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Sample records for atomistic simulation study

  1. Parallel Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    HEFFELFINGER,GRANT S.

    2000-01-18

    Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.

  2. Ionic diffusion in quartz studied by transport measurements, SIMS and atomistic simulations

    International Nuclear Information System (INIS)

    Sartbaeva, Asel; Wells, Stephen A; Redfern, Simon A T; Hinton, Richard W; Reed, Stephen J B

    2005-01-01

    Ionic diffusion in the quartz-β-eucryptite system is studied by DC transport measurements, SIMS and atomistic simulations. Transport data show a large transient increase in ionic current at the α-β phase transition of quartz (the Hedvall effect). The SIMS data indicate two diffusion processes, one involving rapid Li + motion and the other involving penetration of Al and Li atoms into quartz at the phase transition. Atomistic simulations explain why the fine microstructure of twin domain walls in quartz near the transition does not hinder Li + diffusion

  3. Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

    Science.gov (United States)

    Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

    2000-01-01

    We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

  4. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction...... of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol....

  5. Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

    Science.gov (United States)

    Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

    2018-05-01

    Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

  6. Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

    Directory of Open Access Journals (Sweden)

    Zhiwei Zhang

    2018-05-01

    Full Text Available Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young’s modulus, ultimate tensile strength (UTS, and strain at fracture is observed.

  7. Atomistic simulation studies of iron sulphide, platinum antimonide and platinum arsenide

    CSIR Research Space (South Africa)

    Ngoepe, PE

    2005-09-01

    Full Text Available The authors present the results of atomistic simulations using derived interatomic potentials for the pyrite-structured metal chalcogenides FeS2, PtSb2 and PtAs2. Structural and elastic constants were calculated and compared with experimental...

  8. Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

    Directory of Open Access Journals (Sweden)

    Elena ePapaleo

    2015-05-01

    Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  9. Quantum Corrections to the 'Atomistic' MOSFET Simulations

    Science.gov (United States)

    Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

    2000-01-01

    We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

  10. Atomistic Monte Carlo Simulation of Lipid Membranes

    Directory of Open Access Journals (Sweden)

    Daniel Wüstner

    2014-01-01

    Full Text Available Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA for the phospholipid dipalmitoylphosphatidylcholine (DPPC. We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.

  11. Atomistic computer simulations a practical guide

    CERN Document Server

    Brazdova, Veronika

    2013-01-01

    Many books explain the theory of atomistic computer simulations; this book teaches you how to run them This introductory ""how to"" title enables readers to understand, plan, run, and analyze their own independent atomistic simulations, and decide which method to use and which questions to ask in their research project. It is written in a clear and precise language, focusing on a thorough understanding of the concepts behind the equations and how these are used in the simulations. As a result, readers will learn how to design the computational model and which parameters o

  12. Dynamic aspects of dislocation motion: atomistic simulations

    International Nuclear Information System (INIS)

    Bitzek, Erik; Gumbsch, Peter

    2005-01-01

    Atomistic simulations of accelerating edge and screw dislocations were carried out to study the dynamics of dislocations in a face centered cubic metal. Using two different embedded atom potentials for nickel and a simple slab geometry, the Peierls stress, the effective mass, the line tension and the drag coefficient were determined. A dislocation intersecting an array of voids is used to study dynamic effects in dislocation-obstacle interactions. A pronounced effect caused by inertial overshooting is found. A dynamic line tension model is developed which reproduces the simulation results. The model can be used to easily estimate the magnitude of inertial effects in the interaction of dislocations with localized obstacles for different obstacle strengths, -spacings and temperatures

  13. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction...... into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches...

  14. Atomistic Simulation of Initiation in Hexanitrostilbene

    Science.gov (United States)

    Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

    2015-06-01

    We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  15. Atomistic simulations of dislocation processes in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Jacobsen, K.W.

    2002-01-01

    We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example......, the stability of screw dislocation dipoles is discussed. We show that the presence of jogs will strongly influence cross slip barriers and dipole stability. We furthermore present some new results on jogged edge dislocations and edge dislocation dipoles. The jogs are found to be extended, and simulations...

  16. Random Telegraph Signal Amplitudes in Sub 100 nm (Decanano) MOSFETs: A 3D 'Atomistic' Simulation Study

    Science.gov (United States)

    Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.; Saini, Subhash

    2000-01-01

    In this paper we use 3D simulations to study the amplitudes of random telegraph signals (RTS) associated with the trapping of a single carrier in interface states in the channel of sub 100 nm (decanano) MOSFETs. Both simulations using continuous doping charge and random discrete dopants in the active region of the MOSFETs are presented. We have studied the dependence of the RTS amplitudes on the position of the trapped charge in the channel and on the device design parameters. We have observed a significant increase in the maximum RTS amplitude when discrete random dopants are employed in the simulations.

  17. Random telegraph signal amplitudes in sub 100 nm (decanano) MOSFETs: a 3D `Atomistic' simulation study

    OpenAIRE

    Asenov, A.; Balasubramaniam, R.; Brown, A.R.; Davies, J.H.; Saini, S.

    2000-01-01

    In this paper we use 3D simulations to study the amplitudes of random telegraph signals (RTS) associated with the trapping of a single carrier in interface states in the channel of sub 100 nm (decanano) MOSFETs. Both simulations using continuous doping charge and random discrete dopants in the active region of the MOSFETs are presented. We have studied the dependence of the RTS amplitudes on the position of the trapped charge in the channel and on the device design parameters. We have observe...

  18. Atomistic simulation study of deformation twinning of nanocrystalline body-centered cubic Mo

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Xiaofeng [The College of Nuclear Technology and Automation Engineering, Chengdu University of Technology, Chengdu (China); Li, Dan, E-mail: txf8378@163.com [The College of Nuclear Technology and Automation Engineering, Chengdu University of Technology, Chengdu (China); Yu, You [College of Optoelectronic Technology, Chengdu University of Information Technology, Chengdu (China); You, Zhen Jiang [Australian School of Petroleum, University of Adelaide, SA 5005 (Australia); Li, Tongye [The National Key Laboratory of Nuclear Fuel and Materials, Nuclear Power Institute of China, Chengdu (China); Ge, Liangquan [The College of Nuclear Technology and Automation Engineering, Chengdu University of Technology, Chengdu (China)

    2017-04-06

    Deformation twinning of nanocrystalline body-centered cubic Mo was studied using molecular dynamics simulations, and the effects of grain sizes and temperatures on the deformation were evaluated. With small grain size, grain rotation accompanying grain growth was found to play important role in nanocrystalline Mo during tensile deformation. Additionally, grain rotation and the deformation controlled by GB-mediated processes induce to the difficulty of creating crack. Twin was formed by successive emission of twinning partials from grain boundaries in small grain size systems. However, the twin mechanisms of GB splitting and overlapping of two extended dislocations were also found in larger size grain. Twin induced crack tips were observed in our simulation, and this confirmed the results of previous molecular dynamics simulations. At higher temperatures, GB activities can be thermally activated, resulting in suppression of twinning tendency and improvement of ductility of nanocrystalline Mo.

  19. Scalable Atomistic Simulation Algorithms for Materials Research

    Directory of Open Access Journals (Sweden)

    Aiichiro Nakano

    2002-01-01

    Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

  20. Atomistic simulation study of the shear-band deformation mechanism in Mg-Cu metallic glasses

    DEFF Research Database (Denmark)

    Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel

    2006-01-01

    We have simulated plastic deformation of a model Mg-Cu metallic glass in order to study shear banding. In uniaxial tension, we find a necking instability occurs rather than shear banding. We can force the latter to occur by deforming in plane strain, forbidding the change of length in one...... of the transverse directions. Furthermore, in most of the simulations a notch is used to initiate shear bands, which lie at a 45 degrees angle to the tensile loading direction. The shear bands are characterized by the Falk and Langer local measure of plastic deformation D-min(2), averaged here over volumes...... observe a slight decrease in density, up to 1%, within the shear band, which is consistent with notions of increased free volume or disorder within a plastically deforming amorphous material....

  1. Thermally activated magnetization reversal in monatomic magnetic chains on surfaces studied by classical atomistic spin-dynamics simulations

    International Nuclear Information System (INIS)

    Bauer, David S G; Mavropoulos, Phivos; Bluegel, Stefan; Lounis, Samir

    2011-01-01

    We analyse the spontaneous magnetization reversal of supported monatomic chains of finite length due to thermal fluctuations via atomistic spin-dynamics simulations. Our approach is based on the integration of the Landau-Lifshitz equation of motion of a classical spin Hamiltonian in the presence of stochastic forces. The associated magnetization lifetime is found to obey an Arrhenius law with an activation barrier equal to the domain wall energy in the chain. For chains longer than one domain wall width, the reversal is initiated by nucleation of a reversed magnetization domain primarily at the chain edge followed by a subsequent propagation of the domain wall to the other edge in a random-walk fashion. This results in a linear dependence of the lifetime on the chain length, if the magnetization correlation length is not exceeded. We studied chains of uniaxial and triaxial anisotropy and found that a triaxial anisotropy leads to a reduction of the magnetization lifetime due to a higher reversal attempt rate, even though the activation barrier is not changed.

  2. Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study.

    Directory of Open Access Journals (Sweden)

    Vijayan ManickamAchari

    Full Text Available The rational design of a glycolipid application (e.g. drug delivery with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20% in the hydrophobic region of the lamellar crystal (LC phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.

  3. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  4. Si-coated single-walled carbon nanotubes under axial loads: An atomistic simulation study

    International Nuclear Information System (INIS)

    Song Haiyang; Zha Xinwei

    2007-01-01

    The mechanical properties of the Si-coated imperfect (5, 5) single-walled carbon nanotube (SWCNT), the imperfect (5, 5) SWCNT and several perfect armchair SWCNTs under axial loads were investigated using molecular dynamics simulation. The interactions between atoms were modeled using the empirical Tersoff potential and the Tersoff-Brenner potential coupled with the Lennard-Jones potential. We get Young's modulus of the defective (5, 5) nanotube with and without the Si coating under axial tension 1107.92 and 1076.02 GPa, respectively. The results also show that the structure failure of the Si-coated imperfect (5, 5) SWCNT under axial compression occurs at a slightly higher strain than for the perfect (5, 5) SWCNT. Therefore, we can confirm the protective effect of Si as a coating material for defective SWCNTs. We also obtain the critical buckling strains of perfect SWCNTs

  5. Dynamic characteristics of nanoindentation using atomistic simulation

    International Nuclear Information System (INIS)

    Fang, Te-Hua; Chang, Wen-Yang; Huang, Jian-Jin

    2009-01-01

    Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0 o , is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

  6. Dynamic characteristics of nanoindentation using atomistic simulation

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China); Chang, Wen-Yang [Microsystems Technology Center, Industrial Technology Research Institute, Tainan 709, Taiwan (China); Huang, Jian-Jin [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China)

    2009-06-15

    Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0{sup o}, is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

  7. Atomistic simulations of bulk, surface and interfacial polymer properties

    Science.gov (United States)

    Natarajan, Upendra

    In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin

  8. Atomistic simulations of graphite etching at realistic time scales.

    Science.gov (United States)

    Aussems, D U B; Bal, K M; Morgan, T W; van de Sanden, M C M; Neyts, E C

    2017-10-01

    Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 20 m -2 s -1 . The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.

  9. Atomistic simulations of Mg-Cu metallic glasses: Mechanical properties

    DEFF Research Database (Denmark)

    Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel

    2004-01-01

    The atomistic mechanisms of plastic deformation in amorphous metals are far from being understood. We have derived potential parameters for molecular dynamics simulations of Mg-Cu amorphous alloys using the Effective Medium Theory. We have simulated the formation of alloys by cooling from the melt...

  10. Atomistic simulations of contact area and conductance at nanoscale interfaces.

    Science.gov (United States)

    Hu, Xiaoli; Martini, Ashlie

    2017-11-09

    Atomistic simulations were used to study conductance across the interface between a nanoscale gold probe and a graphite surface with a step edge. Conductance on the graphite terrace was observed to increase with load and be approximately proportional to contact area calculated from the positions of atoms in the interface. The relationship between area and conductance was further explored by varying the position of the contact relative to the location of the graphite step edge. These simulations reproduced a previously-reported current dip at step edges measured experimentally and the trend was explained by changes in both contact area and the distribution of distances between atoms in the interface. The novel approach reported here provides a foundation for future studies of the fundamental relationships between conductance, load and surface topography at the atomic scale.

  11. Atomistic simulations of surfactant adsorption kinetics at interfaces

    Science.gov (United States)

    Iskrenova, Eugeniya; Patnaik, Soumya

    2014-03-01

    Heat transfer control and enhancement is an important and challenging problem in a variety of industrial and technological applications including aircraft thermal management. The role of additives in nucleate boiling and phase change in general has long been recognized and studied experimentally and modeled theoretically but in-depth description and atomistic understanding of the multiscale processes involved are still needed for better prediction and control of the heat transfer efficiency. Surfactant additives have been experimentally observed to either enhance or inhibit the boiling heat transfer depending on the surfactant concentration and chemistry and, on a molecular level, their addition leads to dynamic surface tension and changes in interfacial and transfer properties, thus contributing to the complexity of the problem. We present our atomistic modeling study of the interfacial adsorption kinetics of aqueous surfactant (sodium dodecyl sulfate) systems at a range of concentrations at room and boiling temperatures. Classical molecular dynamics and Umbrella Sampling simulations were used to study the surfactant transport properties and estimate the adsorption and desorption rates at liquid-vacuum and liquid-solid interfaces. The authors gratefully acknowledge funding from AFOSR Thermal Science Program and the Air Force Research Laboratory DoD Supercomputing Resource Center for computing time and resources.

  12. An object oriented Python interface for atomistic simulations

    Science.gov (United States)

    Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

    2016-01-01

    Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

  13. Definition and detection of contact in atomistic simulations

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    2015-01-01

    In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

  14. Definition and detection of contact in atomistic simulations

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

  15. Atomistic simulation of graphene-based polymer nanocomposites

    International Nuclear Information System (INIS)

    Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

    2016-01-01

    Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

  16. Deformation behavior of Cu bicrystals with the Σ9(110)(221) symmetric tilt grain boundary under pure shear studied by atomistic simulation method

    International Nuclear Information System (INIS)

    Wan Liang; Wang Shaoqing

    2010-01-01

    The deformation behavior of Cu bicrystals with the symmetric tilt grain boundary (STGB) under pure shear has been studied by atomistic simulation method with the embedded atom method (EAM) interatomic potentials. By using an energy minimization method, it shows that there are two optimized structures of this grain boundary (GB) which correspond to two local energy minima on the potential energy surface of the GB. The structure with lower energy is the stable one while the other is a metastable structure. The pure shear process of the bicrystals at ambient temperature has been studied by molecular dynamics (MD) simulation method. The simulated results indicate that there are three structure transformation modes of this GB depending on the shear direction: (1) pure GB sliding; (2) GB atomic shuffling accompanied by dislocation emission from GB; (3) GB migration coupled GB sliding, namely, GB coupling motion. In addition, an analysis of the structure evolution of the GB shows that, there are two mechanisms for GB coupling motion depending on the shear direction. One is the collective motion of GB atoms and the other is structure transformation realized by uncorrelated atomic shuffling processes. The former mechanism can induce structure transition of GB between the stable one and the metastable one, while the latter introduces faceting of the GB. (authors)

  17. Drug design: Insights from atomistic simulations

    International Nuclear Information System (INIS)

    Collu, F.; Spiga, E.; Kumar, A.; Hajjar, E.; Vargiu, A.V.; Ceccarelli, M.; Ruggerone, P.

    2009-01-01

    Computer simulations have become a widely used and powerful tool to study the behaviour of many-particle and many-interaction systems and processes such as nucleic acid dynamics, drug-DNA interactions, enzymatic processes, membrane, antibiotics. The increased reliability of computational techniques has made possible to plane a bottom-up approach in drug design, i.e. designing molecules with improved properties starting from the knowledge of the molecular mechanisms. However, the in silico techniques have to face the fact that the number of degrees of freedom involved in biological systems is very large while the time scale of several biological processes is not accessible to standard simulations. Algorithms and methods have been developed and are still under construction to bridge these gaps. Here we review the activities of our group focussed on the time-scale bottleneck and, in particular, on the use of the meta dynamics scheme that allows the investigation of rare events in reasonable computer time without reducing the accuracy of the calculation. In particular, we have devoted particular attention to the characterization at microscopic level of translocation of antibiotics through membrane pores, aiming at the identification of structural and dynamical features helpful for a rational drug design.

  18. Atomistic simulation of nanoformed metallic glass

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Cheng-Da, E-mail: nanowu@cycu.edu.tw

    2015-07-15

    Highlights: • STZ forms at substrate surface underneath punch. • Atoms underneath punch have higher speeds at larger mold displacement. • Stick-slip phenomenon becomes more obvious with increasing imprint speed. • Great pattern transfer is obtained with unloading at low temperatures. - Abstract: The effects of forming speed and temperature on the forming mechanism and mechanics of Cu{sub 50}Zr{sub 25}Ti{sub 25} metallic glass are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. These effects are investigated in terms of atomic trajectories, flow field, slip vectors, internal energy, radial distribution function, and elastic recovery of nanoimprint lithography (NIL) patterns. The simulation results show that a shear transformation zone (STZ) forms at the substrate surface underneath the mold during the forming process. The STZ area increases with mold displacement (D). The movement speed of substrate atoms underneath the mold increases with increasing D value. The movement directions of substrate atoms underneath the mold are more agreeable for a larger D value. The stick-slip phenomenon becomes more obvious with increasing D value and imprint speed. The substrate energy increases with increasing imprint speed and temperature. Great NIL pattern transfer is obtained with unloading at low temperatures (e.g., room temperature)

  19. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    Science.gov (United States)

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  20. Elastic dipoles of point defects from atomistic simulations

    Science.gov (United States)

    Varvenne, Céline; Clouet, Emmanuel

    2017-12-01

    The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

  1. Thermodynamics of grain boundary premelting in alloys. II. Atomistic simulation

    International Nuclear Information System (INIS)

    Williams, P.L.; Mishin, Y.

    2009-01-01

    We apply the semi-grand-canonical Monte Carlo method with an embedded-atom potential to study grain boundary (GB) premelting in Cu-rich Cu-Ag alloys. The Σ5 GB chosen for this study becomes increasingly disordered near the solidus line while its local chemical composition approaches the liquidus composition at the same temperature. This behavior indicates the formation of a thin layer of the liquid phase in the GB when the grain composition approaches the solidus. The thickness of the liquid layer remains finite and the GB can be overheated/oversaturated to metastable states slightly above the solidus. The premelting behavior found by the simulations is qualitatively consistent with the phase-field model of the same binary system presented in Part I of this work [Mishin Y, Boettinger WJ, Warren JA, McFadden GB. Acta Mater, in press]. Although this agreement is encouraging, we discuss several problems arising when atomistic simulations are compared with phase-field modeling.

  2. A coupled atomistics and discrete dislocation plasticity simulation of nanoindentation into single crystal thin films

    International Nuclear Information System (INIS)

    Miller, Ronald E.; Shilkrot, L.E.; Curtin, William A.

    2004-01-01

    The phenomenon of 2D nanoindentation of circular 'Brinell' indenter into a single crystal metal thin film bonded to a rigid substrate is investigated. The simulation method is the coupled atomistics and discrete dislocation (CADD) model recently developed by the authors. The CADD model couples a continuum region containing any number of discrete dislocations to an atomistic region, and permits accurate, automatic detection and passing of dislocations between the atomistic and continuum regions. The CADD model allows for a detailed study of nanoindentation to large penetration depths (up to 60 A here) using only a small region of atoms just underneath the indenter where dislocation nucleation, cross-slip, and annihilation occur. Indentation of a model hexagonal aluminum crystal shows: (i) the onset of homogeneous dislocation nucleation at points away from the points of maximum resolved shear stress; (ii) size-dependence of the material hardness, (iii) the role of dislocation dissociation on deformation; (iv) reverse plasticity, including nucleation of dislocations on unloading and annihilation; (v) permanent deformation, including surface uplift, after full unloading; (vi) the effects of film thickness on the load-displacement response; and (vii) the differences between displacement and force controlled loading. This application demonstrates the power of the CADD method in capturing both long-range dislocation plasticity and short-range atomistic phenomena. The use of CADD permits for a clear study of the physical and mechanical influence of both complex plastic flow and non-continuum atomistic-level processes on the macroscopic response of material under indentation loading

  3. Atomistic simulations of the yielding of gold nanowires

    International Nuclear Information System (INIS)

    Diao Jiankuai; Gall, Ken; Dunn, Martin L.; Zimmerman, Jonathan A.

    2006-01-01

    We performed atomistic simulations to study the effect of free surfaces on the yielding of gold nanowires. Tensile surface stresses on the surfaces of the nanowires cause them to contract along the length with respect to the bulk face-centered cubic lattice and induce compressive stress in the interior. When the cross-sectional area of a nanowire is less than 2.45 nm x 2.45 nm, the wire yields under its surface stresses. Under external forces and surface stresses, nanowires yield via the nucleation and propagation of the {1 1 1} partial dislocations. The magnitudes of the tensile and compressive yield stress of nanowires increase and decrease, respectively, with a decrease of the wire width. The magnitude of the tensile yield stress is much larger than that of the compressive yield stress for small nanowires, while for small nanowires, tensile and compressive yield stresses have similar magnitudes. The critical resolved shear stress (RSS) by external forces depends on wire width, orientation and loading condition (tension vs. compression). However, the critical RSS in the interior of the nanowires, which is exerted by both the external force and the surface-stress-induced compressive stress, does not change significantly with wire width for same orientation and same loading condition, and can thus serve as a 'local' criterion. This local criterion is invoked to explain the observed size dependence of yield behavior and tensile/compressive yield stress asymmetry, considering surface stress effects and different slip systems active in tensile and compressive yielding

  4. Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

    Science.gov (United States)

    Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

    1999-01-01

    We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

  5. Redox reactions with empirical potentials: Atomistic battery discharge simulations

    OpenAIRE

    Dapp, Wolf B.; Müser, Martin H.

    2013-01-01

    Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each ...

  6. Atomistic simulation study of short pulse laser interactions with a metal target under conditions of spatial confinement by a transparent overlayer

    Energy Technology Data Exchange (ETDEWEB)

    Karim, Eaman T.; Shugaev, Maxim; Wu, Chengping; Zhigilei, Leonid V., E-mail: lz2n@virginia.edu [Department of Materials Science and Engineering, University of Virginia, 395 McCormick Road, Charlottesville, Virginia 22904-4745 (United States); Lin, Zhibin; Hainsey, Robert F. [Electro Scientific Industries, Inc., 13900 NW Science Park Drive, Portland, Oregon 97229 (United States)

    2014-05-14

    The distinct characteristics of short pulse laser interactions with a metal target under conditions of spatial confinement by a solid transparent overlayer are investigated in a series of atomistic simulations. The simulations are performed with a computational model combining classical molecular dynamics (MD) technique with a continuum description of the laser excitation, electron-phonon equilibration, and electronic heat transfer based on two-temperature model (TTM). Two methods for incorporation of the description of a transparent overlayer into the TTM-MD model are designed and parameterized for Ag-silica system. The material response to the laser energy deposition is studied for a range of laser fluences that, in the absence of the transparent overlayer, covers the regimes of melting and resolidification, photomechanical spallation, and phase explosion of the overheated surface region. In contrast to the irradiation in vacuum, the spatial confinement by the overlayer facilitates generation of sustained high-temperature and high-pressure conditions near the metal-overlayer interface, suppresses the generation of unloading tensile wave, decreases the maximum depth of melting, and prevents the spallation and explosive disintegration of the surface region of the metal target. At high laser fluences, when the laser excitation brings the surface region of the metal target to supercritical conditions, the confinement prevents the expansion and phase decomposition characteristic for the vacuum conditions leading to a gradual cooling of the hot compressed supercritical fluid down to the liquid phase and eventual solidification. The target modification in this case is limited to the generation of crystal defects and the detachment of the metal target from the overlayer.

  7. Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Paavilainen, S.; Rog, T.; Vattulainen, I.

    2011-01-01

    We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile......, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril....

  8. Adaptive resolution simulation of an atomistic protein in MARTINI water

    International Nuclear Information System (INIS)

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-01-01

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations

  9. 3d visualization of atomistic simulations on every desktop

    Science.gov (United States)

    Peled, Dan; Silverman, Amihai; Adler, Joan

    2013-08-01

    Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

  10. 3d visualization of atomistic simulations on every desktop

    International Nuclear Information System (INIS)

    Peled, Dan; Silverman, Amihai; Adler, Joan

    2013-01-01

    Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given

  11. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

  12. Amp: A modular approach to machine learning in atomistic simulations

    Science.gov (United States)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

    Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which

  13. Quantum-based Atomistic Simulation of Transition Metals

    International Nuclear Information System (INIS)

    Moriarty, J A; Benedict, L X; Glosli, J N; Hood, R Q; Orlikowski, D A; Patel, M V; Soderlind, P; Streitz, F H; Tang, M; Yang, L H

    2005-01-01

    First-principles generalized pseudopotential theory (GPT) provides a fundamental basis for transferable multi-ion interatomic potentials in d-electron transition metals within density-functional quantum mechanics. In mid-period bcc metals, where multi-ion angular forces are important to structural properties, simplified model GPT or MGPT potentials have been developed based on canonical d bands to allow analytic forms and large-scale atomistic simulations. Robust, advanced-generation MGPT potentials have now been obtained for Ta and Mo and successfully applied to a wide range of structural, thermodynamic, defect and mechanical properties at both ambient and extreme conditions of pressure and temperature. Recent algorithm improvements have also led to a more general matrix representation of MGPT beyond canonical bands allowing increased accuracy and extension to f-electron actinide metals, an order of magnitude increase in computational speed, and the current development of temperature-dependent potentials

  14. Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

    International Nuclear Information System (INIS)

    Ogawa, Hiroshi

    2015-01-01

    Highlights: • Hydrogen–dislocation interaction was simulated by molecular dynamics method. • Different distribution of H atoms were observed at edge and screw dislocation. • Planner distribution of hydrogen may be caused by partialized edge dislocation. • Hydrogen diffusivity was reduced in both edge and screw dislocation models. • Pipe diffusion was observed for edge dislocation but not for screw dislocation. - Abstract: Kinetics of interstitial hydrogen atoms near dislocation cores were analyzed by atomistic simulation. Classical molecular dynamics method was applied to model structures of edge and screw dislocations in α-phase vanadium hydride. Simulation showed that hydrogen atoms aggregate near dislocation cores. The spatial distribution of hydrogen has a planner shape at edge dislocation due to dislocation partialization, and a cylindrical shape at screw dislocation. Simulated self-diffusion coefficients of hydrogen atoms in dislocation models were a half- to one-order lower than that of dislocation-free model. Arrhenius plot of self-diffusivity showed slightly different activation energies for edge and screw dislocations. Directional dependency of hydrogen diffusion near dislocation showed high and low diffusivity along edge and screw dislocation lines, respectively, hence so called ‘pipe diffusion’ possibly occur at edge dislocation but does not at screw dislocation

  15. A continuum-atomistic simulation of heat transfer in micro- and nano-flows

    International Nuclear Information System (INIS)

    Liu Jin; Chen Shiyi; Nie Xiaobo; Robbins, Mark O.

    2007-01-01

    We develop a hybrid atomistic-continuum scheme for simulating micro- and nano-flows with heat transfer. The approach is based on spatial 'domain decomposition' in which molecular dynamics (MD) is used in regions where atomistic details are important, while classical continuum fluid dynamics is used in the remaining regions. The two descriptions are matched in a coupling region where we ensure continuity of mass, momentum, energy and their fluxes. The scheme for including the energy equation is implemented in 1-D and 2-D, and used to study steady and unsteady heat transfer in channel flows with and without nano roughness. Good agreement between hybrid results and analytical or pure MD results is found, demonstrating the accuracy of this multiscale method and its potential applications in thermal engineering

  16. Redox reactions with empirical potentials: atomistic battery discharge simulations.

    Science.gov (United States)

    Dapp, Wolf B; Müser, Martin H

    2013-08-14

    Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

  17. Ion beam processing of surfaces and interfaces. Modeling and atomistic simulations

    International Nuclear Information System (INIS)

    Liedke, Bartosz

    2011-01-01

    Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In general

  18. Ion beam processing of surfaces and interfaces. Modeling and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liedke, Bartosz

    2011-03-24

    Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In

  19. Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

    KAUST Repository

    Hong, Bingbing; Panagiotopoulos, Athanassios Z.

    2013-01-01

    We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide

  20. Atomistic simulation of the premelting of iron and aluminum : Implications for high-pressure melting-curve measurements

    NARCIS (Netherlands)

    Starikov, Sergey V.; Stegailov, Vladimir V.

    2009-01-01

    Using atomistic simulations we show the importance of the surface premelting phenomenon for the melting-curve measurements at high pressures. The model under consideration mimics the experimental conditions deployed for melting studies with diamond-anvil cells. The iron is considered in this work

  1. Atomistic simulation of fatigue in face centred cubic metals

    International Nuclear Information System (INIS)

    Fan, Zhengxuan

    2016-01-01

    Fatigue is one of the major damage mechanisms of metals. It is characterized by strong environmental effects and wide lifetime dispersions which must be better understood. Different face centred cubic metals, al, Cu, Ni, and Ag are analyzed. The mechanical behaviour of surface steps naturally created by the glide of dislocations subjected to cyclic loading is examined using molecular dynamics simulations in vacuum and in air for Cu and Ni. an atomistic reconstruction phenomenon is observed at these surface steps which can induce strong irreversibility. Three different mechanisms of reconstruction are defined. Surface slip irreversibility under cyclic loading is analyzed. all surface steps are intrinsically irreversible under usual fatigue laboratory loading amplitude without the arrival of opposite sign dislocations on direct neighbor plane.With opposite sign dislocations on non direct neighbour planes, irreversibility cumulates cycle by cycle and a micro-notch is produced whose depth gradually increases.Oxygen environment affects the surface (first stage of oxidation) but does not lead to higher irreversibility as it has no major influence on the different mechanisms linked to surface relief evolution.a rough estimation of surface irreversibility is carried out for pure edge dislocations in persistent slip bands in so-called wavy materials. It gives an irreversibility fraction between 0.5 and 0.75 in copper in vacuum and in air, in agreement with recent atomic force microscopy measurements.Crack propagation mechanisms are simulated in inert environment. Cracks can propagate owing to the irreversibility of generated dislocations because of their mutual interactions up to the formation of dislocation junctions. (author) [fr

  2. Solid solution hardening in face centered binary alloys: Gliding statistics of a dislocation in random solid solution by atomistic simulation

    International Nuclear Information System (INIS)

    Patinet, S.

    2009-12-01

    The glide of edge and screw dislocation in solid solution is modeled through atomistic simulations in two model alloys of Ni(Al) and Al(Mg) described within the embedded atom method. Our approach is based on the study of the elementary interaction between dislocations and solutes to derive solid solution hardening of face centered cubic binary alloys. We identify the physical origins of the intensity and range of the interaction between a dislocation and a solute atom. The thermally activated crossing of a solute atom by a dislocation is studied at the atomistic scale. We show that hardening of edge and screw segments are similar. We develop a line tension model that reproduces quantitatively the atomistic calculations of the flow stress. We identify the universality class to which the dislocation depinning transition in solid solution belongs. (author)

  3. Atomistic simulation and continuum modeling of graphene nanoribbons under uniaxial tension

    International Nuclear Information System (INIS)

    Lu, Qiang; Gao, Wei; Huang, Rui

    2011-01-01

    Atomistic simulations are performed to study the nonlinear mechanical behavior of graphene nanoribbons under quasistatic uniaxial tension, emphasizing the effects of edge structures (armchair and zigzag, without and with hydrogen passivation) on elastic modulus and fracture strength. The numerical results are analyzed within a theoretical model of thermodynamics, which enables determination of the bulk strain energy density, the edge energy density and the hydrogen adsorption energy density as nonlinear functions of the applied strain based on static molecular mechanics simulations. These functions can be used to describe mechanical behavior of graphene nanoribbons from the initial linear elasticity to fracture. It is found that the initial Young's modulus of a graphene nanoribbon depends on the ribbon width and the edge chirality. Furthermore, it is found that the nominal strain to fracture is considerably lower for graphene nanoribbons with armchair edges than for ribbons with zigzag edges. Molecular dynamics simulations reveal two distinct fracture nucleation mechanisms: homogeneous nucleation for the zigzag-edged graphene nanoribbons and edge-controlled heterogeneous nucleation for the armchair-edged ribbons. The modeling and simulations in this study highlight the atomistic mechanisms for the nonlinear mechanical behavior of graphene nanoribbons with the edge effects, which is potentially important for developing integrated graphene-based devices

  4. Crack growth and fracture toughness of amorphous Li-Si anodes: Mechanisms and role of charging/discharging studied by atomistic simulations

    Science.gov (United States)

    Khosrownejad, S. M.; Curtin, W. A.

    2017-10-01

    Fracture is the main cause of degradation and capacity fading in lithiated silicon during cycling. Experiments on the fracture of lithiated silicon show conflicting results, and so mechanistic models can help interpret experiments and guide component design. Here, large-scale K-controlled atomistic simulations of crack propagation (R-curve KI vs. Δa) are performed at LixSi compositions x = 0.5 , 1.0 , 1.5 for as-quenched/relaxed samples and at x = 0.5 , 1.0 for samples created by discharging from higher Li compositions. In all cases, the fracture mechanism is void nucleation, growth, and coalescence. In as-quenched materials, with increasing Li content the plastic flow stress and elastic moduli decrease but void nucleation and growth happen at smaller stress, so that the initial fracture toughness KIc ≈ 1.0 MPa√{ m} decreases slightly but the initial fracture energy JIc ≈ 10.5J/m2 is similar. After 10 nm of crack growth, the fracture toughnesses increase and become similar at KIc ≈ 1.9 MPa√{ m} across all compositions. Plane-strain equi-biaxial expansion simulations of uncracked samples provide complementary information on void nucleation and growth. The simulations are interpreted within the framework of Gurson model for ductile fracture, which predicts JIc = ασy D where α ≃ 1 and D is the void spacing, and good agreement is found. In spite of flowing plastically, the fracture toughness of LixSi is low because voids nucleate within nano-sized distances ahead of the crack (D ≈ 1nm). Scaling simulation results to experimental conditions, reasonable agreement with experimentally-estimated fracture toughnesses is obtained. The discharging process facilitates void nucleation but decreases the flow stress (as shown previously), leading to enhanced fracture toughness at all levels of crack growth. Therefore, the fracture behavior of lithiated silicon at a given composition is not a material property but instead depends on the history of charging

  5. Atomistic simulations in Si processing: Bridging the gap between atoms and experiments

    International Nuclear Information System (INIS)

    Marques, Luis A.; Pelaz, Lourdes; Lopez, Pedro; Aboy, Maria; Santos, Ivan; Barbolla, Juan

    2005-01-01

    With devices shrinking to nanometric scale, process simulation tools have to shift from continuum models to an atomistic description of the material. However, the limited sizes and time scales accessible for detailed atomistic techniques usually lead to the difficult task of relating the information obtained from simulations to experimental data. The solution consists of the use of a hierarchical simulation scheme: more fundamental techniques are employed to extract parameters and models that are then feed into less detailed simulators which allow direct comparison with experiments. This scheme will be illustrated with the modeling of the amorphization and recrystallization of Si, which has been defined as a key challenge in the last edition of the International Technology Roadmap for Semiconductors. The model is based on the bond defect or IV pair, which is used as the building block of the amorphous phase. The properties of this defect have been studied using ab initio methods and classical molecular dynamics techniques. It is shown that the recombination of this defect depends on the surrounding bond defects, which accounts for the cooperative nature of the amorphization and recrystallization processes. The implementation of this model in a kinetic Monte Carlo code allows extracting data directly comparable with experiments. This approach provides physical insight on the amorphization and recrystallization mechanisms and a tool for the optimization of solid-phase epitaxial-related processes

  6. Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

    2013-10-01

    In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.

  7. Simulating Surface-Enhanced Hyper-Raman Scattering Using Atomistic Electrodynamics-Quantum Mechanical Models.

    Science.gov (United States)

    Hu, Zhongwei; Chulhai, Dhabih V; Jensen, Lasse

    2016-12-13

    Surface-enhanced hyper-Raman scattering (SEHRS) is the two-photon analogue of surface-enhanced Raman scattering (SERS), which has proven to be a powerful tool to study molecular structures and surface enhancements. However, few theoretical approaches to SEHRS exist and most neglect the atomistic descriptions of the metal surface and molecular resonance effects. In this work, we present two atomistic electrodynamics-quantum mechanical models to simulate SEHRS. The first is the discrete interaction model/quantum mechanical (DIM/QM) model, which combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule. The second model is a dressed-tensors method that describes the molecule as a point-dipole and point-quadrupole object interacting with the enhanced local field and field-gradients (FG) from the nanoparticle. In both of these models, the resonance effects are treated efficiently by means of damped quadratic response theory. Using these methods, we simulate SEHRS spectra for benzene and pyridine. Our results show that the FG effects in SEHRS play an important role in determining both the surface selection rules and the enhancements. We find that FG effects are more important in SEHRS than in SERS. We also show that the spectral features of small molecules can be accurately described by accounting for the interactions between the molecule and the local field and FG of the nanoparticle. However, at short distances between the metal and molecule, we find significant differences in the SEHRS enhancements predicted using the DIM/QM and the dressed-tensors methods.

  8. Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

    Science.gov (United States)

    Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash; hide

    2002-01-01

    A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

  9. An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhi [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Jiang, Xiang-Wei; Li, Shu-Shen [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Wang, Lin-Wang, E-mail: lwwang@lbl.gov [Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2014-03-24

    We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10{sup 5} atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose.

  10. An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

    International Nuclear Information System (INIS)

    Wang, Zhi; Jiang, Xiang-Wei; Li, Shu-Shen; Wang, Lin-Wang

    2014-01-01

    We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10 5 atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose

  11. An atomistic study of the deformation behavior of tungsten nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Shuozhi [University of California, California NanoSystems Institute, Santa Barbara, CA (United States); Su, Yanqing [University of California, Department of Mechanical Engineering, Santa Barbara, CA (United States); Chen, Dengke [Georgia Institute of Technology, GWW School of Mechanical Engineering, Atlanta, GA (United States); Li, Longlei [Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA (United States)

    2017-12-15

    Large-scale atomistic simulations are performed to study tensile and compressive left angle 112 right angle loading of single-crystalline nanowires in body-centered cubic tungsten (W). Effects of loading mode, wire cross-sectional shape, wire size, strain rate, and crystallographic orientations of the lateral surfaces are explored. Uniaxial deformation of a W bulk single crystal is also investigated for reference. Our results reveal a strong tension-compression asymmetry in both the stress-strain response and the deformation behavior due to different yielding/failure modes: while the nanowires fail by brittle fracture under tensile loading, they yield by nucleation of dislocations from the wire surface under compressive loading. It is found that (1) nanowires have a higher strength than the bulk single crystal; (2) with a cross-sectional size larger than 10 nm, there exists a weak dependence of strength on wire size; (3) when the wire size is equal to or smaller than 10 nm, nanowires buckle under compressive loading; (4) the cross-sectional shape, strain rate, and crystallographic orientations of the lateral surfaces affect the strength and the site of defect initiation but not the overall deformation behavior. (orig.)

  12. Hierarchical Statistical 3D ' Atomistic' Simulation of Decanano MOSFETs: Drift-Diffusion, Hydrodynamic and Quantum Mechanical Approaches

    Science.gov (United States)

    Asenov, Asen; Brown, A. R.; Slavcheva, G.; Davies, J. H.

    2000-01-01

    When MOSFETs are scaled to deep submicron dimensions the discreteness and randomness of the dopant charges in the channel region introduces significant fluctuations in the device characteristics. This effect, predicted 20 year ago, has been confirmed experimentally and in simulation studies. The impact of the fluctuations on the functionality, yield, and reliability of the corresponding systems shifts the paradigm of the numerical device simulation. It becomes insufficient to simulate only one device representing one macroscopical design in a continuous charge approximation. An ensemble of macroscopically identical but microscopically different devices has to be characterized by simulation of statistically significant samples. The aims of the numerical simulations shift from predicting the characteristics of a single device with continuous doping towards estimating the mean values and the standard deviations of basic design parameters such as threshold voltage, subthreshold slope, transconductance, drive current, etc. for the whole ensemble of 'atomistically' different devices in the system. It has to be pointed out that even the mean values obtained from 'atomistic' simulations are not identical to the values obtained from continuous doping simulations. In this paper we present a hierarchical approach to the 'atomistic' simulation of aggressively scaled decanano MOSFETs. A full scale 3D drift-diffusion'atomostic' simulation approach is first described and used for verification of the more economical, but also more restricted, options. To reduce the processor time and memory requirements at high drain voltage we have developed a self-consistent option based on a thin slab solution of the current continuity equation only in the channel region. This is coupled to the Poisson's equation solution in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison with the full self-consistent solution. At low drain

  13. Long-time atomistic simulations with the Parallel Replica Dynamics method

    Science.gov (United States)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  14. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    International Nuclear Information System (INIS)

    Seppä, Jeremias; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Lassila, Antti; Reischl, Bernhard; Raiteri, Paolo; Rohl, Andrew L; Nordlund, Kai

    2017-01-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation. (paper)

  15. Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

    Science.gov (United States)

    Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

    2005-09-01

    Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

  16. Molecular cooperativity and compatibility via full atomistic simulation

    Science.gov (United States)

    Kwan Yang, Kenny

    Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules

  17. Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

    Science.gov (United States)

    Xiao, HuiFang; Huang, Bin; Yao, Ge; Kang, WenBin; Gong, Sheng; Pan, Hai; Cao, Yi; Wang, Jun; Zhang, Jian; Wang, Wei

    2018-03-01

    Understanding the processes of protein adsorption/desorption on nanoparticles' surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for these processes and for the simultaneous protein conformational change is missing. Here, we report the adsorption of protein GB1 on a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states, each involving both the adsorbed and desorbed modes. We also studied the change of the secondary and tertiary structures of GB1 during adsorption and the dominant interactions between the protein and surface in different adsorption stages. The results we obtained from simulation were found to be more adequate and complete than the previous one. We believe the model presented in this paper, in comparison with the previous ones, is a better theoretical model to understand and explain the experimental results.

  18. Atomistic Simulation of Frictional Sliding Between Cellulose Iß Nanocrystals

    Science.gov (United States)

    Xiawa Wu; Robert J. Moon; Ashlie Martini

    2013-01-01

    Sliding friction between cellulose Iß nanocrystals is studied using molecular dynamics simulation. The effects of sliding velocity, normal load, and relative angle between sliding surface are predicted, and the results analyzed in terms of the number of hydrogen bonds within and between the cellulose chains. We find that although the observed friction trends can be...

  19. Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

    Science.gov (United States)

    Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas

    2018-01-01

    We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

  20. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

    Science.gov (United States)

    Yang, Shengfeng; Chen, Youping

    2015-03-08

    In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

  1. Atomistic Simulations of Small-scale Materials Tests of Nuclear Materials

    International Nuclear Information System (INIS)

    Shin, Chan Sun; Jin, Hyung Ha; Kwon, Jun Hyun

    2012-01-01

    Degradation of materials properties under neutron irradiation is one of the key issues affecting the lifetime of nuclear reactors. Evaluating the property changes of materials due to irradiations and understanding the role of microstructural changes on mechanical properties are required for ensuring reliable and safe operation of a nuclear reactor. However, high dose of neuron irradiation capabilities are rather limited and it is difficult to discriminate various factors affecting the property changes of materials. Ion beam irradiation can be used to investigate radiation damage to materials in a controlled way, but has the main limitation of small penetration depth in the length scale of micro meters. Over the past decade, the interest in the investigations of size-dependent mechanical properties has promoted the development of various small-scale materials tests, e.g. nanoindentation and micro/nano-pillar compression tests. Small-scale materials tests can address the issue of the limitation of small penetration depth of ion irradiation. In this paper, we present small-scale materials tests (experiments and simulation) which are applied to study the size and irradiation effects on mechanical properties. We have performed molecular dynamics simulations of nanoindentation and nanopillar compression tests. These atomistic simulations are expected to significantly contribute to the investigation of the fundamental deformation mechanism of small scale irradiated materials

  2. Fatigue mechanisms in an austenitic steel under cyclic loading: Experiments and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Soppa, E.A., E-mail: ewa.soppa@mpa.uni-stuttgart.de; Kohler, C., E-mail: christopher.kohler@mpa.uni-stuttgart.de; Roos, E., E-mail: eberhard.roos@mpa.uni-stuttgart.de

    2014-03-01

    Experimental investigations on the austenitic stainless steel X6CrNiNb18-10 (AISI – 347) and concomitant atomistic simulations of a FeNi nanocrystalline model system have been performed in order to understand the basic mechanisms of fatigue damage under cyclic loading. Using electron backscatter diffraction (EBSD) the influence of deformation induced martensitic transformation and NbC size distribution on the fatigue crack formation has been demonstrated. The martensite nucleates prevalently at grain boundaries, triple points and at the specimen free surface and forms small (∼1 µm sized) differently oriented grains. The atomistic simulations show the role of regions of a high density of stacking faults for the martensitic transformation.

  3. Free-energy landscape of protein oligomerization from atomistic simulations

    Science.gov (United States)

    Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K.; Parrinello, Michele

    2013-01-01

    In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. PMID:24248370

  4. Nanometric mechanical cutting of metallic glass investigated using atomistic simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Cheng-Da, E-mail: nanowu@cycu.edu.tw [Department of Mechanical Engineering, Chung Yuan Christian University, 200, Chung Pei Rd., Chung Li District, Taoyuan City 32023, Taiwan (China); Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Department of Mechanical Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 807, Taiwan (China); Su, Jih-Kai, E-mail: yummy_2468@yahoo.com.tw [Department of Mechanical Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 807, Taiwan (China)

    2017-02-28

    Highlights: • A nanoscale chip with a shear plane of 135° is extruded by the tool. • Tangential force and normal force increase with increasing tool nose radius. • Resistance factor increases with increasing cutting depth and temperature. - Abstract: The effects of cutting depth, tool nose radius, and temperature on the cutting mechanism and mechanics of amorphous NiAl workpieces are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. These effects are investigated in terms of atomic trajectories and flow field, shear strain, cutting force, resistance factor, cutting ratio, and pile-up characteristics. The simulation results show that a nanoscale chip with a shear plane of 135° is extruded by the tool from a workpiece surface during the cutting process. The workpiece atoms underneath the tool flow upward due to the adhesion force and elastic recovery. The required tangential force and normal force increase with increasing cutting depth and tool nose radius; both forces also increase with decreasing temperature. The resistance factor increases with increasing cutting depth and temperature, and decreases with increasing tool nose radius.

  5. Atomistic simulations of the radiation resistance of oxides

    International Nuclear Information System (INIS)

    Chartier, A.; Van Brutzel, L.; Crocombette, J.-P.

    2012-01-01

    Fluorite compounds such as urania and ceria, or related compounds such as pyrochlores and also spinels show different behaviors under irradiations, which ranges from perfect radiation resistance to crystalline phase change or even complete amorphization depending on their structure and/or their composition. Displacement cascades – dedicated to the understanding of the ballistic regime and performed by empirical potentials molecular dynamics simulations – have revealed that the remaining damages of the above mentioned oxides are reduced to point defects unlike what is observed in zircon and zirconolite, which directly amorphize during the cascade. The variable behavior of these point defects is the key of the various responses of these materials to irradiations. This behavior can be investigated by two specific molecular dynamics methodologies that will be reviewed here: (i) the method of point defects accumulation as a function of temperature that gives access to the dose effects and to the critical doses for amorphization; (ii) the study Frenkel pairs life-time – i.e. their time of recombination as function of temperature – that may be used as a tool to understand the results obtained in displacements cascades or to identify the microscopic mechanisms responsible for the amorphization/re-crystallization during the point defects accumulations.

  6. Atomistic Molecular Dynamics Simulations of the Electrical Double

    Science.gov (United States)

    Li, Zifeng; Milner, Scott; Fichthorn, Kristen

    2015-03-01

    The electrical double layer (EDL) near the polymer/water interface plays a key role in the colloidal stability of latex paint. To elucidate the structure of the EDL at the molecular level, we conducted an all-atom molecular dynamics simulations. We studied two representative surface charge groups in latex, the ionic surfactant sodium dodecyl sulfate (SDS) and the grafted short polyelectrolyte charged by dissociated methyl methacrylic acid (MAA) monomers. Our results confirm that the Poisson-Boltzmann theory works well outside the Stern layer. Our calculated electrostatic potential at the Outer Helmholtz Plane (OHP) is close to the zeta potential measured experimentally, which suggests that the potential at the OHP is a good estimate of the zeta potential. We found that the position of the OHP for the MAA polyelectrolyte system extends much further into the aqueous phase than that in the SDS system, resulting in a Stern layer that is twice as thick. This model will allow for future investigations of the interactions of the surface with different surfactants and rheology modifiers, which may serve as a guide to tune the rheology of latex formulations. We thank Dow Chemical Company for financial support.

  7. Analyzing and Driving Cluster Formation in Atomistic Simulations.

    Science.gov (United States)

    Tribello, Gareth A; Giberti, Federico; Sosso, Gabriele C; Salvalaglio, Matteo; Parrinello, Michele

    2017-03-14

    In this paper a set of computational tools for identifying the phases contained in a system composed of atoms or molecules is introduced. The method is rooted in graph theory and combines atom centered symmetry functions, adjacency matrices, and clustering algorithms to identify regions of space where the properties of the system constituents can be considered uniform. We show how this method can be used to define collective variables and how these collective variables can be used to enhance the sampling of nucleation events. We then show how this method can be used to analyze simulations of crystal nucleation and growth by using it to analyze simulations of the nucleation of the molecular crystal urea and simulations of nucleation in a semiconducting alloy. The semiconducting alloy example we discuss is particular challenging as multiple nucleation centers are formed. We show, however, that our algorithm is able to detect the grain boundaries in the resulting polycrystal.

  8. Atomistic Simulation of Interfaces in Materials of Solid State Ionics

    Science.gov (United States)

    Ivanov-Schitz, A. K.; Mazo, G. N.

    2018-01-01

    The possibilities of describing correctly interfaces of different types in solids within a computer experiment using molecular statics simulation, molecular dynamics simulation, and quantum chemical calculations are discussed. Heterophase boundaries of various types, including grain boundaries and solid electrolyte‒solid electrolyte and ionic conductor‒electrode material interfaces, are considered. Specific microstructural features and mechanisms of the ion transport in real heterophase structures (cationic conductor‒metal anode and anionic conductor‒cathode) existing in solid state ionics devices (such as solid-state batteries and fuel cells) are discussed.

  9. Voltage equilibration for reactive atomistic simulations of electrochemical processes

    International Nuclear Information System (INIS)

    Onofrio, Nicolas; Strachan, Alejandro

    2015-01-01

    We introduce electrochemical dynamics with implicit degrees of freedom (EChemDID), a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and their effect on the self-consistent partial atomic charges used in reactive molecular dynamics. An additional variable assigned to each atom denotes the local potential in its vicinity and we use fictitious, but computationally convenient, dynamics to describe its equilibration within connected metallic structures on-the-fly during the molecular dynamics simulation. This local electrostatic potential is used to dynamically modify the atomic electronegativities used to compute partial atomic changes via charge equilibration. Validation tests show that the method provides an accurate description of the electric fields generated by the applied voltage and the driving force for electrochemical reactions. We demonstrate EChemDID via simulations of the operation of electrochemical metallization cells. The simulations predict the switching of the device between a high-resistance to a low-resistance state as a conductive metallic bridge is formed and resistive currents that can be compared with experimental measurements. In addition to applications in nanoelectronics, EChemDID could be useful to model electrochemical energy conversion devices

  10. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    Science.gov (United States)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  11. Voronoi Based Nanocrystalline Generation Algorithm for Atomistic Simulations

    Science.gov (United States)

    2016-12-22

    shown by the screen shot in Fig. 4. First, a 10-nm grain structure is created in a 15- × 15- × 15-nm simulation cell. Here, each grain con - tains an...configuration file saved as Cu_NC_centroids.config. The nanocrystal_builder.py script is invoked a second time to demonstrate the Con - fig Mode in the lower...distributionisunlimited. output_name = raw_input(’Input desired output basename:\

  12. A fast mollified impulse method for biomolecular atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)

    2017-03-15

    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  13. Control of density fluctuations in atomistic-continuum simulations of dense liquids

    DEFF Research Database (Denmark)

    Kotsalis, E.M.; Walther, Jens Honore; Koumoutsakos, P.

    2007-01-01

    with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force...... is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity...

  14. Molecular Simulations of Cyclic Loading Behavior of Carbon Nanotubes Using the Atomistic Finite Element Method

    Directory of Open Access Journals (Sweden)

    Jianfeng Wang

    2009-01-01

    Full Text Available The potential applications of carbon nanotubes (CNT in many engineered bionanomaterials and electromechanical devices have imposed an urgent need on the understanding of the fatigue behavior and mechanism of CNT under cyclic loading conditions. To date, however, very little work has been done in this field. This paper presents the results of a theoretical study on the behavior of CNT subject to cyclic tensile and compressive loads using quasi-static molecular simulations. The Atomistic Finite Element Method (AFEM has been applied in the study. It is shown that CNT exhibited extreme cyclic loading resistance with yielding strain and strength becoming constant within limited number of loading cycles. Viscoelastic behavior including nonlinear elasticity, hysteresis, preconditioning (stress softening, and large strain have been observed. Chiral symmetry was found to have appreciable effects on the cyclic loading behavior of CNT. Mechanisms of the observed behavior have been revealed by close examination of the intrinsic geometric and mechanical features of tube structure. It was shown that the accumulated residual defect-free morphological deformation was the primary mechanism responsible for the cyclic failure of CNT, while the bond rotating and stretching experienced during loading/unloading played a dominant role on the strength, strain and modulus behavior of CNT.

  15. Atomistic simulation of rapid compression of fractured silicon carbide

    International Nuclear Information System (INIS)

    Romano, A.; Li, J.; Yip, S.

    2006-01-01

    Deformation mechanisms of a crack in silicon carbide under high-rate compression are investigated by molecular dynamics simulation. The penny-shaped crack is in tension throughout the simulation while a variable compression is applied in an in-plane direction. Two different mechanisms of crack-tip response are observed: (1) At low tension, a disordered band forms from the crack surface in the direction orthogonal to the compression, which grows as the compressional force is increased in a manner suggesting a stress-induced transition from an ordered to a disordered phase. Moreover the crack is observed to close. (2) At a tension sufficient to allow the crack to remain open, the compressional stress induces formation of disordered regions along the boundaries of the opened crack, which grow and merge into a band as the compression proceeds. This process is driven by bending of the initial crack, which transforms into a curved slit. This mechanism induces incorporation of fragments of perfect crystal into the disordered band. Similar mechanisms have been experimentally observed to occur in porous SiC under high-strain rate compression

  16. From HADES to PARADISE-atomistic simulation of defects in minerals

    Energy Technology Data Exchange (ETDEWEB)

    Parker, Stephen C; Cooke, David J; Kerisit, Sebastien; Marmier, Arnaud S; Taylor, Sarah L; Taylor, Stuart N [Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom)

    2004-07-14

    The development of the HADES code by Michael Norgett in the 1970s enabled, for the first time, the routine simulation of point defects in inorganic solids at the atomic scale. Using examples from current research we illustrate how the scope and applications of atomistic simulations have widened with time and yet still follow an approach readily identifiable with this early work. Firstly we discuss the use of the Mott-Littleton methodology to study the segregation of various isovalent cations to the (00.1) and (01.2) surfaces of haematite ({alpha}-Fe{sub 2}O{sub 3}). The results show that the size of the impurities has a considerable effect on the magnitude of the segregation energy. We then extend these simulations to investigate the effect of the concentration of the impurities at the surface on the segregation process using a supercell approach. We consider next the effect of segregation to stepped surfaces illustrating this with recent work on segregation of La{sup 3+} to CaF{sub 2} surfaces, which show enhanced segregation to step edges. We discuss next the application of lattice dynamics to modelling point defects in complex oxide materials by applying this to the study of hydrogen incorporation into {beta}-Mg{sub 2}SiO{sub 4}. Finally our attention is turned to a method for considering the surface energy of physically defective surfaces and we illustrate its approach by considering the low index surfaces of {alpha}-Al{sub 2}O{sub 3}.

  17. Atomistic simulation of helium bubble nucleation in palladium

    Energy Technology Data Exchange (ETDEWEB)

    Wang Liang [Department of Applied Physics, Hunan University, Changsha 410082 (China); Hu, Wangyu [Department of Applied Physics, Hunan University, Changsha 410082 (China)], E-mail: wangyuhu2001cn@yahoo.com.cn; Xiao Shifang [Department of Applied Physics, Hunan University, Changsha 410082 (China)], E-mail: sfxiao@yahoo.com.cn; Yang Jianyu [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China); Deng Huiqiu [Department of Applied Physics, Hunan University, Changsha 410082 (China)

    2009-09-15

    A palladium crystal has been constructed with 11808 atoms. 55 helium atoms occupied the octahedral position of palladium crystal are introduced and retained in a spherical region. Molecular dynamic simulations are performed in a constant temperature and constant volume ensemble (NVT) with temperature controlled by Nose-Hoover thermostat. The interactions between palladium atoms are described with modified analytic embedded atom method (MAEAM), the interactions between palladium atom and helium atom are in the form of Morse potential, and the interactions between helium atoms are in the form of L-J potential function. With the analysis of the radial distribution function (RDF) and microstructure, it reveals that some of helium atoms form a series of clusters with different size, and the nucleation core is random at low temperature, and which is the embryo of helium bubble. Increasing temperature can accelerate the process of bubble nucleation, and the clusters will aggregate and coalesce into a bigger one in which there are no palladium atoms, and it is considered as a helium bubble.

  18. How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations.

    Directory of Open Access Journals (Sweden)

    Tarja Äijänen

    2014-11-01

    Full Text Available Cholesteryl ester transfer protein (CETP mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity and thereby raise high density lipoprotein (HDL-cholesterol and decrease low density lipoprotein (LDL-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site of anacetrapib turns out to reside in the tunnel inside CETP, near the residues surrounding the N-terminal opening. Free energy calculations show that when anacetrapib resides in this area, it hinders the ability of cholesteryl ester to diffuse out from CETP. The simulations further bring out the ability of anacetrapib to regulate the structure-function relationships of phospholipids and helix X, the latter representing the structural region of CETP important to the process of neutral lipid exchange with lipoproteins. Altogether, the simulations propose CETP inhibition to be realized when anacetrapib is transferred into the lipid binding pocket. The novel insight gained in this study has potential use in the development of new molecular agents capable of preventing the progression of cardiovascular diseases.

  19. Atomistic simulation of the structural and elastic properties of ...

    Indian Academy of Sciences (India)

    experimental data and previous theoretical results, showing no phase transition ... and theoretical [2,9–11] studies have been dedicated to deter- ..... [33] introduced a simple relationship that empirically links the plastic properties of materials with their elastic moduli. The shear modulus G represents the resistance to plastic.

  20. Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

    Science.gov (United States)

    Tiwary, Pratyush

    This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

  1. Atomistic Simulation of Intrinsic Defects and Trivalent and Tetravalent Ion Doping in Hydroxyapatite

    Directory of Open Access Journals (Sweden)

    Ricardo D. S. Santos

    2014-01-01

    Full Text Available Atomistic simulation techniques have been employed in order to investigate key issues related to intrinsic defects and a variety of dopants from trivalent and tetravalent ions. The most favorable intrinsic defect is determined to be a scheme involving calcium and hydroxyl vacancies. It is found that trivalent ions have an energetic preference for the Ca site, while tetravalent ions can enter P sites. Charge compensation is predicted to occur basically via three schemes. In general, the charge compensation via the formation of calcium vacancies is more favorable. Trivalent dopant ions are more stable than tetravalent dopants.

  2. Near-ideal strength in metal nanotubes revealed by atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Mingfei; Xiao, Fei [Department of Materials Science, Fudan University, 220 Handan Road, Shanghai 200433 (China); Deng, Chuang, E-mail: dengc@ad.umanitoba.ca [Department of Mechanical and Manufacturing Engineering, The University of Manitoba, 15Gillson Street, Winnipeg, Manitoba R3T 5V6 (Canada)

    2013-12-02

    Here we report extraordinary mechanical properties revealed by atomistic simulations in metal nanotubes with hollow interior that have been long overlooked. Particularly, the yield strength in [1 1 1] Au nanotubes is found to be up to 60% higher than the corresponding solid Au nanowire, which approaches the theoretical ideal strength in Au. Furthermore, a remarkable transition from sharp to smooth yielding is observed in Au nanotubes with decreasing wall thickness. The ultrahigh tensile strength in [1 1 1] Au nanotube might originate from the repulsive image force exerted by the interior surface against dislocation nucleation from the outer surface.

  3. Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

    International Nuclear Information System (INIS)

    Stukowski, Alexander

    2010-01-01

    The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/

  4. Atomistic simulations of dislocation-precipitate interactions emphasize importance of cross-slip

    International Nuclear Information System (INIS)

    Singh, C.V.; Mateos, A.J.; Warner, D.H.

    2011-01-01

    This work examines the interaction of screw dislocations with Guinier-Preston (GP) zones using atomistic simulations. Both Orowan looping and cross-slip mechanisms are found to control the interactions. Cross-slip, occurring both at zero and finite temperatures, is found to either significantly reduce or enhance precipitate strengthening, depending upon the orientation of the dislocation-GP zone interaction. The orientation dependence, and its dependence on temperature, provides a micromechanical explanation for the experiments of Muraishi et al. (Philos. Mag. A 82 (2002) 2755).

  5. Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Orlowski, A.; St-Pierre, J. F.; Magarkar, A.

    2011-01-01

    We used atomistic simulations to study the membrane-bound form of catechol-O-methyltransferase (MB-COMT). In particular we investigated the 26-residue transmembrane a-helical segment of MB-COMT together with the 24-residue fragment that links the transmembrane component to the main protein unit...... that was not included in our model. In numerous independent simulations we observed the formation of a salt bridge between ARC 27 and GLU40. The salt bridge closed the flexible loop that formed in the linker and kept it in the vicinity of the membrane-water interface. All simulations supported this conclusion...... that the linker has a clear affinity for the interface and preferentially arranges its residues to reside next to the membrane, without a tendency to relocate into the water phase. Furthermore, an extensive analysis of databases for sequences of membrane proteins that have a single transmembrane helical segment...

  6. Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

    Science.gov (United States)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

  7. Investigating dislocation motion through a field of solutes with atomistic simulations and reaction rate theory

    International Nuclear Information System (INIS)

    Saroukhani, S.; Warner, D.H.

    2017-01-01

    The rate of thermally activated dislocation motion across a field of solutes is studied using traditional and modern atomistically informed rate theories. First, the accuracy of popular variants of the Harmonic Transition State Theory, as the most common approach, is examined by comparing predictions to direct MD simulations. It is shown that HTST predictions are grossly inaccurate due to the anharmonic effect of thermal softening. Next, the utility of the Transition Interface Sampling was examined as the method was recently shown to be effective for predicting the rate of dislocation-precipitate interactions. For dislocation-solute interactions studied here, TIS is found to be accurate only when the dislocation overcomes multiple obstacles at a time, i.e. jerky motion, and it is inaccurate in the unpinning regime where the energy barrier is of diffusive nature. It is then shown that the Partial Path TIS method - designed for diffusive barriers - provides accurate predictions in the unpinning regime. The two methods are then used to study the temperature and load dependence of the rate. It is shown that Meyer-Neldel (MN) rule prediction of the entropy barrier is not as accurate as it is in the case of dislocation-precipitate interactions. In response, an alternative model is proposed that provides an accurate prediction of the entropy barrier. This model can be combined with TST to offer an attractively simple rate prediction approach. Lastly, (PP)TIS is used to predict the Strain Rate Sensitivity (SRS) factor at experimental strain rates and the predictions are compared to experimental values.

  8. DoGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

    DEFF Research Database (Denmark)

    Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector

    2017-01-01

    Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would...... be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools...

  9. Atomistic studies of cation transport in tetragonal ZrO2 during zirconium corrosion

    International Nuclear Information System (INIS)

    Bai, Xian-Ming; Zhang, Yongfeng; Tonks, Michael R.

    2015-01-01

    Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is a significant degradation mechanism of these alloys. During corrosion, the transport of oxidizing species in zirconium dioxide (ZrO 2 ) determines the corrosion kinetics. Previously, it has been argued that the outward diffusion of cations is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO 2 is studied with temperature accelerated dynamics and molecular dynamics simulations. The results show that Zr interstitials have anisotropic diffusion and migrate preferentially along the [001] or c direction in tetragonal ZrO 2 . The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration of Zr interstitials at a grain boundary is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed. (authors)

  10. Atomistic Simulation of the Rate-Dependent Ductile-to-Brittle Failure Transition in Bicrystalline Metal Nanowires.

    Science.gov (United States)

    Tao, Weiwei; Cao, Penghui; Park, Harold S

    2018-02-14

    The mechanical properties and plastic deformation mechanisms of metal nanowires have been studied intensely for many years. One of the important yet unresolved challenges in this field is to bridge the gap in properties and deformation mechanisms reported for slow strain rate experiments (∼10 -2 s -1 ), and high strain rate molecular dynamics (MD) simulations (∼10 8 s -1 ) such that a complete understanding of strain rate effects on mechanical deformation and plasticity can be obtained. In this work, we use long time scale atomistic modeling based on potential energy surface exploration to elucidate the atomistic mechanisms governing a strain-rate-dependent incipient plasticity and yielding transition for face centered cubic (FCC) copper and silver nanowires. The transition occurs for both metals with both pristine and rough surfaces for all computationally accessible diameters (ductile-to-brittle transition in failure mode similar to previous experimental studies on bicrystalline silver nanowires is observed, which is driven by differences in dislocation activity and grain boundary mobility as compared to the high strain rate case.

  11. Thermodynamics of low-temperature phyllosilicates: from a macroscopic perspective towards achieving atomistic simulation

    International Nuclear Information System (INIS)

    Dubacq, B.

    2008-12-01

    suggest several improvements to these methods. We used atomistic simulation to calculate the mixing enthalpy along two solid solutions binaries of interest in low-temperature petrology. Results are in agreement with observations in natural systems and confirm the importance of hydration in clay minerals stability. (author)

  12. Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations

    DEFF Research Database (Denmark)

    Franova, M. D.; Vattulainen, I.; Ollila, O. H. S.

    2014-01-01

    The lateral pressure profile of lipid bilayers has gained a lot of attention, since changes in the pressure profile have been suggested to shift the membrane protein conformational equilibrium. This relation has been mostly studied with theoretical methods, especially with molecular dynamics....../monomer fluorescence ratio has been assumed to represent the lateral pressure in the location of the pyrene moieties. Here, we consider the validity of this assumption through atomistic molecular dynamics simulations in a DOPC (dioleoylphosphatidylcholine) membrane, which hosts di-pyr-PC probes with different acyl...... simulations, since established methods to measure the lateral pressure profile experimentally have not been available. The only experiments that have attempted to gauge the lateral pressure profile have been done by using di-pyrenyl-phosphatidylcholine (di-pyr-PC) probes. In these experiments, the excimer...

  13. Computer code for the atomistic simulation of lattice defects and dynamics

    International Nuclear Information System (INIS)

    Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

    1980-04-01

    This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability

  14. Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code

    Energy Technology Data Exchange (ETDEWEB)

    Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

    1980-04-01

    This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.

  15. Atomistic computer simulations of FePt nanoparticles. Thermodynamic and kinetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, M.

    2007-12-20

    In the present dissertation, a hierarchical multiscale approach for modeling FePt nanoparticles by atomistic computer simulations is developed. By describing the interatomic interactions on different levels of sophistication, various time and length scales can be accessed. Methods range from static quantum-mechanic total-energy calculations of small periodic systems to simulations of whole particles over an extended time by using simple lattice Hamiltonians. By employing these methods, the energetic and thermodynamic stability of non-crystalline multiply twinned FePt nanoparticles is investigated. Subsequently, the thermodynamics of the order-disorder transition in FePt nanoparticles is analyzed, including the influence of particle size, composition and modified surface energies by different chemical surroundings. In order to identify processes that reduce or enhance the rate of transformation from the disordered to the ordered state, the kinetics of the ordering transition in FePt nanoparticles is finally investigated by assessing the contributions of surface and volume diffusion. (orig.)

  16. Atomistic spin dynamics simulations on Mn-doped GaAs and CuMn

    Energy Technology Data Exchange (ETDEWEB)

    Hellsvik, Johan, E-mail: johan.hellsvik@fysik.uu.s [Department of Physics and Materials Science, Uppsala University, Box 530, SE-751 21 Uppsala (Sweden)

    2010-01-01

    The magnetic dynamical behavior of two random alloys have been investigated in atomistic spin dynamics (ASD) simulations. For both materials, magnetic exchange parameters calculated with first principles electronic structure methods were used. From experiments it is well known that CuMn is a highly frustrated magnetic system and a good manifestation of a Heisenberg spin glass. In our ASD simulations the behavior of the autocorrelation function indicate spin glass behavior. The diluted magnetic semiconductor (DMS) Mn-doped GaAs is engineered with hopes of high enough Curie temperatures to operate in spintronic devices. Impurities such as As antisites and Mn interstitials change the exhange couplings from being mainly ferromagnetic to also have antiferromagnetic components. We explore how the resulting frustration affects the magnetization dynamics for a varying rate of As antisites.

  17. Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

    Science.gov (United States)

    Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

    2009-01-01

    Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

  18. Radiation damage in Fe-Cr alloys: Atomistic studies

    International Nuclear Information System (INIS)

    Terentyev, Dmitry; Malerba, Lorenzo; Bonny, Giovanni; Castin, Nicolas

    2009-01-01

    High-Cr ferritic-martensitic steels are the most promising candidate structural materials for future advanced fission reactors, as well as for fusion systems, due to their better thermomechanical properties and higher radiation resistance as compared to austenitic steels. The performance of these steels, especially under irradiation, appears to be largely determined by the Cr content. For instance, the current choice of steel compositions around ∼9 wt% Cr is mainly based on the observation of a local minimum in the ductile-brittle transition temperature shift at this composition. On the other hand, reduced void swelling is observed between 3 and 12 wt% Cr. The origin of these and other Cr-dependent effects remained unexplained for a long time, thereby calling for a physical modelling effort addressing these questions. In this presentation, an overview is given on the effort made in recent years to construct a whole modelling framework, from ab initio to dislocations, to provide explanations to the above-mentioned issues. Ab initio calculations combined to the development of the interatomic potentials capable of grasping key features of Cr atoms embedded in perfect and defected Fe matrix, were required. Primary damage, defect migration, Cr mass transport, phase separation, Cr-defect segregation and dislocation-defect interactions could then be studied using fully atomistic approaches. Our research shows that many of the effects of Cr content on the behaviour of these alloys under irradiation can be attributed to the only recently highlighted high solubility of Cr in Fe (∼10 wt%), below which, in addition, Cr atoms tend to order. The presentation will clarify how this aspect, combined with the high affinity between Cr atoms and self-interstitials defects, influences and partly explain both microstructure evolution and mechanical behaviour of high-Cr steels under irradiation. (author)

  19. Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

    Science.gov (United States)

    Hofman, G. L.; Bozzolo, G.; Mosca, H. O.; Yacout, A. M.

    2011-07-01

    Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

  20. Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

    Energy Technology Data Exchange (ETDEWEB)

    Hofman, G.L. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Bozzolo, G., E-mail: guille_bozzolo@yahoo.com [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Mosca, H.O. [Gerencia de Investigaciones y Aplicaciones, CNEA, Av. Gral Paz 1499, B165KNA, San Martin, Buenos Aires (Argentina); Yacout, A.M. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States)

    2011-07-15

    Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

  1. Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

    Directory of Open Access Journals (Sweden)

    Pavel V. Komarov

    2013-09-01

    Full Text Available Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic and minority (hydrophilic subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping mechanism as a significant contributor to the proton conductivity.

  2. How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations

    DEFF Research Database (Denmark)

    Aijanen, T.; Koivuniemi, A.; Javanainen, M.

    2014-01-01

    Cholesteryl ester transfer protein (CETP) mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides) and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity...... and thereby raise high density lipoprotein (HDL)-cholesterol and decrease low density lipoprotein (LDL)-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics...... simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site...

  3. Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores

    Science.gov (United States)

    Yang, Guomin; Neretnieks, Ivars; Holmboe, Michael

    2017-08-01

    During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and

  4. Multiscale modeling of dislocation processes in BCC tantalum: bridging atomistic and mesoscale simulations

    International Nuclear Information System (INIS)

    Yang, L H; Tang, M; Moriarty, J A

    2001-01-01

    Plastic deformation in bcc metals at low temperatures and high-strain rates is controlled by the motion of a/2 screw dislocations, and understanding the fundamental atomistic processes of this motion is essential to develop predictive multiscale models of crystal plasticity. The multiscale modeling approach presented here for bcc Ta is based on information passing, where results of simulations at the atomic scale are used in simulations of plastic deformation at mesoscopic length scales via dislocation dynamics (DD). The relevant core properties of a/2 screw dislocations in Ta have been obtained using quantum-based interatomic potentials derived from model generalized pseudopotential theory and an ab-initio data base together with an accurate Green's-function simulation method that implements flexible boundary conditions. In particular, the stress-dependent activation enthalpy for the lowest-energy kink-pair mechanism has been calculated and fitted to a revealing analytic form. This is the critical quantity determining dislocation mobility in the DD simulations, and the present activation enthalpy is found to be in good agreement with the previous empirical form used to explain the temperature dependence of the yield stress

  5. Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

    Science.gov (United States)

    Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.

    2011-01-01

    Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

  6. Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

    KAUST Repository

    French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

    2013-01-01

    We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

  7. On the atomistic mechanisms of alkane (methane-pentane) separation by distillation: a molecular dynamics study.

    Science.gov (United States)

    Zahn, Dirk

    2007-11-01

    Insights into the liquid-vapor transformation of methane-pentane mixtures were obtained from transition path sampling molecular dynamics simulations. This case study of the boiling of non-azeotropic mixtures demonstrates an unprejudiced identification of the atomistic mechanisms of phase separation in the course of vaporization which form the basis of distillation processes. From our simulations we observe spontaneous segregation events in the liquid mixture to trigger vapor nucleation. The formation of vapor domains stabilizes and further promotes the separation process by preferential evaporation of methane molecules. While this discrimination holds for all mixtures of different composition studied, a full account of the boiling process requires a more complex picture. At low methane concentration the nucleation of the vapor domains includes both methane and pentane molecules. The pentane molecules, however, tend to form small aggregates and undergo rapid re-condensation within picoseconds to nanoseconds scales. Accordingly, two aspects of selectivity accounting for methane-pentane separation in the course of liquid-vapor transformations were made accessible to molecular dynamics simulations: spontaneous segregation in the liquid phase leading to selective vapor nucleation and growth favoring methane vaporization and selective re-condensation of pentane molecules.

  8. Atomistic simulation of MgO nanowires subject to electromagnetic wave

    International Nuclear Information System (INIS)

    Wang, Xianqiao; Lee, James D

    2010-01-01

    This work is concerned with the application of atomistic field theory (AFT) in modeling and simulation of polarizable materials under an electromagnetic (EM) field. AFT enables us to express an atomic scale local property of a multi-element crystalline (which has more than one kind of atom in the unit cell) system in terms of the distortions of lattice cells and the rearrangement of atoms within the lattice cell, thereby making AFT suitable to fully reproduce both acoustic and optical branches in phonon dispersion relations. Due to the applied EM field, the inhomogeneous motions of discrete atoms in the polarizable crystal give rise to the rearrangement of microstructure and polarization. The AFT and its corresponding finite element implementation are briefly introduced. Single-crystal MgO nanowires under an EM field is modeled and simulated. The numerical results have demonstrated that AFT can serve as a tool to analyze the electromagnetic phenomena of multi-element crystal materials at micro/nano-level within a field framework

  9. Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

    Science.gov (United States)

    Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

    2012-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

  10. ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

    Science.gov (United States)

    Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

    2010-04-15

    We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

  11. Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

    KAUST Repository

    Hong, Bingbing

    2013-10-02

    We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH 2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henrys constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henrys constant. Dependence of the calculated Henrys constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. © 2013 Taylor & Francis.

  12. Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

    Energy Technology Data Exchange (ETDEWEB)

    Djurabekova, F.G. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Domingos, R. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Cerchiara, G. [Department of Nuclear and Production Engineering, University of Pisa (Italy); Castin, N. [Catholic University of Louvain-la-Neuve (Belgium); Vincent, E. [LMPGM UMR-8517, University of Lille I, Villeneuve d' Ascq (France); Malerba, L. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium)]. E-mail: lmalerba@sckcen.be

    2007-02-15

    Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed.

  13. Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

    International Nuclear Information System (INIS)

    Djurabekova, F.G.; Domingos, R.; Cerchiara, G.; Castin, N.; Vincent, E.; Malerba, L.

    2007-01-01

    Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed

  14. De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, A; Kalia, R K; Nomura, K; Sharma, A; Vashishta, P; Shimojo, F; van Duin, A; Goddard, III, W A; Biswas, R; Srivastava, D; Yang, L H

    2006-09-04

    We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) simulations explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) simulations are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling simulation algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto Petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/computation structures, as well as its implementation using hybrid Grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations--1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids--in addition to 134 billion-atom non-reactive space-time multiresolution MD, with the parallel efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM

  15. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  16. Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

    Science.gov (United States)

    Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

    2018-01-01

    The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

  17. Critical assessment of Pt surface energy - An atomistic study

    Science.gov (United States)

    Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

    2018-04-01

    Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

  18. Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

    Science.gov (United States)

    Soisson, F.; Becquart, C. S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

    2010-11-01

    Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using "on-the-fly" calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

  19. Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

    International Nuclear Information System (INIS)

    Soisson, F.; Becquart, C.S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

    2010-01-01

    Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using 'on-the-fly' calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

  20. On the use of atomistic simulations to aid bulk metallic glasses structural elucidation with solid-state NMR.

    Science.gov (United States)

    Ferreira, Ary R; Rino, José P

    2017-08-24

    Solid-state nuclear magnetic resonance (ssNMR) experimental 27 Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.

  1. Shape evolution of nanostructures by thermal and ion beam processing. Modeling and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Roentzsch, L.

    2007-07-01

    Single-crystalline nanostructures often exhibit gradients of surface (and/or interface) curvature that emerge from fabrication and growth processes or from thermal fluctuations. Thus, the system-inherent capillary force can initiate morphological transformations during further processing steps or during operation at elevated temperature. Therefore and because of the ongoing miniaturization of functional structures which causes a general rise in surface-to-volume ratios, solid-state capillary phenomena will become increasingly important: On the one hand diffusion-mediated capillary processes can be of practical use in view of non-conventional nanostructure fabrication methods based on self-organization mechanisms, on the other hand they can destroy the integrity of nanostructures which can go along with the failure of functionality. Additionally, capillarity-induced shape transformations are effected and can thereby be controlled by applied fields and forces (guided or driven evolution). With these prospects and challenges at hand, formation and shape transformation of single-crystalline nanostructures due to the system-inherent capillary force in combination with external fields or forces are investigated in the frame of this dissertation by means of atomistic computer simulations. For the exploration (search, description, and prediction) of reaction pathways of nanostructure shape transformations, kinetic Monte Carlo (KMC) simulations are the method of choice. Since the employed KMC code is founded on a cellular automaton principle, the spatio-temporal development of lattice-based N-particle systems (N up to several million) can be followed for time spans of several orders of magnitude, while considering local phenomena due to atomic-scale effects like diffusion, nucleation, dissociation, or ballistic displacements. In this work, the main emphasis is put on nanostructures which have a cylindrical geometry, for example, nanowires (NWs), nanorods, nanotubes etc

  2. Degenerate Ising model for atomistic simulation of crystal-melt interfaces

    International Nuclear Information System (INIS)

    Schebarchov, D.; Schulze, T. P.; Hendy, S. C.

    2014-01-01

    One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level

  3. Degenerate Ising model for atomistic simulation of crystal-melt interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Schebarchov, D., E-mail: Dmitri.Schebarchov@gmail.com [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Schulze, T. P., E-mail: schulze@math.utk.edu [Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996-1300 (United States); Hendy, S. C. [The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140 (New Zealand); Department of Physics, University of Auckland, Auckland 1010 (New Zealand)

    2014-02-21

    One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level.

  4. Shape evolution of nanostructures by thermal and ion beam processing. Modeling and atomistic simulations

    International Nuclear Information System (INIS)

    Roentzsch, L.

    2007-01-01

    Single-crystalline nanostructures often exhibit gradients of surface (and/or interface) curvature that emerge from fabrication and growth processes or from thermal fluctuations. Thus, the system-inherent capillary force can initiate morphological transformations during further processing steps or during operation at elevated temperature. Therefore and because of the ongoing miniaturization of functional structures which causes a general rise in surface-to-volume ratios, solid-state capillary phenomena will become increasingly important: On the one hand diffusion-mediated capillary processes can be of practical use in view of non-conventional nanostructure fabrication methods based on self-organization mechanisms, on the other hand they can destroy the integrity of nanostructures which can go along with the failure of functionality. Additionally, capillarity-induced shape transformations are effected and can thereby be controlled by applied fields and forces (guided or driven evolution). With these prospects and challenges at hand, formation and shape transformation of single-crystalline nanostructures due to the system-inherent capillary force in combination with external fields or forces are investigated in the frame of this dissertation by means of atomistic computer simulations. For the exploration (search, description, and prediction) of reaction pathways of nanostructure shape transformations, kinetic Monte Carlo (KMC) simulations are the method of choice. Since the employed KMC code is founded on a cellular automaton principle, the spatio-temporal development of lattice-based N-particle systems (N up to several million) can be followed for time spans of several orders of magnitude, while considering local phenomena due to atomic-scale effects like diffusion, nucleation, dissociation, or ballistic displacements. In this work, the main emphasis is put on nanostructures which have a cylindrical geometry, for example, nanowires (NWs), nanorods, nanotubes etc

  5. Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension

    Science.gov (United States)

    Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.

    2017-10-01

    We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.

  6. Deformation behaviors of three-dimensional graphene honeycombs under out-of-plane compression: Atomistic simulations and predictive modeling

    Science.gov (United States)

    Meng, Fanchao; Chen, Cheng; Hu, Dianyin; Song, Jun

    2017-12-01

    Combining atomistic simulations and continuum modeling, a comprehensive study of the out-of-plane compressive deformation behaviors of equilateral three-dimensional (3D) graphene honeycombs was performed. It was demonstrated that under out-of-plane compression, the honeycomb exhibits two critical deformation events, i.e., elastic mechanical instability (including elastic buckling and structural transformation) and inelastic structural collapse. The above events were shown to be strongly dependent on the honeycomb cell size and affected by the local atomic bonding at the cell junction. By treating the 3D graphene honeycomb as a continuum cellular solid, and accounting for the structural heterogeneity and constraint at the junction, a set of analytical models were developed to accurately predict the threshold stresses corresponding to the onset of those deformation events. The present study elucidates key structure-property relationships of 3D graphene honeycombs under out-of-plane compression, and provides a comprehensive theoretical framework to predictively analyze their deformation responses, and more generally, offers critical new knowledge for the rational bottom-up design of 3D networks of two-dimensional nanomaterials.

  7. From empirical to ab initio: transferable potentials in the atomistic simulation of amorphous carbons

    International Nuclear Information System (INIS)

    Marks, N.A.; Goringe, C.M.; McKenzie, D.R.; McCulloch, D.G.; Royal Melbourne Institute of Technology University, Melbourne, VIC

    2000-01-01

    Full text: Silicon is often described as the prototype covalent material, and when it comes to developing atomistic models this situation is well described by the sentiment that 'everything works for silicon'. The same cannot be said for carbon though, where the interaction potential has always proved problematical, be it with empirical, tight-binding or ab initio methods. Thus far the most decisive contributions to understanding amorphous carbon networks have come from ab initio simulations using the Car-Parrinello method, where the fully quantum treatment of the valence electrons has provided unexpected insight into the local structure. However such first principles calculations are restricted spatially and temporally to systems with approximately 100 atoms and times of order one picosecond. There is therefore demand for less expensive techniques capable of resolving important questions whose solution can only to found with larger simulations running for longer times. In the case of tetrahedral amorphous carbon, such issues include the release of compressive stress through annealing, the origin of graphitic surface layers and the nature of the film growth process and thermal spike. Against this background tight-binding molecular dynamics has emerged as a popular alternative to first principles methods, and our group has an ongoing program to understand film growth using one of the efficient variants of tight-binding. Another direction of research is a new empirical potential based on the Environment Dependent Interaction Potential (EDIP) recently developed for silicon. The EDIP approach represents a promising direction for empirical potentials through its use of ab initio data to motivate the functional form as well as the more conventional parametrisation. By inverting ab initio cohesive energy curves the authors of EDIP arrived at a pair potential expression which reduces to the well-known Stillinger-Weber form at integer coordination, while providing

  8. Atomistic simulation of solid solution hardening in Mg/Al alloys: Examination of composition scaling and thermo-mechanical relationships

    International Nuclear Information System (INIS)

    Yi, Peng; Cammarata, Robert C.; Falk, Michael L.

    2016-01-01

    Dislocation mobility in a solid solution was studied using atomistic simulations of an Mg/Al system. The critical resolved shear stress (CRSS) for the dislocations on the basal plane was calculated at temperatures from 0 K to 500 K with solute concentrations from 0 to 7 at%, and with four different strain rates. Solute hardening of the CRSS is decomposed into two contributions: one scales with c 2/3 , where c is the solute concentration, and the other scales with c 1 . The former was consistent with the Labusch model for local solute obstacles, and the latter was related to the athermal plateau stress due to the long range solute effect. A thermo-mechanical model was then used to analyze the temperature and strain rate dependences of the CRSS, and it yielded self-consistent and realistic results. The scaling laws were confirmed and the thermo-mechanical model was successfully parameterized using experimental measurements of the CRSS for Mg/Al alloys under quasi-static conditions. The predicted strain rate sensitivity from the experimental measurements of the CRSS is in reasonable agreement with separate mechanical tests. The concentration scaling and the thermo-mechanical relationships provide a potential tool to analytically relate the structural and thermodynamic parameters on the microscopic level with the macroscopic mechanical properties arising from dislocation mediated deformation.

  9. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

    NARCIS (Netherlands)

    Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.

    2016-01-01

    We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell

  10. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

    Science.gov (United States)

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

    2012-07-01

    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

  11. Automated Algorithms for Quantum-Level Accuracy in Atomistic Simulations: LDRD Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Aidan Patrick; Schultz, Peter Andrew; Crozier, Paul; Moore, Stan Gerald; Swiler, Laura Painton; Stephens, John Adam; Trott, Christian Robert; Foiles, Stephen Martin; Tucker, Garritt J. (Drexel University)

    2014-09-01

    This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel computers

  12. Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers

    Science.gov (United States)

    Badalkhani-Khamseh, Farideh; Ebrahim-Habibi, Azadeh; Hadipour, Nasser L.

    2017-12-01

    Poly(amidoamine) (PAMAM) dendrimers have been extensively studied as delivery vectors in biomedical applications. A limited number of molecular dynamics (MD) simulation studies have investigated the effect of surface chemistry on therapeutic molecules loading, with the aim of providing insights for biocompatibility improvement and increase in drug loading capacity of PAMAM dendrimers. In this work, fully atomistic MD simulations were employed to study the association of 5-Fluorouracil (5-FU) with amine (NH2)- and hydroxyl (OH)-terminated PAMAM dendrimers of generations 3 and 4 (G3 and G4). MD results show a 1:12, 1:1, 1:27, and 1:4 stoichiometry, respectively, for G3NH2-FU, G3OH-FU, G4NH2-FU, and G4OH-FU complexes, which is in good agreement with the isothermal titration calorimetry results. The results obtained showed that NH2-terminated dendrimers assume segmented open structures with large cavities and more drug molecules can encapsulate inside the dendritic cavities of amine terminated dendrimers. However, OH-terminated have a densely packed structure and therefore, 5-FU drug molecules are more stable to locate close to the surface of the dendrimers. Intermolecular hydrogen bonding analysis showed that 5-FU drug molecules have more tendency to form hydrogen bonds with terminal monomers of OH-terminated dendrimers, while in NH2-terminated these occur both in the inner region and the surface. Furthermore, MM-PBSA analysis revealed that van der Waals and electrostatic energies are both important to stabilize the complexes. We found that drug molecules are distributed uniformly inside the amine and hydroxyl terminated dendrimers and therefore, both dendrimers are promising candidates as drug delivery systems for 5-FU drug molecules.

  13. Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: Insights from atomistic simulations

    Science.gov (United States)

    Kumari, Pratibha; Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

    2018-04-01

    Modulation of lipid membrane properties due to the permeation of amphiphiles is an important biological process pertaining to many applications in the field of pharmaceutics, toxicology, and biotechnology. Sphingolipids are both structural and functional lipids that constitute an important component of mechanically stable and chemically resistant outer leaflets of plasma membranes. Here, we present an atomistic molecular dynamics simulation study to appreciate the concentration-dependent effects of small amphiphilic molecules, such as ethanol, acetone, and dimethyl sulfoxide (DMSO), on the structure and stability of a fully hydrated homogeneous N-palmitoyl-sphingomyelin (PSM) bilayer. The study reveals an increase in the lateral expansion of the bilayer along with disordering of the hydrophobic lipid tails on increasing the concentration of ethanol. At higher concentrations of ethanol, rupturing of the bilayer is quite evident through the analysis of partial electron density profiles and lipid tail order parameters. For ethanol containing systems, permeation of water molecules in the hydrophobic part of the bilayer is allowed through local defects made due to the entry of ethanol molecules via ethanol-ethanol and ethanol-PSM hydrogen bonds. Moreover, the extent of PSM-PSM hydrogen bonding decreases with increasing ethanol concentration. On the other hand, acetone and DMSO exhibit minimal effects on the stability of the PSM bilayer at their lower concentrations, but at higher concentrations they tend to enhance the stability of the bilayer. The simulated potential of mean force (PMF) profiles for the translocation of the three solutes studied reveal that the free-energy of transfer of an ethanol molecule across the PSM lipid head region is lower than that for acetone and DMSO molecules. However, highest free-energy rise in the core hydrophobic part of the bilayer is observed for the DMSO molecule, whereas the ethanol and acetone PMF profiles show a lower barrier in

  14. Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry

    DEFF Research Database (Denmark)

    Petersen, Michael; Madsen, Jeppe B; Jørgensen, Thomas J D

    2017-01-01

    activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations...... are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1......Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen...

  15. Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

    Science.gov (United States)

    Quevillon, Michael J; Whitmer, Jonathan K

    2018-01-02

    Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure-constant temperature ensemble. These materials exhibit a distinct "smectic" liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

  16. Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia.

    Directory of Open Access Journals (Sweden)

    Ramon Reigada

    Full Text Available The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic and carbon tetrachloride (non-anesthetic. Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.

  17. Atomistic simulations of screw dislocations in bcc tungsten: From core structures and static properties to interaction with vacancies

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Ke [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Niu, Liang-Liang [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Department of Nuclear Engineering and Radiological Science, University of Michigan, Ann Arbor, MI 48109 (United States); Jin, Shuo, E-mail: jinshuo@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Shu, Xiaolin [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Xie, Hongxian [School of Mechanical Engineering, Hebei University of Technology, Tianjin 300132 (China); Wang, Lifang; Lu, Guang-Hong [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China)

    2017-02-15

    Atomistic simulations have been used to investigate the core structures, static properties of isolated 1/2 <1 1 1> screw dislocations, and their interaction with vacancies in bcc tungsten (W) based on three empirical interatomic potentials. Differential displacement maps show that only one embedded atom method potential is able to reproduce the compact non-degenerate core as evidenced by ab initio calculations. The obtained strain energy and stress distribution from atomistic simulations are, in general, consistent with elasticity theory predictions. In particular, one component of the calculated shear stress, which is not present according to elasticity theory, is non-negligible in the core region of our dislocation model. The differences between the results calculated from three interatomic potentials are in details, such as the specific value and the symmetry, but the trend of spatial distributions of static properties in the long range are close to each other. By calculating the binding energies between the dislocations and vacancies, we demonstrate that the dislocations act as vacancy sinks, which may be important for the nucleation and growth of hydrogen bubbles in W under irradiation.

  18. An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

    Science.gov (United States)

    Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.

    2013-12-01

    In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations

  19. Atomistic study of drag, surface and inertial effects on edge dislocations in face-centered cubic metals

    International Nuclear Information System (INIS)

    Bitzek, Erik; Gumbsch, Peter

    2004-01-01

    Atomistic simulations of an accelerating edge dislocation were carried out to study the effects of drag and inertia. Using an embedded atom potential for nickel, the Peierls stress, the effective mass and the drag coefficient of an edge dislocation were determined for different temperatures and stresses in a simple slab geometry. The effect of {1 1 1} surfaces on an intersecting edge dislocation were studied by appropriately cutting the slab. A dislocation intersecting a surface step was used as a model system to demonstrate the importance of inertial effects for dynamically overcoming short range obstacles. Significant effects were found even at room temperature. A simple model based on the dislocation-obstacle interaction energies was used to describe the findings

  20. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)

    2015-12-28

    We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

  1. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    International Nuclear Information System (INIS)

    Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian; Sugii, Taisuke

    2015-01-01

    We investigate the volumetric glass transition temperature T g in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T g increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T g in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T g is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment

  2. Atomistic studies of nucleation of He clusters and bubbles in bcc iron

    International Nuclear Information System (INIS)

    Yang, L.; Deng, H.Q.; Gao, F.; Heinisch, H.L.; Kurtz, R.J.; Hu, S.Y.; Li, Y.L.; Zu, X.T.

    2013-01-01

    Atomistic simulations of the nucleation of He clusters and bubbles in bcc iron at 800 K have been carried out using the newly developed Fe–Fe interatomic potential, along with Ackland potential for the Fe–Fe interactions. Microstructure changes were analyzed in detail. We found that a He cluster with four He atoms is able to push out an iron interstitial from the cluster, creating a Frenkel pair. Small He clusters and self-interstitial atom (SIA) can migrate in the matrix, but He-vacancy (He-V) clusters are immobile. Most SIAs form clusters, and only the dislocation loops with a Burgers vector of b = 1/2 appear in the simulations. SIA clusters (or loops) are attached to He-V clusters for He implantation up to 1372 appm, while the He-V cluster–loop complexes with more than one He-V cluster are formed at the He concentration of 2057 appm and larger

  3. Ab-initio and atomistic study of the ferroelectric properties of Cu doped potassium niobate

    Energy Technology Data Exchange (ETDEWEB)

    Koerbel, Sabine; Elsaesser, Christian [Fraunhofer-Institut fuer Werkstoffmechanik IWM, Woehlerstrasse 11, 79108 Freiburg (Germany)

    2011-07-01

    KNbO{sub 3} is one end member of the solid solution (K,Na)NbO{sub 3} (KNN), which has promising ferroelectric properties to become a future lead-free substitute for lead zirconate titanate Pb(Zr,Ti)O{sub 3} (PZT) in piezoelectric actors and sensors. Both KNN and PZT exhibit a phase transition with composition and a morphotropic phase boundary, at which enhanced piezoelectric coefficients are obtained. The material properties of PZT and KNN are commonly optimized by doping. E.g., CuO can be added when fabricating KNN as a sintering aid. Ab initio density functional theory and atomistic simulation using a classical shell model potential have been combined to investigate low Cu concentrations in the KNbO{sub 3}-CuNbO{sub 3} system. The atomistic model predicts a morphotropic phase boundary at a few percent Cu, analogous to the one found in the LiNbO{sub 3}-KNbO{sub 3} system.

  4. Atomistic simulation of dislocation nucleation barriers from cracktips in α-Fe

    International Nuclear Information System (INIS)

    Gordon, Peter A; Neeraj, T; Luton, Michael J

    2008-01-01

    In this work, we demonstrate that activation pathways for dislocation loop nucleation from cracktips can be explored with full atomistic detail using an efficient form of the nudged elastic band method. The approach is demonstrated in detail with an example of edge emission from an Fe crack under mode II loading, wherein activation energy barriers are obtained as a function of sub-critical stress intensity and the energy barriers for loop formation are compared with 2D calculations. Activation energy barriers are also computed for an intrinsically ductile cracktip orientation under mode I loading, from which we can infer the frequency of nucleation from the cracktip

  5. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

    Science.gov (United States)

    Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

    2015-01-01

    Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  6. Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

    Science.gov (United States)

    Lépinoux, J.; Sigli, C.

    2018-01-01

    In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.

  7. Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc(1) complex

    DEFF Research Database (Denmark)

    Poyry, S.; Cramariuc, O.; Postila, P. A.

    2013-01-01

    by both ensuring the structural integrity of the protein complex and also by taking part in the proton uptake. Yet, the atom-scale understanding of these highly charged four-tail lipids in the cyt bc(1) function has remained quite unclear. We consider this issue through atomistic molecular dynamics...... the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics...... simulations that are applied to the entire cyt bc(1) dimer of the purple photosynthetic bacterium Rhodobacter capsulatus embedded in a lipid bilayer. We find CLs to spontaneously diffuse to the dimer interface to the immediate vicinity of the higher potential heme b groups of the complex's catalytic Q...

  8. Compressive buckling of black phosphorene nanotubes: an atomistic study

    Science.gov (United States)

    Nguyen, Van-Trang; Le, Minh-Quy

    2018-04-01

    We investigate through molecular dynamics finite element method with Stillinger-Weber potential the uniaxial compression of armchair and zigzag black phosphorene nanotubes. We focus especially on the effects of the tube’s diameter with fixed length-diameter ratio, effects of the tube’s length for a pair of armchair and zigzag tubes of equal diameters, and effects of the tube’s diameter with fixed lengths. Their Young’s modulus, critical compressive stress and critical compressive strain are studied and discussed for these 3 case studies. Compressive buckling was clearly observed in the armchair nanotubes. Local bond breaking near the boundary occurred in the zigzag ones under compression.

  9. Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vuorela, T.; Kovanen, P. T.

    2012-01-01

    molecular dynamics simulations to unravel the mechanisms associated with the CETP-mediated lipid exchange. To this end we used both atomistic and coarse-grained models whose results were consistent with each other. We found CETP to bind to the surface of high density lipoprotein (HDL) -like lipid droplets......Cholesteryl ester transfer protein (CETP) transports cholesteryl esters, triglycerides, and phospholipids between different lipoprotein fractions in blood plasma. The inhibition of CETP has been shown to be a sound strategy to prevent and treat the development of coronary heart disease. We employed...... evidence that helix X acts as a lid which conducts lipid exchange by alternating the open and closed states. The findings have potential for the design of novel molecular agents to inhibit the activity of CETP....

  10. Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

    Science.gov (United States)

    Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

    2003-01-01

    Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

  11. Molecular dynamics simulations of the atomistic structure of the intergranular film between silicon nitride grains: Effect of composition, thickness, and surface vacancies

    International Nuclear Information System (INIS)

    Garofalini, Stephen H.

    2006-01-01

    Molecular dynamics computer simulations were used to study the atomistic structure of intergranular films (IGFs) between two basal oriented Si 3 N 4 crystals or between combined basal and prism oriented crystals. Ordering of the ions into the IGF induced by the crystal surfaces was observed using density profiles of the ions, although that ordering is effected by the roughness of the crystal surface. Density profiles of the sum of all ions misleadingly shows a rapid decay in the density oscillations and apparent ordering into the IGF. However, this is an artifact of the coincidence of the maximum in the peaks of one species with the minimum of another species and the actual oscillations of individual species extend into the IGF farther than the sum profile indicates. This result would have important implications regarding the density oscillations observed in physical experiments with regard to the actual extent of ordering into the IGF induced by the crystal surface

  12. Stearic acid spin labels in lipid bilayers :  insight through atomistic simulations

    NARCIS (Netherlands)

    Stimson, L.M.; Dong, L.; Karttunen, M.E.J.; Wisniewska, A.; Dutka, M.; Róg, T.

    2007-01-01

    Spin-labeled stearic acid species are commonly used for electron paramagnetic resonance (EPR) studies of cell membranes to investigate phase transitions, fluidity, and other physical properties. In this paper, we use large-scale molecular dynamics simulations to investigate the position and behavior

  13. An Overview of the State of the Art in Atomistic and Multiscale Simulation of Fracture

    Science.gov (United States)

    Saether, Erik; Yamakov, Vesselin; Phillips, Dawn R.; Glaessgen, Edward H.

    2009-01-01

    The emerging field of nanomechanics is providing a new focus in the study of the mechanics of materials, particularly in simulating fundamental atomic mechanisms involved in the initiation and evolution of damage. Simulating fundamental material processes using first principles in physics strongly motivates the formulation of computational multiscale methods to link macroscopic failure to the underlying atomic processes from which all material behavior originates. This report gives an overview of the state of the art in applying concurrent and sequential multiscale methods to analyze damage and failure mechanisms across length scales.

  14. Evaluating variability with atomistic simulations: the effect of potential and calculation methodology on the modeling of lattice and elastic constants

    Science.gov (United States)

    Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.

    2018-07-01

    Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.

  15. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

    Science.gov (United States)

    2017-01-01

    We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

  16. Effects of alpha decays on nuclear waste glasses, simulation through atomistic models

    International Nuclear Information System (INIS)

    Ghaleb, D.; Delaye, J.M.

    1997-01-01

    In a simplified (SiO 2 , B 2 O 3 , Na 2 O 3 , Al 2 O 3 , ZrO 2 ) nuclear glass we have simulated, by Molecular Dynamics simulations, the effects of displacement cascades created by the slowing-down of the recoil nucleus. The methodology employed to construct and validate the used Molecular Dynamics model representing the basis matrix of the 'light-water' French nuclear glass (R77) and the manner which are simulated atomic displacements are described. Although the energies given to recoil nucleus were relatively low (≤ 1/10 of actual energies) the study has yielded a number of interesting results. Notably we have: - identified the main mechanisms responsible for the depolymerization of the network; - observed, at the atomic level, the kinetic of the structure evolution; - detailed the behavior and displacement mechanisms of every atomic species during the cascade sequences; - made a link with the experimentation through the calculation of some physical properties. (authors)

  17. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Alan [The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Harlen, Oliver G. [University of Leeds, Leeds LS2 9JT (United Kingdom); Harris, Sarah A., E-mail: s.a.harris@leeds.ac.uk [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Leeds, Leeds LS2 9JT (United Kingdom); Khalid, Syma; Leung, Yuk Ming [University of Southampton, Southampton SO17 1BJ (United Kingdom); Lonsdale, Richard [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg (Germany); Mulholland, Adrian J. [University of Bristol, Bristol BS8 1TS (United Kingdom); Pearson, Arwen R. [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Hamburg, Hamburg (Germany); Read, Daniel J.; Richardson, Robin A. [University of Leeds, Leeds LS2 9JT (United Kingdom); The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom)

    2015-01-01

    The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  18. Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations

    Science.gov (United States)

    Piaggi, Pablo M.; Valsson, Omar; Parrinello, Michele

    2017-07-01

    Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. As in all first order first transitions, there is an interplay between enthalpy and entropy. Based on this idea, in order to drive crystallization in molecular simulations, we introduce two collective variables, one enthalpic and the other entropic. Defined in this way, these collective variables do not prejudge the structure into which the system is going to crystallize. We show the usefulness of this approach by studying the cases of sodium and aluminum that crystallize in the bcc and fcc crystalline structures, respectively. Using these two generic collective variables, we perform variationally enhanced sampling and well tempered metadynamics simulations and find that the systems transform spontaneously and reversibly between the liquid and the solid phases.

  19. Study of the embedded atom method of atomistic calculations for metals and alloys

    International Nuclear Information System (INIS)

    Johnson, R.A.

    1990-10-01

    Two projects were completed in the past year. The stability of a series of binary alloys was calculated using the embedded-atom method (EAM) with an analytic form for two-body potentials derived previously. Both disordered alloys and intermetallic compounds with the L1 0 and L1 2 structures were studied. The calculated heats of solution of alloys of Cu, Ag, Au, Ni, and Pt were satisfactory, while results for alloys containing Pd were too high. Atomistic calculations using the EAM were also carried out for point defects in hcp metals. By comparison with results in the literature, it was found that many body effects from the EAM significantly alter predicted physical properties of hcp metals. For example, the EAM calculations yield anisotropic vacancy diffusion with greater vacancy mobility in the basal plane, and imply that diffusion will start at a lower fraction of the melting temperature

  20. Early structural development in melt-quenched polymer PTT from atomistic molecular dynamic simulations

    Science.gov (United States)

    Hsieh, Min-Kang; Lin, Shiang-Tai

    2009-12-01

    Molecular dynamics simulations are performed to study the initial structural development in poly(trimethylene terephthalate) (PTT) when quenched below its melting point. The development of local ordering has been observed in our simulations. The thermal properties, such as the glass transition temperature (Tg) and the melting temperature (Tm), determined from our simulations are in reasonable agreement with experimental values. It is found that, between these two temperatures, the number of local structures quickly increases during the thermal relaxation period soon after the system is quenched and starts to fluctuate afterwards. The formation and development of local structures is found to be driven mainly by the torsional and van der Waals forces and follows the classical nucleation-growth mechanism. The variation of local structures' fraction with temperature exhibits a maximum between Tg and Tm, resembling the temperature dependence of the crystallization rate for most polymers. In addition, the backbone torsion distribution for segments within the local structures preferentially reorganizes to the trans-gauche-gauche-trans (t-g-g-t) conformation, the same as that in the crystalline state. As a consequence, we believe that such local structural ordering could be the baby nuclei that have been suggested to form in the early stage of polymer crystallization.

  1. Elastic deformation and failure in protein filament bundles: Atomistic simulations and coarse-grained modeling.

    Science.gov (United States)

    Hammond, Nathan A; Kamm, Roger D

    2008-07-01

    The synthetic peptide RAD16-II has shown promise in tissue engineering and drug delivery. It has been studied as a vehicle for cell delivery and controlled release of IGF-1 to repair infarcted cardiac tissue, and as a scaffold to promote capillary formation for an in vitro model of angiogenesis. The structure of RAD16-II is hierarchical, with monomers forming long beta-sheets that pair together to form filaments; filaments form bundles approximately 30-60 nm in diameter; branching networks of filament bundles form macroscopic gels. We investigate the mechanics of shearing between the two beta-sheets constituting one filament, and between cohered filaments of RAD16-II. This shear loading is found in filament bundle bending or in tensile loading of fibers composed of partial-length filaments. Molecular dynamics simulations show that time to failure is a stochastic function of applied shear stress, and that for a given loading time behavior is elastic for sufficiently small shear loads. We propose a coarse-grained model based on Langevin dynamics that matches molecular dynamics results and facilities extending simulations in space and time. The model treats a filament as an elastic string of particles, each having potential energy that is a periodic function of its position relative to the neighboring filament. With insight from these simulations, we discuss strategies for strengthening RAD16-II and similar materials.

  2. Atomistic simulations of diffusional creep in a nanocrystalline body-centered cubic material

    International Nuclear Information System (INIS)

    Millett, Paul C.; Desai, Tapan; Yamakov, Vesselin; Wolf, Dieter

    2008-01-01

    Molecular dynamics (MD) simulations are used to study diffusion-accommodated creep deformation in nanocrystalline molybdenum, a body-centered cubic metal. In our simulations, the microstructures are subjected to constant-stress loading at levels below the dislocation nucleation threshold and at high temperatures (i.e., T > 0.75T melt ), thereby ensuring that the overall deformation is indeed attributable to atomic self-diffusion. The initial microstructures were designed to consist of hexagonally shaped columnar grains bounded by high-energy asymmetric tilt grain boundaries (GBs). Remarkably the creep rates, which exhibit a double-exponential dependence on temperature and a double power-law dependence on grain size, indicate that both GB diffusion in the form of Coble creep and lattice diffusion in the form of Nabarro-Herring creep contribute to the overall deformation. For the first time in an MD simulation, we observe the formation and emission of vacancies from high-angle GBs into the grain interiors, thus enabling bulk diffusion

  3. Construction of a kinetics model for liquid-solid transitions built from atomistic simulations

    Science.gov (United States)

    Benedict, Lorin; Zepeda-Ruiz, Luis; Haxhimali, Tomorr; Hamel, Sebastien; Sadigh, Babak; Chernov, Alexander; Belof, Jonathan

    We discuss work in progress towards a kinetics model for dynamically-driven liquid-solid transitions built from MD simulations. The growth of solid particles within a liquid is studied for a range of conditions, and careful attention is paid to the construction of an accurate multi-phase (equilibrium) equation of state for the system under consideration, in order to provide a framework upon which the non-equilibrium physics is based. His work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Lawrence Livermore National Security, LLC.

  4. Atomistic Simulations of Fluid Flow through Graphene Channels and Carbon Nanotubes

    DEFF Research Database (Denmark)

    Zambrano, Harvey A.; Walther, Jens Honore; Oyarzua, Elton E.

    2015-01-01

    conductivity, extremely low surface friction and superior mechanical properties, graphene channels and carbon nanotubes (CNTs) are promising candidates to be implemented as fluid conduits in nanosystems. Performing Non-equilibrium Molecular Dynamics simulations, we study the transport of water......-eletrolyte solutions inside single and multi-wall graphene channels and inside zig-zag and armchair CNTs of similar cross sectional area. In order to calibrate the force fields, we use dedicated criteria relevant to the hydrodynamics of the systems of interest. Different fluid driving mechanisms such as pressure...

  5. A method of integration of atomistic simulations and continuum mechanics by collecting of dynamical systems with dimensional reduction

    International Nuclear Information System (INIS)

    Kaczmarek, J.

    2002-01-01

    Elementary processes responsible for phenomena in material are frequently related to scale close to atomic one. Therefore atomistic simulations are important for material sciences. On the other hand continuum mechanics is widely applied in mechanics of materials. It seems inevitable that both methods will gradually integrate. A multiscale method of integration of these approaches called collection of dynamical systems with dimensional reduction is introduced in this work. The dimensional reduction procedure realizes transition between various scale models from an elementary dynamical system (EDS) to a reduced dynamical system (RDS). Mappings which transform variables and forces, skeletal dynamical system (SDS) and a set of approximation and identification methods are main components of this procedure. The skeletal dynamical system is a set of dynamical systems parameterized by some constants and has variables related to the dimensionally reduced model. These constants are identified with the aid of solutions of the elementary dynamical system. As a result we obtain a dimensionally reduced dynamical system which describes phenomena in an averaged way in comparison with the EDS. Concept of integration of atomistic simulations with continuum mechanics consists in using a dynamical system describing evolution of atoms as an elementary dynamical system. Then, we introduce a continuum skeletal dynamical system within the dimensional reduction procedure. In order to construct such a system we have to modify a continuum mechanics formulation to some degree. Namely, we formalize scale of averaging for continuum theory and as a result we consider continuum with finite-dimensional fields only. Then, realization of dimensional reduction is possible. A numerical example of realization of the dimensional reduction procedure is shown. We consider a one dimensional chain of atoms interacting by Lennard-Jones potential. Evolution of this system is described by an elementary

  6. Atomistic to Continuum Multiscale and Multiphysics Simulation of NiTi Shape Memory Alloy

    Science.gov (United States)

    Gur, Sourav

    Shape memory alloys (SMAs) are materials that show reversible, thermo-elastic, diffusionless, displacive (solid to solid) phase transformation, due to the application of temperature and/ or stress (/strain). Among different SMAs, NiTi is a popular one. NiTi shows reversible phase transformation, the shape memory effect (SME), where irreversible deformations are recovered upon heating, and superelasticity (SE), where large strains imposed at high enough temperatures are fully recovered. Phase transformation process in NiTi SMA is a very complex process that involves the competition between developed internal strain and phonon dispersion instability. In NiTi SMA, phase transformation occurs over a wide range of temperature and/ or stress (strain) which involves, evolution of different crystalline phases (cubic austenite i.e. B2, different monoclinic variant of martensite i.e. B19', and orthorhombic B19 or BCO structures). Further, it is observed from experimental and computational studies that the evolution kinetics and growth rate of different phases in NiTi SMA vary significantly over a wide spectrum of spatio-temporal scales, especially with length scales. At nano-meter length scale, phase transformation temperatures, critical transformation stress (or strain) and phase fraction evolution change significantly with sample or simulation cell size and grain size. Even, below a critical length scale, the phase transformation process stops. All these aspects make NiTi SMA very interesting to the science and engineering research community and in this context, the present focuses on the following aspects. At first this study address the stability, evolution and growth kinetics of different phases (B2 and variants of B19'), at different length scales, starting from the atomic level and ending at the continuum macroscopic level. The effects of simulation cell size, grain size, and presence of free surface and grain boundary on the phase transformation process

  7. Wettability alteration properties of fluorinated silica nanoparticles in liquid-loaded pores: An atomistic simulation

    International Nuclear Information System (INIS)

    Sepehrinia, Kazem; Mohammadi, Aliasghar

    2016-01-01

    Highlights: • Properties of fluorinated silica nanoparticles were investigated in water or decane-loaded pores of mineral silica using molecular dynamics simulation. • The water or decane-loaded pores represent liquid bridging. • Addition of nanoparticles to liquid-loaded pores results in weakening of the liquid bridge. • The hydrophobicity of the pore wall increases in the presence of adsorbed fluorinated silica nanoparticles. - Abstract: Control over the wettability of reservoir rocks is of crucial importance for enhancing oil and gas recovery. In order to develop chemicals for controlling the wettability of reservoir rocks, we present a study of functionalized silica nanoparticles as candidates for wettability alteration and improved gas recovery applications. In this paper, properties of fluorinated silica nanoparticles were investigated in water or decane-loaded pores of mineral silica using molecular dynamics simulation. Trifluoromethyl groups as water and oil repellents were placed on the nanoparticles. Simulating a pore in the presence of trapped water or decane molecules leads to liquid bridging for both of the liquids. Adsorption of nanoparticles on the pore wall reduces the density of liquid molecules adjacent to the wall. The density of liquid molecules around the nanoparticles decreases significantly with increasing the number of trifluoromethyl groups on the nanoparticles’ surfaces. An increased hydrophobicity of the pore wall was observed in the presence of adsorbed fluorinated silica nanoparticles. Also, it is observed that increasing the number of the trifluoromethyl groups results in weakening of liquid bridges. Moreover, the free energy of adsorption on mineral surface was evaluated to be more favorable than that of aggregation of nanoparticles, which suggests nanoparticles adsorb preferably on mineral surface.

  8. Wettability alteration properties of fluorinated silica nanoparticles in liquid-loaded pores: An atomistic simulation

    Energy Technology Data Exchange (ETDEWEB)

    Sepehrinia, Kazem; Mohammadi, Aliasghar, E-mail: amohammadi@sharif.edu

    2016-05-15

    Highlights: • Properties of fluorinated silica nanoparticles were investigated in water or decane-loaded pores of mineral silica using molecular dynamics simulation. • The water or decane-loaded pores represent liquid bridging. • Addition of nanoparticles to liquid-loaded pores results in weakening of the liquid bridge. • The hydrophobicity of the pore wall increases in the presence of adsorbed fluorinated silica nanoparticles. - Abstract: Control over the wettability of reservoir rocks is of crucial importance for enhancing oil and gas recovery. In order to develop chemicals for controlling the wettability of reservoir rocks, we present a study of functionalized silica nanoparticles as candidates for wettability alteration and improved gas recovery applications. In this paper, properties of fluorinated silica nanoparticles were investigated in water or decane-loaded pores of mineral silica using molecular dynamics simulation. Trifluoromethyl groups as water and oil repellents were placed on the nanoparticles. Simulating a pore in the presence of trapped water or decane molecules leads to liquid bridging for both of the liquids. Adsorption of nanoparticles on the pore wall reduces the density of liquid molecules adjacent to the wall. The density of liquid molecules around the nanoparticles decreases significantly with increasing the number of trifluoromethyl groups on the nanoparticles’ surfaces. An increased hydrophobicity of the pore wall was observed in the presence of adsorbed fluorinated silica nanoparticles. Also, it is observed that increasing the number of the trifluoromethyl groups results in weakening of liquid bridges. Moreover, the free energy of adsorption on mineral surface was evaluated to be more favorable than that of aggregation of nanoparticles, which suggests nanoparticles adsorb preferably on mineral surface.

  9. A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

    Science.gov (United States)

    Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

    2017-06-07

    Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.

  10. High-frequency intrinsic dynamics of the electrocaloric effect from direct atomistic simulations

    Science.gov (United States)

    Lisenkov, S.; Ponomareva, I.

    2018-05-01

    We propose a computational methodology capable of harvesting isothermal heat and entropy change in molecular dynamics simulations. The methodology is applied to study high-frequency dynamics of the electrocaloric effect (ECE) in ferroelectric PbTiO3. ECE is associated with a reversible change in temperature under adiabatic application of electric field or with a reversible change in entropy under isothermal application of the electric field. Accurate assessment of electrocaloric performance requires the knowledge of three quantities: isothermal heat, isothermal entropy change, and adiabatic temperature change. Our methodology allows computations of all these quantities directly, that is, without restoring to the reversible thermodynamical models. Consequently, it captures both reversible and irreversible effects, which is critical for ECE simulations. The approach is well suited to address the dynamics of the ECE, which so far remains underexplored. We report the following basic features of the intrinsic dynamics of ECE: (i) the ECE is independent of the electric field frequency, rate of application, or field profile; (ii) the effect persists up to the frequencies associated with the onset of dielectric losses and deteriorates from there due to the creation of irreversible entropy; and (iii) in the vicinity of the phase transition and in the paraelectric phase the onset of irreversible dynamics occurs at lower frequency as compared to the ferroelectric phase. The latter is attributed to lower intrinsic soft-mode frequencies and and larger losses in the paraelectric phase.

  11. Dynamics of Surfactant Clustering at Interfaces and Its Influence on the Interfacial Tension: Atomistic Simulation of a Sodium Hexadecane-Benzene Sulfonate-Tetradecane-Water System.

    Science.gov (United States)

    Paredes, Ricardo; Fariñas-Sánchez, Ana Isabel; Medina-Rodrı Guez, Bryan; Samaniego, Samantha; Aray, Yosslen; Álvarez, Luis Javier

    2018-03-06

    The process of equilibration of the tetradecane-water interface in the presence of sodium hexadecane-benzene sulfonate is studied using intensive atomistic molecular dynamics simulations. Starting as an initial point with all of the surfactants at the interface, it is obtained that the equilibration time of the interface (several microseconds) is orders of magnitude higher than previously reported simulated times. There is strong evidence that this slow equilibration process is due to the aggregation of surfactants molecules on the interface. To determine this fact, temporal evolution of interfacial tension and interfacial formation energy are studied and their temporal variations are correlated with cluster formation. To study cluster evolution, the mean cluster size and the probability that a molecule of surfactant chosen at random is free are obtained as a function of time. Cluster size distribution is estimated, and it is observed that some of the molecules remain free, whereas the rest agglomerate. Additionally, the temporal evolution of the interfacial thickness and the structure of the surfactant molecules on the interface are studied. It is observed how this structure depends on whether the molecules agglomerate or not.

  12. Collapsed adhesion of carbon nanotubes on silicon substrates: continuum mechanics and atomistic simulations

    Science.gov (United States)

    Yuan, Xuebo; Wang, Youshan

    2018-02-01

    Carbon nanotubes (CNTs) can undergo collapse from the ordinary cylindrical configurations to bilayer ribbons when adhered on substrates. In this study, the collapsed adhesion of CNTs on the silicon substrates is investigated using both classical molecular dynamics (MD) simulations and continuum analysis. The governing equations and transversality conditions are derived based on the minimum potential energy principle and the energy-variational method, considering both the van der Waals interactions between CNTs and substrates and those inside CNTs. Closed-form solutions for the collapsed configuration are obtained which show good agreement with the results of MD simulations. The stability of adhesive configurations is investigated by analyzing the energy states. It is found that the adhesive states of single-walled CNTs (SWCNTs) (n, n) on the silicon substrates can be categorized by two critical radii, 0.716 and 0.892 nm. For SWCNTs with radius larger than 0.892 nm, they would fully collapse on the silicon substrates. For SWCNTs with radius less than 0.716 nm, the initial cylindrical configuration is energetically favorable. For SWCNTs with radius between two critical radii, the radially deformed state is metastable. The non-contact ends of all collapsed SWCNTs are identical with the same arc length of 2.38 nm. Finally, the role of number of walls on the adhesive configuration is investigated quantitatively. For multi-walled CNTs with the number of walls exceeding a certain value, the cylindrical configuration is stable due to the increasing bending stiffness. The present study can be useful for the design of CNT-based nanodevices.

  13. Zinc adsorption on clays inferred from atomistic simulations and EXAFS spectroscopy

    International Nuclear Information System (INIS)

    Churakov, S.V.; Daehn, R.

    2012-01-01

    Document available in extended abstract form only. Clay minerals such as illite and montmorillonite are ubiquitous in the environment. Because of their large specific area and high structural charge, they control the migration of heavy metals in the geosphere via different uptake mechanisms. The main processes for the sequestration of trace concentrations of heavy metals are sorption to clay edge sites and incorporation into clay structures. Whereas, sorption is a fast process occurring nearly instantaneously, the incorporation of metal ions into clay minerals occurs over geological time scales. Zn is a divalent transition metal, which shows similar chemical behavior to Ni and Co and can thus also be considered as a natural analogue for radioactive Ni and Co arising from nuclear fuel and radioactive waste from the decommissioning of nuclear power plants. The release of radionuclides from a repository can be considerably retarded due to interactions with clay minerals. For example, bentonite containing >70 wt% di-octahedral alumino-silicate clays is foreseen as a backfill material in the Swiss concept for a high level radioactive waste repository (NAGRA, 2002). Knowing the uptake mechanism of these elements on clays can help to protect the natural environment. In this study ab initio molecular dynamics (MD) calculations were applied to simulate the molecular mechanism of Zn uptake on the edge surfaces of montmorillonite, a di-octahedral clay, and to explain the measured K-edge extended X-ray absorption fine structure (EXAFS) spectra of Zn adsorbed on montmorillonite at different loadings. Two different montmorillonites were chosen for the experimental part of this study: Milos (Island of Milos, Greece) and STx-1 (Gonzales County, Texas, USA) (VANTELON et al., 2003). As a reference for Zn substituted for Al in the clay octahedral sheet a MILOS sample was prepared without adding any Zn. Milos was chosen because it contains 1.8 [mmol/kg] Zn incorporated into the

  14. Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

    Directory of Open Access Journals (Sweden)

    Christopher D. Taylor

    2012-01-01

    Full Text Available Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies of the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.

  15. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    Energy Technology Data Exchange (ETDEWEB)

    Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  16. Atomistic simulation on charge mobility of amorphous tris(8-hydroxyquinoline) aluminum (Alq3): origin of Poole-Frenkel-type behavior.

    Science.gov (United States)

    Nagata, Yuki; Lennartz, Christian

    2008-07-21

    The atomistic simulation of charge transfer process for an amorphous Alq(3) system is reported. By employing electrostatic potential charges, we calculate site energies and find that the standard deviation of site energy distribution is about twice as large as predicted in previous research. The charge mobility is calculated via the Miller-Abrahams formalism and the master equation approach. We find that the wide site energy distribution governs Poole-Frenkel-type behavior of charge mobility against electric field, while the spatially correlated site energy is not a dominant mechanism of Poole-Frenkel behavior in the range from 2x10(5) to 1.4x10(6) V/cm. Also we reveal that randomly meshed connectivities are, in principle, required to account for the Poole-Frenkel mechanism. Charge carriers find a zigzag pathway at low electric field, while they find a straight pathway along electric field when a high electric field is applied. In the space-charge-limited current scheme, the charge-carrier density increases with electric field strength so that the nonlinear behavior of charge mobility is enhanced through the strong charge-carrier density dependence of charge mobility.

  17. Atomistic simulations of thermal transport in Si and SiGe based materials: From bulk to nanostructures

    Science.gov (United States)

    Savic, Ivana; Mingo, Natalio; Donadio, Davide; Galli, Giulia

    2010-03-01

    It has been recently proposed that Si and SiGe based nanostructured materials may exhibit low thermal conductivity and overall promising properties for thermoelectric applications. Hence there is a considerable interest in developing accurate theoretical and computational methods which can help interpret recent measurements, identify the physical origin of the reduced thermal conductivity, as well as shed light on the interplay between disorder and nanostructuring in determining a high figure of merit. In this work, we investigate the capability of an atomistic Green's function method [1] to describe phonon transport in several types of Si and SiGe based systems: amorphous Si, SiGe alloys, planar and nanodot Si/SiGe multilayers. We compare our results with experimental data [2,3], and with the findings of molecular dynamics simulations and calculations based on the Boltzmann transport equation. [1] I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008). [2] S.-M. Lee, D. G. Cahill, and R. Venkatasubramanian, Appl. Phys. Lett. 70, 2957 (1997). [3] G. Pernot et al., submitted.

  18. Large-Scale Reactive Atomistic Simulation of Shock-induced Initiation Processes in Energetic Materials

    Science.gov (United States)

    Thompson, Aidan

    2013-06-01

    Initiation in energetic materials is fundamentally dependent on the interaction between a host of complex chemical and mechanical processes, occurring on scales ranging from intramolecular vibrations through molecular crystal plasticity up to hydrodynamic phenomena at the mesoscale. A variety of methods (e.g. quantum electronic structure methods (QM), non-reactive classical molecular dynamics (MD), mesoscopic continuum mechanics) exist to study processes occurring on each of these scales in isolation, but cannot describe how these processes interact with each other. In contrast, the ReaxFF reactive force field, implemented in the LAMMPS parallel MD code, allows us to routinely perform multimillion-atom reactive MD simulations of shock-induced initiation in a variety of energetic materials. This is done either by explicitly driving a shock-wave through the structure (NEMD) or by imposing thermodynamic constraints on the collective dynamics of the simulation cell e.g. using the Multiscale Shock Technique (MSST). These MD simulations allow us to directly observe how energy is transferred from the shockwave into other processes, including intramolecular vibrational modes, plastic deformation of the crystal, and hydrodynamic jetting at interfaces. These processes in turn cause thermal excitation of chemical bonds leading to initial chemical reactions, and ultimately to exothermic formation of product species. Results will be presented on the application of this approach to several important energetic materials, including pentaerythritol tetranitrate (PETN) and ammonium nitrate/fuel oil (ANFO). In both cases, we validate the ReaxFF parameterizations against QM and experimental data. For PETN, we observe initiation occurring via different chemical pathways, depending on the shock direction. For PETN containing spherical voids, we observe enhanced sensitivity due to jetting, void collapse, and hotspot formation, with sensitivity increasing with void size. For ANFO, we

  19. Atomistic simulations of displacement cascades in Y2O3 single crystal

    International Nuclear Information System (INIS)

    Dholakia, Manan; Chandra, Sharat; Valsakumar, M.C.; Mathi Jaya, S.

    2014-01-01

    Graphical abstract: (a) The averaged distortion index and the Y–O bond length of the Y 2 O 3 octahedra as a function of the simulation time for 5 keV PKA. (b) Shows the nearest neighbourhood of one of the Y ions as a function of simulation time, showing the destruction and the recovery of the YO 6 octahedron during the cascade corresponding to 5 keV Y PKA. - Highlights: • Qualitative difference in displacement cascades exists for Y and O PKA. • Nearest neighbour correlation between Y and O ions exists even at cascade peak. • Cascade core in Y 2 O 3 does not undergo melting. • Topological connectivity of YO 6 polyhedra plays important role in stability of Y 2 O 3 . - Abstract: We study the characteristics of displacement cascades in single crystal Y 2 O 3 using classical molecular dynamics. There are two possible ways to generate the cascades in yttria, using either the Y or the O atoms as the primary knock-on (PKA) atom. It is shown that there is a qualitative difference in the characteristics of the cascades obtained in these two cases. Even though the crystal is seen to be in a highly disordered state in the cascade volume, as seen from the plots of radial distribution function, the correlation between the Y and O atoms is not completely lost. This facilitates a quick recovery of the system during the annealing phase. Topological connectivity of the YO 6 polyhedral units plays an important role in imparting stability to the Y 2 O 3 crystal. These characteristics of the cascades can help explain the stability of the yttria nanoparticles when they are dispersed in oxide dispersion strengthened steels

  20. Local dynamics of glass-forming polystyrene thin films from atomistic simulation

    Science.gov (United States)

    Zhou, Yuxing; Milner, Scott

    Despite a wide technological application ranging from protective coatings to organic solar cells, there still no consensus on the mechanism for the glass transition in polymer thin films a manifestation of the infamous glass problem under confinement. Many experimental and computational studies have observed a large deviation of nanoscale dynamical properties in thin films from the corresponding properties in bulk. In this work, we perform extensive united-atom simulations on atactic polystyrene free-standing thin films near the glass transition temperature and focus on the effect of free surface on the local dynamics. We study the segmental dynamics as a function of distance from the surface for different temperatures, from which relaxation time and thereby local Tg is obtained for each layer. We find the dynamics near free surface is not only enhanced but becomes less strongly temperature dependent as Tg is approached compared to the bulk. We find an increasing length scale associated with mobility propagation from the free surface as temperature decreases, but no correlation between local structure and enhanced relaxation rates near the surface, consistent with studies on bead-spring chains.

  1. Atomistic simulations of cross-slip of jogged screw dislocations in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Rasmussen, T.; Leffers, T.

    2001-01-01

    We have performed atomic-scare simulations of cross-slip processes of screw dislocations in copper, simulating jog-free dislocations as well as different types of jogged screw dislocations. Minimum-energy paths and corresponding transition state energies are obtained using the nudged-elastic...

  2. Subsurface damage mechanism of high speed grinding process in single crystal silicon revealed by atomistic simulations

    International Nuclear Information System (INIS)

    Li, Jia; Fang, Qihong; Zhang, Liangchi; Liu, Youwen

    2015-01-01

    Highlights: • Molecular dynamic model of nanoscale high speed grinding of silicon workpiece has been established. • The effect of grinding speed on subsurface damage and grinding surface integrity by analyzing the chip, dislocation movement, and phase transformation during high speed grinding process are thoroughly investigated. • Subsurface damage is studied by the evolution of surface area at first time for more obvious observation on transition from ductile to brittle. • The hydrostatic stress and von Mises stress by the established analytical model are studied subsurface damage mechanism during nanoscale grinding. - Abstract: Three-dimensional molecular dynamics (MD) simulations are performed to investigate the nanoscale grinding process of single crystal silicon using diamond tool. The effect of grinding speed on subsurface damage and grinding surface integrity by analyzing the chip, dislocation movement, and phase transformation are studied. We also establish an analytical model to calculate several important stress fields including hydrostatic stress and von Mises stress for studying subsurface damage mechanism, and obtain the dislocation density on the grinding subsurface. The results show that a higher grinding velocity in machining brittle material silicon causes a larger chip and a higher temperature, and reduces subsurface damage. However, when grinding velocity is above 180 m s −1 , subsurface damage thickness slightly increases because a higher grinding speed leads to the increase in grinding force and temperature, which accelerate dislocation nucleation and motion. Subsurface damage is studied by the evolution of surface area at first time for more obvious observation on transition from ductile to brittle, that provides valuable reference for machining nanometer devices. The von Mises stress and the hydrostatic stress play an important role in the grinding process, and explain the subsurface damage though dislocation mechanism under high

  3. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N. [Qatar Environment and Energy Research Institute (QEERI), Hamad Ben Khalifa University (HBKU), Qatar Foundation, P.O. Box 5825, Doha (Qatar); Harrabi, K. [Department of Physics, King Fahd University of Petroleum and Minerals, 31261 Dhahran (Saudi Arabia); Mehmood, U.; Hussein, I. A. [Department of Chemical Engineering, King Fahd University of Petroleum and Minerals, 31261 Dharan (Saudi Arabia); Peeters, F. M. [Departement Fysica, Universiteit Antwerpen, Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Zhang, J. [Department of Materials and London Centre for Nanotechnology, Imperial College London, SW7 2AZ London (United Kingdom); McLachlan, M. A. [Department of Materials and Centre for Plastic Electronics, Imperial College London, SW7 2AZ London (United Kingdom)

    2015-07-14

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.

  4. Correlation between self-diffusion in Si and the migration mechanisms of vacancies and self-interstitials: An atomistic study

    International Nuclear Information System (INIS)

    Posselt, M.; Gao, F.; Bracht, H.

    2008-01-01

    The migration of point defects in silicon and the corresponding atomic mobility are investigated by comprehensive classical molecular-dynamics simulations using the Stillinger-Weber potential and the Tersoff potential. In contrast to most of the previous studies both the point defect diffusivity and the self-diffusion coefficient per defect are calculated separately so that the diffusion-correlation factor can be determined. Simulations with both the Stillinger-Weber and the Tersoff potential show that vacancy migration is characterized by the transformation of the tetrahedral vacancy to the split vacancy and vice versa and the diffusion-correlation factor f V is about 0.5. This value was also derived by the statistical diffusion theory under the assumption of the same migration mechanism. The mechanisms of self-interstitial migration are more complex. The detailed study, including a visual analysis and investigations with the nudged elastic band method, reveals a variety of transformations between different self-interstitial configurations. Molecular-dynamics simulations using the Stillinger-Weber potential show that the self-interstitial migration is dominated by a dumbbell mechanism, whereas in the case of the Tersoff potential the interstitialcy mechanism prevails. The corresponding values of the correlation factor f I are different, namely, 0.59 and 0.69 for the dumbbell and the interstitialcy mechanisms, respectively. The latter value is nearly equal to that obtained by the statistical theory which assumes the interstitialcy mechanism. Recent analysis of experimental results demonstrated that in the framework of state-of-the-art diffusion and reaction models the best interpretation of point defect data can be given by assuming f I ≅0.6. The comparison with the present atomistic study leads to the conclusion that the self-interstitial migration in Si should be governed by a dumbbell mechanism

  5. Atomistic simulations of thermodynamic properties of Xe gas bubbles in U10Mo fuels

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Shenyang, E-mail: shenyang.hu@pnnl.gov; Setyawan, Wahyu; Joshi, Vineet V.; Lavender, Curt A.

    2017-07-15

    Xe gas bubble superlattice formation is observed in irradiated uranium–10 wt% molybdenum (U10Mo) fuels. However, the thermodynamic properties of the bubbles (the relationship among bubble size, equilibrium Xe concentration, and bubble pressure) and the mechanisms of bubble superlattice formation are not well known. In this work, the molecular dynamics (MD) method is used to study these properties and mechanisms. The results provide important inputs for quantitative mesoscale models of gas bubble evolution and fuel performance. In the MD simulations, the embedded-atom method (EAM) potential of U10Mo-Xe [1] is employed. Initial gas bubbles with a low Xe concentration (underpressured) are generated in a body-centered cubic (bcc) U10Mo single crystal. Then Xe atoms are sequentially added into the bubbles one by one, and the evolution of pressure and dislocation emission around the bubbles is analyzed. The relationship between pressure, equilibrium Xe concentration, and radius of the bubbles is established. It was found that an overpressured gas bubble emits partial dislocations with a Burgers vector along the <111> direction and a slip plane of (11-2). Meanwhile, dislocation loop punch out was not observed. The overpressured bubble also induces an anisotropic stress field. A tensile stress was found along <110> directions around the bubble, favoring the nucleation and formation of a face-centered cubic bubble superlattice in bcc U10Mo fuels.

  6. Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Wei Ye

    Full Text Available MicroRNAs are endogenous 23-25 nt RNAs that play important gene-regulatory roles in animals and plants. Recently, miR369-3 was found to upregulate translation of TNFα mRNA in quiescent (G0 mammalian cell lines. Knock down and immunofluorescence experiments suggest that microRNA-protein complexes (with FXR1 and AGO2 are necessary for the translation upregulation. However the molecular mechanism of microRNA translation activation is poorly understood. In this study we constructed the microRNA-mRNA-AGO2-FXR1 quadruple complex by bioinformatics and molecular modeling, followed with all atom molecular dynamics simulations in explicit solvent to investigate the interaction mechanisms for the complex. A combined analysis of experimental and computational data suggests that AGO2-FXR1 complex relocalize microRNA:mRNA duplex to polysomes in G0. The two strands of dsRNA are then separated upon binding of AGO2 and FXR1. Finally, polysomes may improve the translation efficiency of mRNA. The mutation research confirms the stability of microRNA-mRNA-FXR1 and illustrates importance of key residue of Ile304. This possible mechanism can shed more light on the microRNA-dependent upregulation of translation.

  7. Atomistic simulations of thermodynamic properties of Xe gas bubbles in U10Mo fuels

    Science.gov (United States)

    Hu, Shenyang; Setyawan, Wahyu; Joshi, Vineet V.; Lavender, Curt A.

    2017-07-01

    Xe gas bubble superlattice formation is observed in irradiated uranium-10 wt% molybdenum (U10Mo) fuels. However, the thermodynamic properties of the bubbles (the relationship among bubble size, equilibrium Xe concentration, and bubble pressure) and the mechanisms of bubble superlattice formation are not well known. In this work, the molecular dynamics (MD) method is used to study these properties and mechanisms. The results provide important inputs for quantitative mesoscale models of gas bubble evolution and fuel performance. In the MD simulations, the embedded-atom method (EAM) potential of U10Mo-Xe [1] is employed. Initial gas bubbles with a low Xe concentration (underpressured) are generated in a body-centered cubic (bcc) U10Mo single crystal. Then Xe atoms are sequentially added into the bubbles one by one, and the evolution of pressure and dislocation emission around the bubbles is analyzed. The relationship between pressure, equilibrium Xe concentration, and radius of the bubbles is established. It was found that an overpressured gas bubble emits partial dislocations with a Burgers vector along the direction and a slip plane of (11-2). Meanwhile, dislocation loop punch out was not observed. The overpressured bubble also induces an anisotropic stress field. A tensile stress was found along directions around the bubble, favoring the nucleation and formation of a face-centered cubic bubble superlattice in bcc U10Mo fuels.

  8. Atomistic simulation of damage production by atomic and molecular ion irradiation in GaN

    International Nuclear Information System (INIS)

    Ullah, M. W.; Kuronen, A.; Nordlund, K.; Djurabekova, F.; Karaseov, P. A.; Titov, A. I.

    2012-01-01

    We have studied defect production during single atomic and molecular ion irradiation having an energy of 50 eV/amu in GaN by molecular dynamics simulations. Enhanced defect recombination is found in GaN, in accordance with experimental data. Instantaneous damage shows non-linearity with different molecular projectile and increasing molecular mass. Number of instantaneous defects produced by the PF 4 molecule close to target surface is four times higher than that for PF 2 molecule and three times higher than that calculated as a sum of the damage produced by one P and four F ion irradiation (P+4×F). We explain this non-linearity by energy spike due to molecular effects. On the contrary, final damage created by PF 4 and PF 2 shows a linear pattern when the sample cools down. Total numbers of defects produced by Ag and PF 4 having similar atomic masses are comparable. However, defect-depth distributions produced by these species are quite different, also indicating molecular effect.

  9. Activated states for cross-slip at screw dislocation intersections in face-centered cubic nickel and copper via atomistic simulation

    International Nuclear Information System (INIS)

    Rao, S.I.; Dimiduk, D.M.; El-Awady, J.A.; Parthasarathy, T.A.; Uchic, M.D.; Woodward, C.

    2010-01-01

    We extend our recent simulation studies where a screw dislocation in face-centered cubic (fcc) Ni was found to spontaneously attain a low energy partially cross-slipped configuration upon intersecting a forest dislocation. Using atomistic (molecular statics) simulations with embedded atom potentials, we evaluated the activation barrier for a dislocation to transform from fully residing on the glide plane to fully residing on a cross-slip plane intersecting a forest dislocation in both Ni and Cu. The activation energies were obtained by determining equilibrium configurations (energies) when variable pure tensile or compressive stresses were applied along the [1 1 1] direction on the partially cross-slipped state. We show that the activation energy is a factor of 2-5 lower than that for cross-slip in isolation via the Escaig process. The cross-slip activation energies obtained at the intersection in Cu were in reasonable accord with the experimentally determined cross-slip activation energy for Cu. Further, the activation barrier for cross-slip at these intersections was shown to be linearly proportional to (d/b)[ln(√(3)d/b)] 1/2 , as in the Escaig process, where d is the Shockley partial dislocation spacing and b is the Burgers vector of the screw dislocation. These results suggest that cross-slip should be preferentially observed at selected screw dislocation intersections in fcc materials.

  10. Viscosity of nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation.

    Science.gov (United States)

    Eslami, Hossein; Müller-Plathe, Florian

    2010-01-14

    Our new simulation scheme in isosurface-isothermal-isobaric ensemble [Eslami, H.; Mozaffari, F.; Moghadasi, J.; Müller-Plathe, F. J. Chem. Phys. 2008, 129, 194702], developed to simulate confined fluids in equilibrium with bulk, is applied to simulate polyamide-6,6 oligomers confined between graphite surfaces. The reverse nonequilibrium molecular dynamics simulation technique is employed to shear the graphite surfaces. In this work, six confined systems, with different surface separations, as well as the bulk fluid are simulated. Our results show a viscosity increase with respect to the bulk fluid, with decreasing distance between surfaces. Also, the calculated viscosities of the confined systems show an oscillatory behavior with maxima corresponding to well-formed layers between the surfaces. We observe a substantial slip at the surfaces, with the slip length depending on the shear rate and on the slit width. The slip length and the slip velocity show oscillatory behavior with out-of-phase oscillations with respect to the solvation force oscillations. Moreover, the temperature difference between coldest and hottest parts of the simulation box depends on the shear rate and on the layering effect (solvation force oscillations). An analysis of oligomer deformation under flow shows preferential alignment of oligomers parallel to the surfaces with increasing shear rate.

  11. Passing waves from atomistic to continuum

    Science.gov (United States)

    Chen, Xiang; Diaz, Adrian; Xiong, Liming; McDowell, David L.; Chen, Youping

    2018-02-01

    Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

  12. Atomistic simulations of void migration under thermal gradient in UO2

    International Nuclear Information System (INIS)

    Desai, Tapan G.; Millett, Paul; Tonks, Michael; Wolf, Dieter

    2010-01-01

    It is well known that within a few hours after startup of a nuclear reactor, the temperature gradient within a fuel element causes migration of voids/bubbles radially inwards to form a central hole. To understand the atomic processes that control this migration of voids, we performed molecular dynamics (MD) simulations on single crystal UO 2 with voids of diameter 2.2 nm. An external temperature gradient was applied across the simulation cell. At the end of the simulation run, it was observed that the voids had moved towards the hot end of the simulation cell. The void migration velocity obtained from the simulations was compared with the available phenomenological equations for void migration due to different transport mechanisms. Surface diffusion of the slowest moving specie, i.e. uranium, was found to be the dominant mechanism for void migration. The contribution from lattice diffusion and the thermal stress gradient to the void migration was analyzed and found to be negligible. By extrapolation, a crossover from the surface-diffusion-controlled mechanism to the lattice-diffusion-controlled mechanism was found to occur for voids with sizes in the μm range.

  13. Atomistic simulations of the formation of -component dislocation loops in α-zirconium

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Cong, E-mail: dai.cong@queensu.ca; Balogh, Levente; Yao, Zhongwen; Daymond, Mark R., E-mail: mark.daymond@queensu.ca

    2016-09-15

    The formation of -component dislocation loops in α-Zr is believed to be responsible for the breakaway irradiation growth experimentally observed under high irradiation fluences. However, while -loop growth is well described by existing models, the atomic mechanisms responsible for the nucleation of -component dislocation loops are still not clear. In the present work, both interstitial and vacancy -type dislocation loops are initially equilibrated at different temperatures. Cascades simulations in the vicinity of the -type loops are then performed by selecting an atom as the primary knock-on atoms (PKAs) with different kinetic energies, using molecular dynamics simulations. No -component dislocation loop was formed in cascades simulations with a 10 keV PKA, but -component interstitial loops were observed after the interaction between discontinuous 50 keV PKAs and pre-existing -type interstitial loops. The comparisons of cascades simulations in volumes having pre-existing -type interstitial and vacancy loops suggest that the reaction between the PKAs and -type interstitial loops is responsible for the formation of -component interstitial loops.

  14. Stretching and breaking of monolayer MoS2—an atomistic simulation

    International Nuclear Information System (INIS)

    Lorenz, Tommy; Joswig, Jan-Ole; Seifert, Gotthard

    2014-01-01

    We report on the simulation of the nanoindentation process of monolayer MoS 2 using molecular-dynamics simulations and a density-functional based tight-binding method. A circular sheet of MoS 2 with clamped boundaries was indented by a slowly moved tip, which deformed and finally pierced the layer. We found the Young’s modulus of monolayer MoS 2 to be 262 GPa, which is in good agreement with experimental observations. Furthermore, the energetic and structural behavior during the indentation process was analyzed. Elasticity theory supplies the necessary equations to explain the experiment. Thereby, the nature of the linear term in the force-deflection relation is discussed. (letter)

  15. Atomistic simulations of diffusion mechanisms in off-stoichiometric Al-rich Ni3Al

    International Nuclear Information System (INIS)

    Duan, Jinsong

    2007-01-01

    This paper presents dynamics simulation results of diffusion in off-stoichiometric Al-rich Ni 3 Al (Ni 73 Al 27 ) at temperature ranging from 1300 to 1550 K. The interatomic forces are described by the Finnis-Sinclair type N-body potentials. Particular attention is devoted to the effect of the extra 2% of Al atoms sitting on the Ni sublattice as antisite point defects (Al Ni ) on diffusion. Simulation results show that Ni atoms mainly diffuse through the Ni sublattice at the temperatures investigated. Al atoms diffuse via both the intrasublattice and antistructure bridge (ASB) mechanisms. The contribution to Al diffusion from the ASB mechanism decreases at the lower temperature (T Ni ) enhances both Al and Ni diffusion in Ni 73 Al 27 . The Ni-Al coupled diffusion effect is observed and understood at the atomic level for the first time

  16. Microcanonical Monte Carlo approach for computing melting curves by atomistic simulations

    OpenAIRE

    Davis, Sergio; Gutiérrez, Gonzalo

    2017-01-01

    We report microcanonical Monte Carlo simulations of melting and superheating of a generic, Lennard-Jones system starting from the crystalline phase. The isochoric curve, the melting temperature $T_m$ and the critical superheating temperature $T_{LS}$ obtained are in close agreement (well within the microcanonical temperature fluctuations) with standard molecular dynamics one-phase and two-phase methods. These results validate the use of microcanonical Monte Carlo to compute melting points, a ...

  17. Mechanism of crack healing at room temperature revealed by atomistic simulations

    International Nuclear Information System (INIS)

    Li, J.; Fang, Q.H.; Liu, B.; Liu, Y.; Liu, Y.W.; Wen, P.H.

    2015-01-01

    Three dimensional molecular dynamics (MD) simulations are systematically carried out to reveal the mechanism of the crack healing at room temperature, in terms of the dislocation shielding and the atomic diffusion to control the crack closure, in a copper (Cu) plate suffering from a shear loading. The results show that the process of the crack healing is actualized through the dislocation emission at a crack tip accompanied with intrinsic stacking faults ribbon forming in the crack tip wake, the dislocation slipping in the matrix and the dislocation annihilation in the free surface. Dislocation included stress compressing the crack tip is examined from the MD simulations and the analytical models, and then the crack closes rapidly due to the assistance of the atomic diffusion induced by the thermal activation when the crack opening displacement is less than a threshold value. This phenomenon is very different from the previous results for the crack propagation under the external load applied because of the crack healing (advancing) largely dependent on the crystallographic orientations of crack and the directions of external loading. Furthermore, based on the energy characteristic and considering the crack size effect, a theoretical model is established to predict the relationships between the crack size and the shear stress which qualitatively agree well with that obtained in the MD simulations

  18. Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

    Science.gov (United States)

    Riniker, Sereina

    2018-03-26

    In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

  19. Key role of water in proton transfer at the Q(o)-site of the cytochrome bc(1) complex predicted by atomistic molecular dynamics simulations

    DEFF Research Database (Denmark)

    Postila, P. A.; Kaszuba, K.; Sarewicz, M.

    2013-01-01

    of the cyt bc(1) function have remained unclear especially regarding the substrate binding at the Q(o)-site. In this work we address this issue by performing extensive atomistic molecular dynamics simulations with the cyt bc(1) complex of Rhodobacter capsulatus embedded in a lipid bilayer. Based...... on the simulations we are able to show the atom-level binding modes of two substrate forms: quinol (QH(2)) and quinone (Q). The QH(2) binding at the Q(o)-site involves a coordinated water arrangement that produces an exceptionally close and stable interaction between the cyt b and iron sulfur protein subunits...

  20. On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Garrido, J. M. [Departamento de Ingeniería Química, Universidad de Concepción, POB 160-C Concepción (Chile); Algaba, J.; Blas, F. J., E-mail: felipe@uhu.es [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Física Aplicada, Universidad de Huelva, 21007 Huelva (Spain); Míguez, J. M. [Laboratoire des Fluides Complexes et Leurs Reservoirs, Université de Pau et des Pays de l’Adour, CNRS, TOTAL–UMR 5150, Avenue de l’Université, B.P. 1155, Pau F-64013 (France); Departamento de Física Aplicada, Universidade de Vigo, E36310 Vigo (Spain); Mendiboure, B. [Laboratoire des Fluides Complexes et Leurs Reservoirs, Université de Pau et des Pays de l’Adour, CNRS, TOTAL–UMR 5150, Avenue de l’Université, B.P. 1155, Pau F-64013 (France); Moreno-Ventas Bravo, A. I. [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Geología, Universidad de Huelva, 21007 Huelva (Spain); Piñeiro, M. M. [Departamento de Física Aplicada, Universidade de Vigo, E36310 Vigo (Spain)

    2016-04-14

    We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

  1. On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation

    International Nuclear Information System (INIS)

    Garrido, J. M.; Algaba, J.; Blas, F. J.; Míguez, J. M.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.; Piñeiro, M. M.

    2016-01-01

    We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

  2. Influence of Cholesterol on the Oxygen Permeability of Membranes: Insight from Atomistic Simulations.

    Science.gov (United States)

    Dotson, Rachel J; Smith, Casey R; Bueche, Kristina; Angles, Gary; Pias, Sally C

    2017-06-06

    Cholesterol is widely known to alter the physical properties and permeability of membranes. Several prior works have implicated cell membrane cholesterol as a barrier to tissue oxygenation, yet a good deal remains to be explained with regard to the mechanism and magnitude of the effect. We use molecular dynamics simulations to provide atomic-resolution insight into the influence of cholesterol on oxygen diffusion across and within the membrane. Our simulations show strong overall agreement with published experimental data, reproducing the shapes of experimental oximetry curves with high accuracy. We calculate the upper-limit transmembrane oxygen permeability of a 1-palmitoyl,2-oleoylphosphatidylcholine phospholipid bilayer to be 52 ± 2 cm/s, close to the permeability of a water layer of the same thickness. With addition of cholesterol, the permeability decreases somewhat, reaching 40 ± 2 cm/s at the near-saturating level of 62.5 mol % cholesterol and 10 ± 2 cm/s in a 100% cholesterol mimic of the experimentally observed noncrystalline cholesterol bilayer domain. These reductions in permeability can only be biologically consequential in contexts where the diffusional path of oxygen is not water dominated. In our simulations, cholesterol reduces the overall solubility of oxygen within the membrane but enhances the oxygen transport parameter (solubility-diffusion product) near the membrane center. Given relatively low barriers to passing from membrane to membrane, our findings support hydrophobic channeling within membranes as a means of cellular and tissue-level oxygen transport. In such a membrane-dominated diffusional scheme, the influence of cholesterol on oxygen permeability is large enough to warrant further attention. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  3. Atomistic simulations of anionic Au-144(SR)(60) nanoparticles interacting with asymmetric model lipid membranes

    DEFF Research Database (Denmark)

    Heikkila, E.; Martinez-Seara, H.; Gurtovenko, A. A.

    2014-01-01

    whose lipid composition and transmembrane distribution are to a large extent consistent with real plasma membranes of eukaryotic cells. To this end, we use a model system which comprises two cellular compartments, extracellular and cytosolic, divided by two asymmetric lipid bilayers. The simulations...... clearly show that AuNP- attaches to the extracellular membrane surface within a few tens of nanoseconds, while it avoids contact with the membrane on the cytosolic side. This behavior stems from several factors. In essence, when the nanoparticle interacts with lipids in the extracellular compartment...

  4. Harnessing atomistic simulations to predict the rate at which dislocations overcome obstacles

    Science.gov (United States)

    Saroukhani, S.; Nguyen, L. D.; Leung, K. W. K.; Singh, C. V.; Warner, D. H.

    2016-05-01

    Predicting the rate at which dislocations overcome obstacles is key to understanding the microscopic features that govern the plastic flow of modern alloys. In this spirit, the current manuscript examines the rate at which an edge dislocation overcomes an obstacle in aluminum. Predictions were made using different popular variants of Harmonic Transition State Theory (HTST) and compared to those of direct Molecular Dynamics (MD) simulations. The HTST predictions were found to be grossly inaccurate due to the large entropy barrier associated with the dislocation-obstacle interaction. Considering the importance of finite temperature effects, the utility of the Finite Temperature String (FTS) method was then explored. While this approach was found capable of identifying a prominent reaction tube, it was not capable of computing the free energy profile along the tube. Lastly, the utility of the Transition Interface Sampling (TIS) approach was explored, which does not need a free energy profile and is known to be less reliant on the choice of reaction coordinate. The TIS approach was found capable of accurately predicting the rate, relative to direct MD simulations. This finding was utilized to examine the temperature and load dependence of the dislocation-obstacle interaction in a simple periodic cell configuration. An attractive rate prediction approach combining TST and simple continuum models is identified, and the strain rate sensitivity of individual dislocation obstacle interactions is predicted.

  5. Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation.

    Science.gov (United States)

    Berryman, Joshua T; Radford, Sheena E; Harris, Sarah A

    2009-07-08

    Amyloid fibrils are long, helically symmetric protein aggregates that can display substantial variation (polymorphism), including alterations in twist and structure at the beta-strand and protofilament levels, even when grown under the same experimental conditions. The structural and thermodynamic origins of this behavior are not yet understood. We performed molecular-dynamics simulations to determine the thermodynamic properties of different polymorphs of the peptide GNNQQNY, modeling fibrils containing different numbers of protofilaments based on the structure of amyloid-like cross-beta crystals of this peptide. We also modeled fibrils with new orientations of the side chains, as well as a de novo designed structure based on antiparallel beta-strands. The simulations show that these polymorphs are approximately isoenergetic under a range of conditions. Structural analysis reveals a dynamic reorganization of electrostatics and hydrogen bonding in the main and side chains of the Gln and Asn residues that characterize this peptide sequence. Q/N-rich stretches are found in several amyloidogenic proteins and peptides, including the yeast prions Sup35-N and Ure2p, as well as in the human poly-Q disease proteins, including the ataxins and huntingtin. Based on our results, we propose that these residues imbue a unique structural plasticity to the amyloid fibrils that they comprise, rationalizing the ability of proteins enriched in these amino acids to form prion strains with heritable and different phenotypic traits.

  6. Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering.

    Science.gov (United States)

    Ho, Tuan Anh; Greathouse, Jeffery A; Wang, Yifeng; Criscenti, Louise J

    2017-11-10

    The porosity of clay aggregates is an important property governing chemical reactions and fluid flow in low-permeability geologic formations and clay-based engineered barrier systems. Pore spaces in clays include interlayer and interparticle pores. Under compaction and dewatering, the size and geometry of such pore spaces may vary significantly (sub-nanometer to microns) depending on ambient physical and chemical conditions. Here we report a molecular dynamics simulation method to construct a complex and realistic clay-like nanoparticle aggregate with interparticle pores and grain boundaries. The model structure is then used to investigate the effect of dewatering and water content on micro-porosity of the aggregates. The results suggest that slow dewatering would create more compact aggregates compared to fast dewatering. Furthermore, the amount of water present in the aggregates strongly affects the particle-particle interactions and hence the aggregate structure. Detailed analyses of particle-particle and water-particle interactions provide a molecular-scale view of porosity and texture development of the aggregates. The simulation method developed here may also aid in modeling the synthesis of nanostructured materials through self-assembly of nanoparticles.

  7. Atomistic simulation of orientation dependence in shock-induced initiation of pentaerythritol tetranitrate.

    Science.gov (United States)

    Shan, Tzu-Ray; Wixom, Ryan R; Mattsson, Ann E; Thompson, Aidan P

    2013-01-24

    The dependence of the reaction initiation mechanism of pentaerythritol tetranitrate (PETN) on shock orientation and shock strength is investigated with molecular dynamics simulations using a reactive force field and the multiscale shock technique. In the simulations, a single crystal of PETN is shocked along the [110], [001], and [100] orientations with shock velocities in the range 3-10 km/s. Reactions occur with shock velocities of 6 km/s or stronger, and reactions initiate through the dissociation of nitro and nitrate groups from the PETN molecules. The most sensitive orientation is [110], while [100] is the most insensitive. For the [001] orientation, PETN decomposition via nitro group dissociation is the dominant reaction initiation mechanism, while for the [110] and [100] orientations the decomposition is via mixed nitro and nitrate group dissociation. For shock along the [001] orientation, we find that CO-NO(2) bonds initially acquire more kinetic energy, facilitating nitro dissociation. For the other two orientations, C-ONO(2) bonds acquire more kinetic energy, facilitating nitrate group dissociation.

  8. Atomistic simulation of fcc—bcc phase transition in single crystal Al under uniform compression

    International Nuclear Information System (INIS)

    Li Li; Liang Jiu-Qing; Shao Jian-Li; Duan Su-Qing; Li Yan-Fang

    2012-01-01

    By molecular dynamics simulations employing an embedded atom model potential, we investigate the fcc-to-bcc phase transition in single crystal Al, caused by uniform compression. Results show that the fcc structure is unstable when the pressure is over 250 GPa, in reasonable agreement with the calculated value through the density functional theory. The morphology evolution of the structural transition and the corresponding transition mechanism are analysed in detail. The bcc (011) planes are transited from the fcc (111-bar) plane and the (11-bar1) plane. We suggest that the transition mechanism consists mainly of compression, shear, slid and rotation of the lattice. In addition, our radial distribution function analysis explicitly indicates the phase transition of Al from fcc phase to bcc structure. (condensed matter: structural, mechanical, and thermal properties)

  9. Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification

    Science.gov (United States)

    Swinburne, Thomas D.; Perez, Danny

    2018-05-01

    A massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.

  10. Structure Based Modeling of Small Molecules Binding to the TLR7 by Atomistic Level Simulations

    Directory of Open Access Journals (Sweden)

    Francesco Gentile

    2015-05-01

    Full Text Available Toll-Like Receptors (TLR are a large family of proteins involved in the immune system response. Both the activation and the inhibition of these receptors can have positive effects on several diseases, including viral pathologies and cancer, therefore prompting the development of new compounds. In order to provide new indications for the design of Toll-Like Receptor 7 (TLR7-targeting drugs, the mechanism of interaction between the TLR7 and two important classes of agonists (imidazoquinoline and adenine derivatives was investigated through docking and Molecular Dynamics simulations. To perform the computational analysis, a new model for the dimeric form of the receptors was necessary and therefore created. Qualitative and quantitative differences between agonists and inactive compounds were determined. The in silico results were compared with previous experimental observations and employed to define the ligand binding mechanism of TLR7.

  11. Atomistic simulation of the pinning of edge dislocations in Ni by Ni3Al precipitates

    International Nuclear Information System (INIS)

    Kohler, Christopher; Kizler, Peter; Schmauder, Siegfried

    2005-01-01

    Classical molecular dynamics simulations of the interaction of edge dislocations in Ni with chains of spherical Ni 3 Al precipitates are performed using EAM potentials. The order hardening is investigated at temperature T=0 -bar K by determining the critical resolved shear stresses (CRSSs) for a superdislocation that is dissociated into four partial dislocations. The CRSS is computed as a function of the radius and the distance of the precipitates. It is found that for precipitates with a diameter smaller than the dissociation width of perfect edge dislocation in Ni, the CRSS of the trailing dislocation of the superdislocation is a fraction of about 0.4 of the CRSS of the leading dislocation

  12. Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

    Science.gov (United States)

    Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

    2014-07-21

    In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

  13. The glide of screw dislocations in bcc Fe: Atomistic static and dynamic simulations

    International Nuclear Information System (INIS)

    Chaussidon, Julien; Fivel, Marc; Rodney, David

    2006-01-01

    We present atomic-scale simulations of screw dislocation glide in bcc iron. Using two interatomic potentials that, respectively, predict degenerate and non-degenerate core structures, we compute the static 0 K dependence of the screw dislocation Peierls stress on crystal orientation and show strong boundary condition effects related to the generation of non-glide stress components. At finite temperatures we show that, with a non-degenerate core, glide by nucleation/propagation of kink-pairs in a {1 1 0} glide plane is obtained at low temperatures. A transition in the twinning region, towards an average {1 1 2} glide plane, with the formation of debris loops is observed at higher temperatures

  14. Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

    Science.gov (United States)

    Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

    2014-10-14

    Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

  15. Atomistic simulations of dislocations in a model BCC multicomponent concentrated solid solution alloy

    International Nuclear Information System (INIS)

    Rao, S.I.; Varvenne, C.; Woodward, C.; Parthasarathy, T.A.; Miracle, D.; Senkov, O.N.; Curtin, W.A.

    2017-01-01

    Molecular statics and molecular dynamics simulations are presented for the structure and glide motion of a/2〈111〉 dislocations in a randomly-distributed model-BCC Co 16.67 Fe 36.67 Ni 16.67 Ti 30 alloy. Core structure variations along an individual dislocation line are found for a/2〈111〉 screw and edge dislocations. One reason for the core structure variations is the local variation in composition along the dislocation line. Calculated unstable stacking fault energies on the (110) plane as a function of composition vary significantly, consistent with this assessment. Molecular dynamics simulations of the critical glide stress as a function of temperature show significant strengthening, and much shallower temperature dependence of the strengthening, as compared to pure BCC Fe as well as a reference mean-field BCC alloy material of the same overall composition, lattice and elastic constants as the target alloy. Interpretation of the strength versus temperature in terms of an effective kink-pair activation model shows the random alloy to have a much larger activation energy than the mean-field alloy or BCC Fe. This is interpreted as due to the core structure variations along the dislocation line that are often unfavorable for glide in the direction of the load. The configuration of the gliding dislocation is wavy, and significant debris is left behind, demonstrating the role of local composition and core structure in creating kink pinning (super jogs) and/or deflection of the glide plane of the dislocation. - Graphical abstract: Measured critical resolved shear stress scaled by the (111) shear modulus (39 GPa) necessary to achieve on-going glide as a function of temperature, for the a/2[111] screw dislocation in the model BCC Co 16.67 Fe 36.67 Ni 16.67 Ti 30 alloy. The upper and lower bounds of the critical resolved shear stress is shown in the plot. Also shown in is the measured strength for the mean-field A-atom material and BCC Fe as a function of

  16. Atomistic simulation of the point defects in B2-type MoTa alloy

    International Nuclear Information System (INIS)

    Zhang Jianmin; Wang Fang; Xu Kewei; Ji, Vincent

    2009-01-01

    The formation and migration mechanisms of three different point defects (mono-vacancy, anti-site defect and interstitial atom) in B 2 -type MoTa alloy have been investigated by combining molecular dynamics (MD) simulation with modified analytic embedded-atom method (MAEAM). From minimization of the formation energy, we find that the anti-site defects Mo Ta and Ta Mo are easier to form than Mo and Ta mono-vacancies, while Mo and Ta interstitial atoms are difficult to form in the alloy. In six migration mechanisms of Mo and Ta mono-vacancies, one nearest-neighbor jump (1NNJ) is the most favorable due to its lowest activation and migration energies, but it will cause a disorder in the alloy. One next-nearest-neighbor jump (1NNNJ) and one third-nearest-neighbor jump (1TNNJ) can maintain the ordered property of the alloy but require higher activation and migration energies, so the 1NNNJ and 1TNNJ should be replaced by straight [1 0 0] six nearest-neighbor cyclic jumps (S[1 0 0]6NNCJ) or bent [1 0 0] six nearest-neighbor cyclic jumps (B[1 0 0]6NNCJ) and [1 1 0] six nearest-neighbor cyclic jumps ([1 1 0]6NNCJ), respectively. Although the migrations of Mo and Ta interstitial atoms need much lower energy than Mo and Ta mono-vacancies, they are not main migration mechanisms due to difficult to form in the alloy.

  17. Understanding and revisiting the most complex perovskite system via atomistic simulations

    Science.gov (United States)

    Yang, Yali; Xu, Bin; Xu, Changsong; Ren, Wei; Bellaiche, Laurent

    2018-05-01

    A first-principles-based effective Hamiltonian is developed and used, along with direct ab initio techniques, to investigate finite-temperature properties of the system commonly coined the most complex perovskite, that is NaNbO3. Such simulations successfully reproduce the existence of seven different phases in its phase diagram. The decomposition of the total energy of this effective Hamiltonian into different terms, altogether with the values of the parameters associated with these terms, also allow us to shed some light into puzzling features of such a compound. Examples include revealing the microscopic reasons of why R 3 c is its ground state and why it solely adopts in-phase tiltings at high temperatures versus complex nanotwins for intermediate temperatures. The results of the computations also call for a revisiting of the so-called P ,R , and S states, in the sense that an unexpected and previously overlooked inhomogeneous electrical polarization is numerically found in the P state while complex tiltings associated with the simultaneous condensation of several k points are predicted for the controversial R and S phases.

  18. Computer code for the atomistic simulation of lattice defects and dynamics

    International Nuclear Information System (INIS)

    Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

    1980-04-01

    The computer code COMENT used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect properties, defect migration, and defect stability. This report documents Version IV of COMENT (models, methods, and implementation) and defines current code options. Version IV of COMENT generates only face-centered-cubic (fcc) crystal lattices. However, an effort was made to structure COMENT to allow addition of new options with a minimum of change in the existing version of the code. This document describes the calling program and thirty-two user-defined subroutines. Fourteen subroutines (ALOYORD, DASPKA, DFCT, DSLOAN, DSLOIN, EXPAND, POT1, POT2, POT3, POT4, POT5, POT6, POT7, and THRMAL) are associated with the selection of program options; only a few of these are used in any given analysis. Seven of the other subroutines (CRYSTL, IEAF, INCBOX, LABLE, MINILAT, SPEFORS, and SQUEZ are used to establish a variety of arrays and conditions required for each analysis; most of them are used once in a given calculation. The remaining eleven subroutines (DAMP, DIRECT, IDDEF, NEAF, INBIN, FILBIN, FTBIN, PAC3, UNPAC3, PACF, and UNPACF) are used many times in each calculation; the last eight of these are used many times in each time step during the integration and, therefore, are written in COMPASS (CDC assembly language). The COMPASS subroutines are described in sufficient detail to permit easy conversion to some other assembly language or to FORTRAN

  19. Atomistic simulation on the plastic deformation and fracture of bio-inspired graphene/Ni nanocomposites

    Science.gov (United States)

    Yang, Zhenyu; Wang, Dandan; Lu, Zixing; Hu, Wenjun

    2016-11-01

    Molecular dynamics simulations were performed to investigate the plastic deformation and fracture behaviors of bio-inspired graphene/metal nanocomposites, which have a "brick-and-mortar" nanostructure, consisting of hard graphene single-layers embedded in a soft Ni matrix. The plastic deformation mechanisms of the nanocomposites were analyzed as well as their effects on the mechanical properties with various geometrical variations. It was found that the strength and ductility of the metal matrix can be highly enhanced with the addition of the staggered graphene layers, and the plastic deformation can be attributed to the interfacial sliding, dislocation nucleation, and cracks' combination. The strength of the nanocomposites strongly depends on the length scale of the nanostructure and the interlayer distance as well. In addition, slip at the interface releases the stress in graphene layers, leading to the stress distribution on the graphene more uniform. The present results are expected to contribute to the design of the nanolayered graphene/metal composites with high performance.

  20. Verification of experimental dynamic strength methods with atomistic ramp-release simulations

    Science.gov (United States)

    Moore, Alexander P.; Brown, Justin L.; Lim, Hojun; Lane, J. Matthew D.

    2018-05-01

    Material strength and moduli can be determined from dynamic high-pressure ramp-release experiments using an indirect method of Lagrangian wave profile analysis of surface velocities. This method, termed self-consistent Lagrangian analysis (SCLA), has been difficult to calibrate and corroborate with other experimental methods. Using nonequilibrium molecular dynamics, we validate the SCLA technique by demonstrating that it accurately predicts the same bulk modulus, shear modulus, and strength as those calculated from the full stress tensor data, especially where strain rate induced relaxation effects and wave attenuation are small. We show here that introducing a hold in the loading profile at peak pressure gives improved accuracy in the shear moduli and relaxation-adjusted strength by reducing the effect of wave attenuation. When rate-dependent effects coupled with wave attenuation are large, we find that Lagrangian analysis overpredicts the maximum unload wavespeed, leading to increased error in the measured dynamic shear modulus. These simulations provide insight into the definition of dynamic strength, as well as a plausible explanation for experimental disagreement in reported dynamic strength values.

  1. Exploration of Structural Changes in Lactose Permease on Sugar Binding and Proton Transport through Atomistic Simulations

    Science.gov (United States)

    Liu, Jin; Jewel, Yead; Dutta, Prashanta

    2017-11-01

    Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule to a wild-type LacY. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from microsecond simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with experiments. Our analysis suggest that the conformational changes of LacY are a cumulative consequence of inter-domain H-bonds breaking at the periplasmic side, inter-domain salt-bridge formation at the cytoplasmic side, as well as the TDG orientational changes during the transition. This work is supported by US National Science Foundation under Grant No. CBET-1604211.

  2. Microchemical effects in irradiated Fe–Cr alloys as revealed by atomistic simulation

    Energy Technology Data Exchange (ETDEWEB)

    Malerba, L., E-mail: lmalerba@sckcen.be [Structural Materials Modelling and Microstructure Unit, SMA/NMS, Studiecentrum voor Kernenergie, Centre d’Etudes de l’Energie Nucléaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Bonny, G.; Terentyev, D. [Structural Materials Modelling and Microstructure Unit, SMA/NMS, Studiecentrum voor Kernenergie, Centre d’Etudes de l’Energie Nucléaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Zhurkin, E.E. [Experimental Nuclear Physics Department, K-89, Faculty of Physics and Mechanics, Saint-Petersburg State Polytechnical University, 29 Polytekhnicheskaya Str., 195251 St. Petersburg (Russian Federation); Hou, M. [Physique des Solides Irradiés et des Nanostructures CP234, Faculté des Sciences, Université Libre de Bruxelles, Bd du Triomphe, B-1050 Bruxelles (Belgium); Vörtler, K.; Nordlund, K. [Association EURATOM-Tekes, Department of Physics, P.O. Box 43, FI-00014, University of Helsinki (Finland)

    2013-11-15

    Neutron irradiation produces evolving nanostructural defects in materials, that affect their macroscopic properties. Defect production and evolution is expected to be influenced by the chemical composition of the material. In turn, the accumulation of defects in the material results in microchemical changes, which may induce further changes in macroscopic properties. In this work we review the results of recent atomic-level simulations conducted in Fe–Cr alloys, as model materials for high-Cr ferritic–martensitic steels, to address the following questions: 1. Is the primary damage produced in displacement cascades influenced by the Cr content? If so, how? 2. Does Cr change the stability of radiation-produced defects? 3. Is the diffusivity of cascade-produced defects changed by Cr content? 4. How do Cr atoms redistribute under irradiation inside the material under the action of thermodynamic driving forces and radiation-defect fluxes? It is found that the presence of Cr does not influence the type of damage created by displacement cascades, as compared to pure Fe, while cascades do contribute to redistributing Cr, in the same direction as thermodynamic driving forces. The presence of Cr does change the stability of point-defects: the effect is weak in the case of vacancies, stronger in the case of self-interstitials. In the latter case, Cr increases the stability of self-interstitial clusters, especially those so small to be invisible to the electron microscope. Cr reduces also significantly the diffusivity of self-interstitials and their clusters, in a way that depends in a non-monotonic way on Cr content, as well as on cluster size and temperature; however, the effect is negligible on the mobility of self-interstitial clusters large enough to become visible dislocation loops. Finally, Cr-rich precipitate formation is favoured in the tensile region of edge dislocations, while it appears not to be influenced by screw dislocations; prismatic dislocation loops

  3. Atomistic modelling study of lanthanide incorporation in the crystal lattice of an apatite

    International Nuclear Information System (INIS)

    Louis-Achille, V.

    1999-01-01

    Studies of natural and synthetic apatites allow to propose such crystals as matrix for nuclear waste storage. The neodymium substituted britholite, Ca 9 Nd(PO 4 ) 5 (SiO 4 )F 2 . is a model for the trivalent actinide storage Neodymium can be substituted in two types of sites. The aim of this thesis is to compare the chemical nature of this two sites in fluoro-apatite Ca 9 (PO 4 ) 6 F 2 and then in britholite, using ab initio atomistic modeling. Two approaches are used: one considers the infinite crystals and the second considers clusters. The calculations of the electronic structure for both were performed using Kohn and Sham density functional theory in the local approximation. For solids, pseudopotentials were used, and wave functions are expanded in plane waves. For clusters, a frozen core approximation was used, and the wave functions are expanded in a linear combination of Slater type atomic orbitals. The pseudopotential is semi-relativistic for neodymium, and the Hamiltonian is scalar relativistic for the clusters. The validation of the solid approach is performed using two test cases: YPO 4 and ScPO 4 . Two numerical tools were developed to compute electronic deformation density map, and calculate partial density of stases. A full optimisation of the lattice parameters with a relaxation of the atomic coordinates leads to correct structural and thermodynamic properties for the fluoro-apatite, compared to experience. The electronic deformation density maps do not show any significant differences. between the two calcium sites. but Mulliken analysis on the solid and on the clusters point out the more ionic behavior of the calcium in site 2. A neodymium substituted britholite is then studied. Neodymium location only induces local modifications in; the crystalline structure and few changes in the formation enthalpy. The electronic study points out an increase of the covalent character the bonding involving neodymium compared with the one related to calcium

  4. Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations

    DEFF Research Database (Denmark)

    Heikkila, E.; Martinez-Seara, H.; Gurtovenko, A. A.

    2014-01-01

    Despite being chemically inert as a bulk material, nanoscale gold can pose harmful side effects to living organisms. In particular, cationic Au nanoparticles (AuNP+) of 2 nm diameter or less permeate readily through plasma membranes and induce cell death. We report atomistic simulations of cationic...... to be governed by cooperative effects where AuNP+, counterions, water, and the two membrane leaflets all contribute. On the extracellular side, we find that the nanoparticle has to cross a free energy barrier of about 5 k(B)T prior forming a stable contact with the membrane. This results in a rearrangement...

  5. Atomistic simulations of divacancy defects in armchair graphene nanoribbons: Stability, electronic structure, and electron transport properties

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Jun [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Zeng, Hui, E-mail: zenghui@yangtzeu.edu.cn [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Wei, Jianwei [College of Optoelectronic Information, Chongqing University of Technology, Chongqing 400054 (China); Li, Biao; Xu, Dahai [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China)

    2014-01-17

    Using the first principles calculations associated with nonequilibrium Green's function, we have studied the electronic structures and quantum transport properties of defective armchair graphene nanoribbon (AGNR) in the presence of divacancy defects. The triple pentagon–triple heptagon (555–777) defect in the defective AGNR is energetically more favorable than the pentagon–octagon–pentagon (5–8–5) defect. Our calculated results reveal that both 5–8–5-like defect and 555–777-like defect in AGNR could improve the electron transport. It is anticipated that defective AGNRs can exhibit large range variations in transport behaviors, which are strongly dependent on the distributions of the divacancy defect.

  6. Surfactant-nanotube interactions in water and nanotube separation by diameter: atomistic simulations

    Science.gov (United States)

    Carvalho, E. J. F.; Dos Santos, M. C.

    2010-05-01

    A non-destructive sorting method to separate single-walled carbon nanotubes (SWNTs) by diameter was recently proposed. By this method, SWNTs are suspended in water by surfactant encapsulation and the separation is carried out by ultracentrifugation in a density gradient. SWNTs of different diameters are distributed according to their densities along the centrifuge tube. A mixture of two anionic surfactants, namely sodium dodecylsulfate (SDS) and sodium cholate (SC), presented the best performance in discriminating nanotubes by diameter. Unexpectedly, small diameter nanotubes are found at the low density part of the centrifuge tube. We present molecular dynamics studies of the water-surfactant-SWNT system to investigate the role of surfactants in the sorting process. We found that surfactants can actually be attracted towards the interior of the nanotube cage, depending on the relationship between the surfactant radius of gyration and the nanotube diameter. The dynamics at room temperature showed that, as the amphiphile moves to the hollow cage, water molecules are dragged together, thereby promoting the nanotube filling. The resulting densities of filled SWNT are in agreement with measured densities.

  7. The defect chemistry of UO2 ± x from atomistic simulations

    Science.gov (United States)

    Cooper, M. W. D.; Murphy, S. T.; Andersson, D. A.

    2018-06-01

    Control of the defect chemistry in UO2 ± x is important for manipulating nuclear fuel properties and fuel performance. For example, the uranium vacancy concentration is critical for fission gas release and sintering, while all oxygen and uranium defects are known to strongly influence thermal conductivity. Here the point defect concentrations in thermal equilibrium are predicted using defect energies from density functional theory (DFT) and vibrational entropies calculated using empirical potentials. Electrons and holes have been treated in a similar fashion to other charged defects allowing for structural relaxation around the localized electronic defects. Predictions are made for the defect concentrations and non-stoichiometry of UO2 ± x as a function of oxygen partial pressure and temperature. If vibrational entropy is omitted, oxygen interstitials are predicted to be the dominant mechanism of excess oxygen accommodation over only a small temperature range (1265 K-1350 K), in contrast to experimental observation. Conversely, if vibrational entropy is included oxygen interstitials dominate from 1165 K to 1680 K (Busker potential) or from 1275 K to 1630 K (CRG potential). Below these temperature ranges, excess oxygen is predicted to be accommodated by uranium vacancies, while above them the system is hypo-stoichiometric with oxygen deficiency accommodated by oxygen vacancies. Our results are discussed in the context of oxygen clustering, formation of U4O9, and issues for fuel behavior. In particular, the variation of the uranium vacancy concentrations as a function of temperature and oxygen partial pressure will underpin future studies into fission gas diffusivity and broaden the understanding of UO2 ± x sintering.

  8. 3D atomistic studies of fatigue behaviour of edge crack (0 0 1) in bcc iron loaded in mode i and II

    Czech Academy of Sciences Publication Activity Database

    Machová, Anna; Pokluda, J.; Uhnáková, Alena; Hora, Petr

    2014-01-01

    Roč. 66, September (2014), s. 11-19 ISSN 0142-1123 R&D Projects: GA ČR(CZ) GAP108/10/0698 Institutional support: RVO:61388998 Keywords : fatigue crack growth * bcc iron * 3D atomistic simulations * molecular dynamics Subject RIV: JQ - Machines ; Tools Impact factor: 2.275, year: 2014 www.elsevier.com/locate/ijfatigue

  9. Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

    Science.gov (United States)

    Paul, Fabian; Noé, Frank; Weikl, Thomas R

    2018-03-27

    Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109 Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.

  10. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

    International Nuclear Information System (INIS)

    Nishizawa, Manami; Nishizawa, Kazuhisa

    2014-01-01

    Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT OPLS ). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT OPLS PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT CHARMM ) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT OPLS PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA) 3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret

  11. Atomistic simulations of ultra-short pulse laser ablation of aluminum: validity of the Lambert-Beer law

    Science.gov (United States)

    Eisfeld, Eugen; Roth, Johannes

    2018-05-01

    Based on hybrid molecular dynamics/two-temperature simulations, we study the validity of the application of Lambert-Beer's law, which is conveniently used in various modeling approaches of ultra-short pulse laser ablation of metals. The method is compared to a more rigorous treatment, which involves solving the Helmholtz wave equation for different pulse durations ranging from 100 fs to 5 ps and a wavelength of 800 nm. Our simulations show a growing agreement with increasing pulse durations, and we provide appropriate optical parameters for all investigated pulse durations.

  12. Derivation of kinetic coefficients by atomistic methods for studying defect behavior in Mo

    International Nuclear Information System (INIS)

    Insepov, Z.; Rest, J.; Yacout, A.M.; Kuksin, A.Yu.; Norman, G.E.; Stegailov, V.V.; Starikov, S.V.; Yanilkin, A.V.

    2012-01-01

    Highlights: ► A multiscale concept couples molecular dynamics (MD) with ab initio and kinetic rate theory. ► Evolution of a system of self-interstitial atoms and vacancies in Mo is studied by MD. ► Formation of di-SIA clusters and SIA–vacancy recombination is analyzed. ► 1D diffusion of self-interstitials at various temperature and defect concentrations were studied. ► This paper provides a powerful predictive tool for simulating irradiation of nuclear materials. - Abstract: A multiscale concept for irradiated materials simulation is formulated based on coupling molecular dynamics simulations (MD) where the potential was obtained from ab initio data of energies of the basic defect structures, with kinetic mesoscale models. The evolution of a system containing self-interstitial atoms (SIAs) and vacancies in crystalline molybdenum is investigated by means of MD. The kinetics of formation of di-SIA clusters and SIA–vacancy recombination is analyzed via approaches used in the kinetic theory of radiation ageing. The effects of 1D diffusion of SIAs, temperature, and defect concentrations on the reaction rates are also studied. This approach can validate both the kinetic mechanisms and the appropriate kinetic coefficients, offering the potential to significantly reduce the uncertainty of the kinetic methodology and providing a powerful predictive tool for simulating irradiation behavior of nuclear materials.

  13. Giant electrocaloric response in the prototypical Pb(Mg,Nb)O3 relaxor ferroelectric from atomistic simulations

    Science.gov (United States)

    Jiang, Zhijun; Nahas, Y.; Prokhorenko, S.; Prosandeev, S.; Wang, D.; Íñiguez, Jorge; Bellaiche, L.

    2018-03-01

    An atomistic effective Hamiltonian is used to investigate electrocaloric (EC) effects of Pb (Mg1 /3Nb2 /3) O3 relaxor ferroelectrics in its ergodic regime, and subject to electric fields applied along the pseudocubic [111] direction. Such a Hamiltonian qualitatively reproduces (i) the electric field-versus-temperature phase diagram, including the existence of a critical point where first-order and second-order transitions meet each other; and (ii) a giant EC response near such a critical point. It also reveals that such giant response around this critical point is microscopically induced by field-induced percolation of polar nanoregions. Moreover, it is also found that, for any temperature above the critical point, the EC coefficient-versus-electric-field curve adopts a maximum (and thus larger electrocaloric response too), that can be well described by the general Landau-like model proposed by Jiang et al., [Phys. Rev. B 96, 014114 (2017)], 10.1103/PhysRevB.96.014114, and that is further correlated with specific microscopic features related to dipoles lying along different rhombohedral directions. Furthermore, for temperatures being at least 40 K higher than the critical temperature, the (electric field, temperature) line associated with this maximal EC coefficient is below both the Widom line and the line representing percolation of polar nanoregions.

  14. Atomistic simulation of tantalum nanoindentation: Effects of indenter diameter, penetration velocity, and interatomic potentials on defect mechanisms and evolution

    Energy Technology Data Exchange (ETDEWEB)

    Ruestes, C.J., E-mail: cjruestes@hotmail.com [Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States); Facultad de Ciencias Exactas y Naturales, Univ. Nac. de Cuyo, Mendoza 5500 (Argentina); CONICET, Mendoza 5500 (Argentina); Stukowski, A. [Technische Universität Darmstadt, Darmstadt 64287 (Germany); Tang, Y. [Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072 (China); Tramontina, D.R. [Facultad de Ciencias Exactas y Naturales, Univ. Nac. de Cuyo, Mendoza 5500 (Argentina); Erhart, P. [Chalmers University of Technology, Department of Applied Physics, Gothenburg 41296 (Sweden); Remington, B.A. [Lawrence Livermore National Lab, Livermore, CA 94550 (United States); Urbassek, H.M. [Physics Department and Research Center OPTIMAS, University of Kaiserslautern, Kaiserslautern 67663 (Germany); Meyers, M.A. [Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States); Bringa, E.M. [Facultad de Ciencias Exactas y Naturales, Univ. Nac. de Cuyo, Mendoza 5500 (Argentina); CONICET, Mendoza 5500 (Argentina)

    2014-09-08

    Nanoindentation simulations are a helpful complement to experiments. There is a dearth of nanoindentation simulations for bcc metals, partly due to the lack of computationally efficient and reliable interatomic potentials at large strains. We carry out indentation simulations for bcc tantalum using three different interatomic potentials and present the defect mechanisms responsible for the creation and expansion of the plastic deformation zone: twins are initially formed, giving rise to shear loop expansion and the formation of sequential prismatic loops. The calculated elastic constants as function of pressure as well as stacking fault energy surfaces explain the significant differences found in the defect structures generated for the three potentials investigated in this study. The simulations enable the quantification of total dislocation length and twinning fraction. The indenter velocity is varied and, as expected, the penetration depth for the first pop-in (defect emission) event shows a strain rate sensitivity m in the range of 0.037–0.055. The effect of indenter diameter on the first pop-in is discussed. A new intrinsic length-scale model is presented based on the profile of the residual indentation and geometrically necessary dislocation theory.

  15. Atomistic simulation of tantalum nanoindentation: Effects of indenter diameter, penetration velocity, and interatomic potentials on defect mechanisms and evolution

    International Nuclear Information System (INIS)

    Ruestes, C.J.; Stukowski, A.; Tang, Y.; Tramontina, D.R.; Erhart, P.; Remington, B.A.; Urbassek, H.M.; Meyers, M.A.; Bringa, E.M.

    2014-01-01

    Nanoindentation simulations are a helpful complement to experiments. There is a dearth of nanoindentation simulations for bcc metals, partly due to the lack of computationally efficient and reliable interatomic potentials at large strains. We carry out indentation simulations for bcc tantalum using three different interatomic potentials and present the defect mechanisms responsible for the creation and expansion of the plastic deformation zone: twins are initially formed, giving rise to shear loop expansion and the formation of sequential prismatic loops. The calculated elastic constants as function of pressure as well as stacking fault energy surfaces explain the significant differences found in the defect structures generated for the three potentials investigated in this study. The simulations enable the quantification of total dislocation length and twinning fraction. The indenter velocity is varied and, as expected, the penetration depth for the first pop-in (defect emission) event shows a strain rate sensitivity m in the range of 0.037–0.055. The effect of indenter diameter on the first pop-in is discussed. A new intrinsic length-scale model is presented based on the profile of the residual indentation and geometrically necessary dislocation theory

  16. Study of plasticity in metals by numerical simulations

    International Nuclear Information System (INIS)

    Clouet, E.

    2013-01-01

    We present a study of the plastic behaviour in metals based on the modelling of dislocation properties. Different simulation tools have been used and developed to study plasticity in structural materials, in particular metals used in the nuclear industry. In iron or zirconium alloys, plasticity is controlled at low temperature by the glide of screw dislocations. Atomistic simulations can be used to model dislocation core properties and thus to obtain a better knowledge of the mechanisms controlling dislocation glide. Such atomistic simulations need nevertheless some special care because of the long range elastic field induced by the dislocations. We have therefore developed a modelling approach relying both on atomistic simulations, using either empirical interatomic potentials or ab initio calculations, and on elasticity theory. Such an approach has been used to obtain dislocation intrinsic core properties. These simulations allowed us to describe, in iron, the variations of these core properties with the dislocation character. In zirconium, we could identity the origin of the high lattice friction and obtain a better understanding of the competition between the different glide systems. At high temperature, dislocations do not only glide but can also cross-slip or climb. This leads to a motion of the dislocations out of their glide plane which needs to be considered when modelling the plastic flow. We performed a study of dislocation climb at different scales, leading to the implementation of a dislocation climb model in dislocation dynamics simulations. (author) [fr

  17. Mobility and stability of large vacancy and vacancy-copper clusters in iron: An atomistic kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Castin, N., E-mail: ncastin@sckcen.be [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium); Pascuet, M.I., E-mail: pascuet@cnea.gov.ar [Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires (Argentina); Malerba, L. [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium)

    2012-10-15

    The formation of Cu-rich precipitates under irradiation is a major cause for changes in the mechanical response to load of reactor pressure vessel steels. In previous works, it has been shown that the mechanism under which precipitation occurs is governed by diffusion of vacancy-copper (VCu) complexes, also in the absence of irradiation. Coarse-grained computer models (such as object kinetic Monte Carlo) aimed at simulating irradiation processes in model alloys or steels should therefore explicitly include the mobility of Cu precipitates, as a consequence of vacancy hops at their surface. For this purpose, in this work we calculate diffusion coefficients and lifetimes for a large variety of VCu complexes. We use an innovative atomistic model, where vacancy migration energies are calculated with little approximations, taking into account all effects of static relaxation and long-range chemical interaction as predicted by an interatomic potential. Our results show that, contrary to what intuition might suggest, saturation in vacancies tend to slow down the transport of Cu atoms.

  18. Atomistic kinetic Monte Carlo study of atomic layer deposition derived from density functional theory.

    Science.gov (United States)

    Shirazi, Mahdi; Elliott, Simon D

    2014-01-30

    To describe the atomic layer deposition (ALD) reactions of HfO2 from Hf(N(CH3)2)4 and H2O, a three-dimensional on-lattice kinetic Monte-Carlo model is developed. In this model, all atomistic reaction pathways in density functional theory (DFT) are implemented as reaction events on the lattice. This contains all steps, from the early stage of adsorption of each ALD precursor, kinetics of the surface protons, interaction between the remaining precursors (steric effect), influence of remaining fragments on adsorption sites (blocking), densification of each ALD precursor, migration of each ALD precursors, and cooperation between the remaining precursors to adsorb H2O (cooperative effect). The essential chemistry of the ALD reactions depends on the local environment at the surface. The coordination number and a neighbor list are used to implement the dependencies. The validity and necessity of the proposed reaction pathways are statistically established at the mesoscale. The formation of one monolayer of precursor fragments is shown at the end of the metal pulse. Adsorption and dissociation of the H2O precursor onto that layer is described, leading to the delivery of oxygen and protons to the surface during the H2O pulse. Through these processes, the remaining precursor fragments desorb from the surface, leaving the surface with bulk-like and OH-terminated HfO2, ready for the next cycle. The migration of the low coordinated remaining precursor fragments is also proposed. This process introduces a slow reordering motion (crawling) at the mesoscale, leading to the smooth and conformal thin film that is characteristic of ALD. Copyright © 2013 Wiley Periodicals, Inc.

  19. Atomistic simulations of nanocrystalline U0.5Th0.5O2 solid solution under uniaxial tension

    Directory of Open Access Journals (Sweden)

    Hongxing Xiao

    2017-12-01

    Full Text Available Molecular dynamics simulations were performed to investigate the uniaxial tensile properties of nanocrystalline U0.5Th0.5O2 solid solution with the Born–Mayer–Huggins potential. The results indicated that the elastic modulus increased linearly with the density relative to a single crystal, but decreased with increasing temperature. The simulated nanocrystalline U0.5Th0.5O2 exhibited a breakdown in the Hall–Petch relation with mean grain size varying from 3.0 nm to 18.0 nm. Moreover, the elastic modulus of U1-yThyO2 solid solutions with different content of thorium at 300 K was also studied and the results accorded well with the experimental data available in the literature. In addition, the fracture mode of nanocrystalline U0.5Th0.5O2 was inclined to be ductile because the fracture behavior was preceded by some moderate amount of plastic deformation, which is different from what has been seen earlier in simulations of pure UO2.

  20. Multiscale modeling for ferroelectric materials: identification of the phase-field model’s free energy for PZT from atomistic simulations

    International Nuclear Information System (INIS)

    Völker, Benjamin; Landis, Chad M; Kamlah, Marc

    2012-01-01

    Within a knowledge-based multiscale simulation approach for ferroelectric materials, the atomic level can be linked to the mesoscale by transferring results from first-principles calculations into a phase-field model. A recently presented routine (Völker et al 2011 Contin. Mech. Thermodyn. 23 435–51) for adjusting the Helmholtz free energy coefficients to intrinsic and extrinsic ferroelectric material properties obtained by DFT calculations and atomistic simulations was subject to certain limitations: caused by too small available degrees of freedom, an independent adjustment of the spontaneous strains and piezoelectric coefficients was not possible, and the elastic properties could only be considered in cubic instead of tetragonal symmetry. In this work we overcome such restrictions by expanding the formulation of the free energy function, i.e. by motivating and introducing new higher-order terms that have not appeared in the literature before. Subsequently we present an improved version of the adjustment procedure for the free energy coefficients that is solely based on input parameters from first-principles calculations performed by Marton and Elsässer, as documented in Völker et al (2011 Contin. Mech. Thermodyn. 23 435–51). Full sets of adjusted free energy coefficients for PbTiO 3 and tetragonal Pb(Zr,Ti)O 3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed. (paper)

  1. Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

    Science.gov (United States)

    Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

    2012-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

  2. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

    DEFF Research Database (Denmark)

    Kaszuba, K.; Postila, P. A.; Cramariuc, O.

    2013-01-01

    studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...

  3. Atomistic mechanism of graphene growth on a SiC substrate: Large-scale molecular dynamics simulations based on a new charge-transfer bond-order type potential

    Science.gov (United States)

    Takamoto, So; Yamasaki, Takahiro; Nara, Jun; Ohno, Takahisa; Kaneta, Chioko; Hatano, Asuka; Izumi, Satoshi

    2018-03-01

    Thermal decomposition of silicon carbide is a promising approach for the fabrication of graphene. However, the atomistic growth mechanism of graphene remains unclear. This paper describes the development of a new charge-transfer interatomic potential. Carbon bonds with a wide variety of characteristics can be reproduced by the proposed vectorized bond-order term. A large-scale thermal decomposition simulation enables us to observe the continuous growth process of the multiring carbon structure. The annealing simulation reveals the atomistic process by which the multiring carbon structure is transformed to flat graphene involving only six-membered rings. Also, it is found that the surface atoms of the silicon carbide substrate enhance the homogeneous graphene formation.

  4. Investigating interfacial contact configuration and behavior of single-walled carbon nanotube-based nanodevice with atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Jianlei, E-mail: cjlxjtu@mail.xjtu.edu.cn; Zhang, Jianwei [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); He, Xiaoqiao, E-mail: bcxqhe@cityu.edu.hk [City University of Hong Kong, Department of Architecture and Civil Engineering (Hong Kong); Mei, Xuesong; Wang, Wenjun [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); Yang, Xinju [Fudan University, State Key Laboratory of Surface Physics and Department of Physics (China); Xie, Hui; Yang, Lijun; Wang, Yang [Harbin Institute of Technology, State Key Laboratory of Robotics and Systems (China)

    2017-03-15

    Carbon nanotubes (CNTs), including single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs), are considered to be the promising candidates for next-generation interconnects with excellent physical and chemical properties ranging from ultrahigh mechanical strength, to electrical properties, to thermal conductivity, to optical properties, etc. To further study the interfacial contact configurations of SWNT-based nanodevice with a 13.56-Å diameter, the corresponding simulations are carried out with the molecular dynamic method. The nanotube collapses dramatically into the surface with the complete collapse on the Au/Ag/graphite electrode surface and slight distortion on the Si/SiO{sub 2} substrate surface, respectively. The related dominant mechanism is studied and explained. Meanwhile, the interfacial contact configuration and behavior, depended on other factors, are also analyzed in this article.

  5. Atomistic simulation of the influence of Cr on the mobility of the edge dislocation in Fe(Cr) alloys

    International Nuclear Information System (INIS)

    Hafez Haghighat, S.M.; Terentyev, D.; Schaeublin, R.

    2011-01-01

    In this work Fe-Cr compounds, as model alloys for the ferritic base steels that are considered as main candidates for the structural materials of the future fusion reactors, are studied using molecular dynamics simulations. The Cr or so-called α' precipitates, which are obstacles to dislocations, affect mechanical properties, leading to hardening and loss of ductility. The flow stress to move an edge dislocation in a Cr solid solution in pure Fe is studied as a function of Cr content. The strength of a nanometric Cr precipitate as obstacle to an edge dislocation in pure Fe is investigated as a function of its Cr content. Results show that with increasing Cr content the precipitate obstacle strength increases, with a strong sensitivity to the local atomic order. Temperature induces a monotonic decrease of the flow stress of the Cr solid solution and of the Cr precipitate obstacle strength.

  6. An efficient Monte Carlo algorithm for the fast equilibration and atomistic simulation of alkanethiol self-assembled monolayers on a Au(111) substrate.

    Science.gov (United States)

    Alexiadis, Orestis; Daoulas, Kostas Ch; Mavrantzas, Vlasis G

    2008-01-31

    A new Monte Carlo algorithm is presented for the simulation of atomistically detailed alkanethiol self-assembled monolayers (R-SH) on a Au(111) surface. Built on a set of simpler but also more complex (sometimes nonphysical) moves, the new algorithm is capable of efficiently driving all alkanethiol molecules to the Au(111) surface, thereby leading to full surface coverage, irrespective of the initial setup of the system. This circumvents a significant limitation of previous methods in which the simulations typically started from optimally packed structures on the substrate close to thermal equilibrium. Further, by considering an extended ensemble of configurations each one of which corresponds to a different value of the sulfur-sulfur repulsive core potential, sigmass, and by allowing for configurations to swap between systems characterized by different sigmass values, the new algorithm can adequately simulate model R-SH/Au(111) systems for values of sigmass ranging from 4.25 A corresponding to the Hautman-Klein molecular model (J. Chem. Phys. 1989, 91, 4994; 1990, 93, 7483) to 4.97 A corresponding to the Siepmann-McDonald model (Langmuir 1993, 9, 2351), and practically any chain length. Detailed results are presented quantifying the efficiency and robustness of the new method. Representative simulation data for the dependence of the structural and conformational properties of the formed monolayer on the details of the employed molecular model are reported and discussed; an investigation of the variation of molecular organization and ordering on the Au(111) substrate for three CH3-(CH2)n-SH/Au(111) systems with n=9, 15, and 21 is also included.

  7. Atomistic study of a nanometer-scale pump based on the thermal ratchet concept

    DEFF Research Database (Denmark)

    Oyarzua, Elton; Walther, J. H.; Zambrano, Harvey

    In this study, a novel concept of nanoscale pump fabricated using Carbon Nanotubes (CNTs) is presented. The development of nanofluidic systems provides unprecedented possibilities for the control of biology and chemistry at the molecular level with potential applications in low energy cost devices...... dynamics simulations, we explore the possibility to design thermophoretic pumping devices fabricated of CNTs for water transport in nanoconduits. The design of the nanopumps is based on the concept of the Feynman-Smoluchowski ratchet....... of great interest in nanofluidics. Thermophoresisis the phenomenon observed when a mixture of two or more types of motile objects experience a force induced by a thermal gradient and the different types of objects respond to it differently, inducing a motion and segregation of the objects. Using molecular...

  8. Tunable thermodynamic stability of Au-CuPt core-shell trimetallic nanoparticles by controlling the alloy composition: insights from atomistic simulations.

    Science.gov (United States)

    Huang, Rao; Shao, Gui-Fang; Wen, Yu-Hua; Sun, Shi-Gang

    2014-11-07

    A microscopic understanding of the thermal stability of metallic core-shell nanoparticles is of importance for their synthesis and ultimately application in catalysis. In this article, molecular dynamics simulations have been employed to investigate the thermodynamic evolution of Au-CuPt core-shell trimetallic nanoparticles with various Cu/Pt ratios during heating processes. Our results show that the thermodynamic stability of these nanoparticles is remarkably enhanced upon rising Pt compositions in the CuPt shell. The melting of all the nanoparticles initiates at surface and gradually spreads into the core. Due to the lattice mismatch among Au, Cu and Pt, stacking faults have been observed in the shell and their numbers are associated with the Cu/Pt ratios. With the increasing temperature, they have reduced continuously for the Cu-dominated shell while more stacking faults have been produced for the Pt-dominated shell because of the significantly different thermal expansion coefficients of the three metals. Beyond the overall melting, all nanoparticles transform into a trimetallic mixing alloy coated by an Au-dominated surface. This work provides a fundamental perspective on the thermodynamic behaviors of trimetallic, even multimetallic, nanoparticles at the atomistic level, indicating that controlling the alloy composition is an effective strategy to realize tunable thermal stability of metallic nanocatalysts.

  9. From beta-relaxation to alpha-decay: Atomistic picture from molecular dynamics simulations for glass-forming Ni0.5Zr0.5 melt

    Energy Technology Data Exchange (ETDEWEB)

    Teichler, Helmar [Inst. Materialphysik, Univ Goettingen (Germany)

    2013-07-01

    In glass-forming melts the decay of structural fluctuation shows the well known transition from beta-relaxation (von-Schweidler law with exponent b) to alpha-decay (KWW law with exponent beta). Here we present results from molecular dynamics simulations for a metallic glass forming Ni0.5Zr0.5 model aimed at giving an understanding of this transition on the atomistic scale. At the considered temperature below mode coupling Tc, the dynamics of the system can be interpreted by residence of the particles in their neighbour cages and escape from the cages as rare processes. Our analysis yields that the fraction of residing particles is characterized by a hierarchical law in time, with von-Schweidler b explicitly related to the exponent of this law. In the alpha-decay regime the stretching exponent reflects, in addition, floating of the cages due to strain effects of escaped particles. Accordingly, the change from beta-relaxation to alpha-decay indicates the transition from low to large fraction of escaped particles.

  10. Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations

    International Nuclear Information System (INIS)

    Yoon, Gwonchan; Lee, Myeongsang; Kim, Kyungwoo; In Kim, Jae; Joon Chang, Hyun; Baek, Inchul; Na, Sungsoo; Eom, Kilho

    2015-01-01

    Amyloid fibrils are responsible for pathogenesis of various diseases and exhibit the structural feature of an ordered, hierarchical structure such as multi-stranded helical structure. As the multi-strandedness of amyloid fibrils has recently been found to be highly correlated with their toxicity and infectivity, it is necessary to study how the hierarchical (i.e. multi-stranded) structure of amyloid fibril is formed. Moreover, although it has recently been reported that the nanomechanics of amyloid proteins plays a key role on the amyloid-induced pathogenesis, a critical role that the multi-stranded helical structure of the fibrils plays in their nanomechanical properties has not fully characterized. In this work, we characterize the morphology and mechanical properties of multi-stranded amyloid fibrils by using equilibrium molecular dynamics simulation and elastic network model. It is shown that the helical pitch of multi-stranded amyloid fibril is linearly proportional to the number of filaments comprising the amyloid fibril, and that multi-strandedness gives rise to improving the bending rigidity of the fibril. Moreover, we have also studied the morphology and mechanical properties of a single protofilament (filament) in order to understand the effect of cross-β structure and mutation on the structures and mechanical properties of amyloid fibrils. Our study sheds light on the underlying design principles showing how the multi-stranded amyloid fibril is formed and how the structure of amyloid fibrils governs their nanomechanical properties. (paper)

  11. Large-scale atomistic simulations of nanostructured materials based on divide-and-conquer density functional theory

    Directory of Open Access Journals (Sweden)

    Vashishta P.

    2011-05-01

    Full Text Available A linear-scaling algorithm based on a divide-and-conquer (DC scheme is designed to perform large-scale molecular-dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT. This scheme is applied to the thermite reaction at an Al/Fe2O3 interface. It is found that mass diffusion and reaction rate at the interface are enhanced by a concerted metal-oxygen flip mechanism. Preliminary simulations are carried out for an aluminum particle in water based on the conventional DFT, as a target system for large-scale DC-DFT simulations. A pair of Lewis acid and base sites on the aluminum surface preferentially catalyzes hydrogen production in a low activation-barrier mechanism found in the simulations

  12. Integration of NMR And SAXS with Atomistic Simulations for Characterizing the Structure and Dynamics of Multi-Domain Proteins

    Science.gov (United States)

    Debiec, Karl Thomas

    In the seven decades since the first atomic-level structures of biomolecules were determined, the development and application of novel research methods has led to an advanced understanding of biological functions at the molecular level. In addition to experimental methods, key advances have been spurred by computer simulations, which provide an in silico representation of accumulated prior knowledge of biomolecular structure and dynamics. These models can be used both (i) as a complement to experimental results, filling in the gaps where experimental information is not accessible, and (ii) as complete representations, directing future research. Critically, the validity of either application depends on the accuracy of the models used. In this work, I aspired to combine computational and experimental methods to characterize the structure and dynamics of the flexibly linked two-domain protein MoCVNH3. In Chapter 1 I describe my motivation, and the suspected simulation artifacts observed in our preliminary simulations, which led me to investigate how accurately simulation models represent salt bridge interactions. Chapter 2 details my comparison of current models ("force fields"), for which significant variation but consistent overstabilization of salt bridges was discovered. This work motivated the development of a new force field, AMBER ff15ipq, which corrects, to some degree, the overstabilization and introduces extensive improvements, described in Chapter 3. Finally, in Chapter 4, I applied this new force field in simulations of MoCVNH3, for which I collected extensive experimental data leading to the determination of a structural ensemble. I validated the simulations against the experimental data set, and identified further directions for improvement. Overall, the work presented here demonstrates the power of integrating experimental and computational methods.

  13. doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

    Czech Academy of Sciences Publication Activity Database

    Danne, R.; Poojari, C.; Martinez-Seara, Hector; Rissanen, S.; Lolicato, F.; Róg, T.; Vattulainen, I.

    2017-01-01

    Roč. 57, č. 10 (2017), s. 2401-2406 ISSN 1549-9596 Institutional support: RVO:61388963 Keywords : molecular dynamics simulations * GROMOS force field * cellulose nanofibrils Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 3.760, year: 2016 http://pubs.acs.org/doi/full/10.1021/acs.jcim.7b00237

  14. Atomistic study of ternary oxides as high-temperature solid lubricants

    Science.gov (United States)

    Gao, Hongyu

    understanding of lubricious mechanisms of solid lubricants in general. Molecular dynamics (MD) simulations was used as the primary tool in this research, complemented by density-functional theory and experiments from our colleagues. In this research, we first developed empirical potential parameters for AgTaO3 and later Cu- Ta-O ternaries using the modified embedded-atom method (MEAM) formalism. With those parameters, we explored the sliding mechanisms of AgTaO3, CuTaO3 and CuTa2O6 at elevated temperatures. Particularly on AgTaO3, we investigated the effects of applied loads as well as surface terminations on friction and wear as functions of temperature. In addition, to optimize the tribological performance of AgTaO3, film reconstruction mechanisms were investigated on Ta2O5/Ag films with varying amounts of Ag. For the potassium chloride-iron system, we studied the effect of contact pressure on interfacial structure, based on which the origin of the commonly observed pressure-dependent shear strengths was explored. We hope this research will benefit the design and development of solid lubricant materials for a wide range of applications.

  15. Mass and heat transfer between evaporation and condensation surfaces: Atomistic simulation and solution of Boltzmann kinetic equation.

    Science.gov (United States)

    Zhakhovsky, Vasily V; Kryukov, Alexei P; Levashov, Vladimir Yu; Shishkova, Irina N; Anisimov, Sergey I

    2018-04-16

    Boundary conditions required for numerical solution of the Boltzmann kinetic equation (BKE) for mass/heat transfer between evaporation and condensation surfaces are analyzed by comparison of BKE results with molecular dynamics (MD) simulations. Lennard-Jones potential with parameters corresponding to solid argon is used to simulate evaporation from the hot side, nonequilibrium vapor flow with a Knudsen number of about 0.02, and condensation on the cold side of the condensed phase. The equilibrium density of vapor obtained in MD simulation of phase coexistence is used in BKE calculations for consistency of BKE results with MD data. The collision cross-section is also adjusted to provide a thermal flux in vapor identical to that in MD. Our MD simulations of evaporation toward a nonreflective absorbing boundary show that the velocity distribution function (VDF) of evaporated atoms has the nearly semi-Maxwellian shape because the binding energy of atoms evaporated from the interphase layer between bulk phase and vapor is much smaller than the cohesive energy in the condensed phase. Indeed, the calculated temperature and density profiles within the interphase layer indicate that the averaged kinetic energy of atoms remains near-constant with decreasing density almost until the interphase edge. Using consistent BKE and MD methods, the profiles of gas density, mass velocity, and temperatures together with VDFs in a gap of many mean free paths between the evaporation and condensation surfaces are obtained and compared. We demonstrate that the best fit of BKE results with MD simulations can be achieved with the evaporation and condensation coefficients both close to unity.

  16. Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel

    DEFF Research Database (Denmark)

    Bjelkmar, Pär; Niemelä, Perttu S; Vattulainen, Ilpo

    2009-01-01

    transitions occur in membrane proteins-not to mention numerous applications in drug design. Here, we present a full 1 micros atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements......Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how...... and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations....

  17. 3D atomistic simulation of fatigue behavior of a ductile crack in bcc iron loaded in mode II

    Czech Academy of Sciences Publication Activity Database

    Uhnáková, Alena; Pokluda, J.; Machová, Anna; Hora, Petr

    2012-01-01

    Roč. 61, AUG 2012 (2012), s. 12-19 ISSN 0927-0256 R&D Projects: GA ČR(CZ) GAP108/10/0698 Institutional research plan: CEZ:AV0Z20760514 Keywords : fatigue * mode II * bcc iron * molecular dynamic simulations Subject RIV: JG - Metallurgy Impact factor: 1.878, year: 2012 http://www.sciencedirect.com/science/article/pii/S0927025612001929

  18. Atomistic modeling of dropwise condensation

    Energy Technology Data Exchange (ETDEWEB)

    Sikarwar, B. S., E-mail: bssikarwar@amity.edu; Singh, P. L. [Department of Mechanical Engineering, Amity University Uttar Pradesh, Noida (India); Muralidhar, K.; Khandekar, S. [Department of Mechanical Engineering, IIT Kanpur (India)

    2016-05-23

    The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smaller sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.

  19. Atomistic simulation of the thermal conductivity in amorphous SiO2 matrix/Ge nanocrystal composites

    Science.gov (United States)

    Kuryliuk, Vasyl V.; Korotchenkov, Oleg A.

    2017-04-01

    We use nonequilibrium molecular dynamics computer simulations with the Tersoff potential aiming to provide a comprehensive picture of the thermal conductivity of amorphous SiO2 (a-SiO2) matrix with embedded Ge nanocrystals (nc-Ge). The modelling predicts the a-SiO2 matrix thermal conductivity in a temperature range of 50 fair agreement with experiment at around room temperature. It is worth noticing that the predicted room-temperature thermal conductivity in a-SiO2 is in very good agreement with the experimental result, which is in marked contrast with the thermal conductivity calculated employing the widely used van Beest-Kramer-van Santen (BKS) potential. We show that the thermal conductivity of composite nc-Ge/a-SiO2 systems decreases steadily with increasing the volume fraction of Ge inclusions, indicative of enhanced interface scattering of phonons imposed by embedded Ge nanocrystals. We also observe that increasing the volume fractions above a certain threshold value results in a progressively increased thermal conductivity of the nanocomposite, which can be explained by increasing volume fraction of a better thermally conducting Ge. Finally, non-equilibrium molecular dynamics simulations with the Tersoff potential are promising for computing the thermal conductivity of nanocomposites based on amorphous SiO2 and can be readily scaled to more complex composite structures with embedded nanoparticles, which thus help design nanocomposites with desired thermal properties.

  20. Mass-velocity and size-velocity distributions of ejecta cloud from shock-loaded tin surface using atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Durand, O.; Soulard, L. [CEA, DAM, DIF, F-91297 Arpajon (France)

    2015-04-28

    The mass (volume and areal densities) versus velocity as well as the size versus velocity distributions of a shock-induced cloud of particles are investigated using large scale molecular dynamics simulations. A generic three-dimensional tin crystal with a sinusoidal free surface roughness (single wavelength) is set in contact with vacuum and shock-loaded so that it melts directly on shock. At the reflection of the shock wave onto the perturbations of the free surface, two-dimensional sheets/jets of liquid metal are ejected. The simulations show that the distributions may be described by an analytical model based on the propagation of a fragmentation zone, from the tip of the sheets to the free surface, in which the kinetic energy of the atoms decreases as this zone comes closer to the free surface on late times. As this kinetic energy drives (i) the (self-similar) expansion of the zone once it has broken away from the sheet and (ii) the average size of the particles which result from fragmentation in the zone, the ejected mass and the average size of the particles progressively increase in the cloud as fragmentation occurs closer to the free surface. Though relative to nanometric scales, our model may help in the analysis of experimental profiles.

  1. Investigation into diffusion induced plastic deformation behavior in hollow lithium ion battery electrode revealed by analytical model and atomistic simulation

    International Nuclear Information System (INIS)

    Li, Jia; Fang, Qihong; Wu, Hong; Liu, Youwen; Wen, Pihua

    2015-01-01

    Highlights: • Diffusion induced stress is established. • Yield stress is dependent upon concentration. • Plastic deformation induced stress lowers tensile stress. • Plastic deformation suppresses crack nucleation. • Plastic deformation occurs not only at lithiated phase but also at electrode interior. - Abstract: This paper is theoretically suggested to describe diffusion induced stress in the elastoplastic hollow spherical silicon electrode for plastic deformation using both analytical model and molecular simulation. Based on the plastic deformation and the yield criterion, we develop this model accounting for the lithium-ion diffusion effect in hollow electrode, focusing on the concentration and stress distributions undergoing lithium-ion insertion. The results show that the two ways, applied compressive stress to inner surface or limited inner surface with higher concentration using biological membranes maintaining concentration difference, lead to the compressive stress induced by the lithium-ion diffusion effect. Hollow spherical electrode reduces effectively diffusion induced stress through controlling and tuning electrode parameters to obtain the reasonably low yield strength. According to MD simulations, plastic deformation phenomenon not only occurs at interface layer of lithiated phase, but also penetrates at electrode interior owning to confinement imposed by lithiated phase. These criteria that radial and hoop stresses reduce dramatically when plastic deformation occurs near the end faces of hollow electrode, may help guide development of new materials for lithium-ion batteries with enhanced mechanical durability, by means of reasonable designing yield strength to maintain mechanical stress below fracture strength, thereby increasing battery life.

  2. Atomistic study on shock behaviour of NiTi shape memory alloy

    Science.gov (United States)

    Yin, Qiuyun; Wu, Xianqian; Huang, Chenguang

    2017-06-01

    The shock behaviour of NiTi shape memory alloy is investigated by using molecular dynamics simulation. The nano-pillar samples of the alloy are subjected to the impact of a piston with a velocity of 350 m/s at initial environment temperatures of 325 and 500 K. At 325 K, we observe two different pathways of the formation of BCO phase, the gradient twins, and the detwinning phenomena, strongly depending on the local stress and the deformation state. As the initial temperature increases to 500 K, the plasticity is dominated by the dislocation movements rather than the twinning at 325 K. The phase transformation and plasticity result in stress attenuation when the stress wave propagates through the nano-pillar. Furthermore, it is interesting to note that multiple stress peaks occur due to the formation of local complex atomic structures with various wave speeds, leading to the catch up and overlap of the stress waves.

  3. PELE web server: atomistic study of biomolecular systems at your fingertips.

    Science.gov (United States)

    Madadkar-Sobhani, Armin; Guallar, Victor

    2013-07-01

    PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

  4. Atomistic study of self-diffusion in Cu-Ag immiscible alloy system

    International Nuclear Information System (INIS)

    Zhang Jianmin; Chen Gouxiang; Xu Kewei

    2006-01-01

    Combining molecular dynamic (MD) simulation with modified analytic embedded-atom method (MAEAM) potential, the formation, migration and activation energies have been calculated for four-kind migrations of Cu vacancy and three-kind migrations of Ag vacancy in Cu-Ag immiscible alloy system. The equilibrium concentration of Cu vacancies is greater than that of Ag vacancies owing to the formation energy of Cu vacancy (1.012 eV) is lower than that of Ag vacancy (1.169 eV). Comparing the migration or activation energy needed for four-kind migrations of Cu vacancy and three-kind migrations of Ag vacancy show that the favorable migration mechanism is the nearest-neighbor (NN) jump for Cu vacancy, while the straight [0 1 0] six-jump cycle (6JC) for Ag vacancy. Furthermore, the activation energy of the NN jump of Cu vacancy (2.164 eV) is lower than that of straight [0 1 0] 6JC of Ag vacancy (2.404 eV) also show that the former is more favorable. We conclude accordingly that the primary migration mechanism is the NN jump of an abundance of Cu vacancies

  5. Atomistic simulation of radiation-induced amorphization of the B2 ordered intermetallic compound NiTi

    International Nuclear Information System (INIS)

    Sabochick, M.J.

    1990-12-01

    Amorphization of the B2 intermetallic compound NiTi under electron irradiation has been investigated using molecular dynamics. The effect of irradiation was simulated using two processes: (1) Ni and Ti atoms were exchanged, resulting in chemical disorder, and (2) Frenkel pairs were introduced, leading to the formation of stable point defects and also chemical disorder upon mutual recombination of interstitials and vacancies. After ∼0.4 exchanges per atom, the first process resulted in an energy increase of approximately 0.11 eV/atom and a volume increase of 1.91%. On the other hand, after introducing ∼0.5 Frenkel pairs per atom, the second process led to smaller increases of 0.092 eV/atom in energy and 1.43% in volume. The calculated radial distribution functions (RDFs) were essentially identical to each other and to the calculated RDF of a quenched liquid. The structure factor, however, showed that long-range order was still present after atom exchanges, while the introduction of Frenkel pairs resulted in the loss of long-range order. It was concluded that point defects are necessary for amorphization to occur in NiTi, although chemical disorder alone is capable of storing enough energy to make the transition possible. 18 refs., 3 figs

  6. Atomistic simulations on the axial nanowelding configuration and contact behavior between Ag nanowire and single-walled carbon nanotubes

    International Nuclear Information System (INIS)

    Cui, Jianlei; Zhang, Jianwei; He, Xiaoqiao; Yang, Xinjun; Mei, Xuesong; Wang, Wenjun; Jiang, Gedong; Wang, Kedian; Yang, Lijun; Xie, Hui

    2017-01-01

    As for the interesting new building blocks, the Ag nanowires (AgNWs) and single-walled carbon nanotubes (SWNTs) as the interesting new building blocks are viewed as the promising candidates for the next-generation interconnects due to their most remarkable electrical, thermal, optical, mechanical, and other properties. The axial nanowelding of head-to-head style and side-to-side style is relatively simulated with the molecular dynamics method. As for the head-to-head structural style, SWNTs will move toward the AgNWs and contact with the head of AgNWs. And, the part of the Ag nanowire may be subsequently encapsulated in SWNT with the core-filling Ag atom chain as the final atomic contact configuration during nanowelding, which is related to the nanowelding temperature. When the SWNTs and AgNWs are arranged by the side-to-side contact style, the SWNTs will move along the SWNT surface and may eventually catch up with the AgNW being neck and neck. Aiming at the final axial atomic configurations and the contact behavior during nanowelding process, the related dominant mechanism is revealed in this paper.

  7. Atomistic simulations on the axial nanowelding configuration and contact behavior between Ag nanowire and single-walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Jianlei, E-mail: cjlxjtu@mail.xjtu.edu.cn; Zhang, Jianwei [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); He, Xiaoqiao, E-mail: bcxqhe@cityu.edu.hk [City University of Hong Kong, Department of Architecture and Civil Engineering (Hong Kong); Yang, Xinjun [Fudan University, State Key Laboratory of Surface Physics and Department of Physics (China); Mei, Xuesong; Wang, Wenjun; Jiang, Gedong; Wang, Kedian [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); Yang, Lijun; Xie, Hui [Harbin Institute of Technology, State Key Laboratory of Robotics and Systems (China)

    2017-03-15

    As for the interesting new building blocks, the Ag nanowires (AgNWs) and single-walled carbon nanotubes (SWNTs) as the interesting new building blocks are viewed as the promising candidates for the next-generation interconnects due to their most remarkable electrical, thermal, optical, mechanical, and other properties. The axial nanowelding of head-to-head style and side-to-side style is relatively simulated with the molecular dynamics method. As for the head-to-head structural style, SWNTs will move toward the AgNWs and contact with the head of AgNWs. And, the part of the Ag nanowire may be subsequently encapsulated in SWNT with the core-filling Ag atom chain as the final atomic contact configuration during nanowelding, which is related to the nanowelding temperature. When the SWNTs and AgNWs are arranged by the side-to-side contact style, the SWNTs will move along the SWNT surface and may eventually catch up with the AgNW being neck and neck. Aiming at the final axial atomic configurations and the contact behavior during nanowelding process, the related dominant mechanism is revealed in this paper.

  8. Atomistic simulations of the effect of embedded hydrogen and helium on the tensile properties of monocrystalline and nanocrystalline tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Zhe [Department of Physics, Beihang University, Beijing 100191 (China); Department of Mechanical Engineering, University of North Carolina at Charlotte, Charlotte, NC 28223-0001 (United States); Kecskes, Laszlo J. [US Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, MD 21005 (United States); Zhu, Kaigui, E-mail: kgzhu@buaa.edu.cn [Department of Physics, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Energy Materials and Physics, Beihang University, Beijing 100191 (China); Wei, Qiuming, E-mail: qwei@uncc.edu [Department of Mechanical Engineering, University of North Carolina at Charlotte, Charlotte, NC 28223-0001 (United States)

    2016-12-01

    Uniaxial tensile properties of monocrystalline tungsten (MC-W) and nanocrystalline tungsten (NC-W) with embedded hydrogen and helium atoms have been investigated using molecular dynamics (MD) simulations in the context of radiation damage evolution. Different strain rates have been imposed to investigate the strain rate sensitivity (SRS) of the samples. Results show that the plastic deformation processes of MC-W and NC-W are dominated by different mechanisms, namely dislocation-based for MC-W and grain boundary-based activities for NC-W, respectively. For MC-W, the SRS increases and a transition appears in the deformation mechanism with increasing embedded atom concentration. However, no obvious embedded atom concentration dependence of the SRS has been observed for NC-W. Instead, in the latter case, the embedded atoms facilitate GB sliding and intergranular fracture. Additionally, a strong strain enhanced He cluster growth has been observed. The corresponding underlying mechanisms are discussed. - Highlights: • Uniaxial tensile behavior of monocrystal tungsten (C-W) and nanocrystalline W (NC-W) have been investigated. • Dislocation-based activities dominate the plastic deformation of MC-W. • Grain boundary-based activities dominate the plastic deformation of NC-W. • H/He atoms have significant impacts on the tensile behavior of MC-W and NC-W. • Strong strain enhanced He cluster growth has been revealed.

  9. Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

    Science.gov (United States)

    Anwar, Muhammad Ayaz; Choi, Sangdun

    2017-03-01

    Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

  10. Insights into the charge carrier terahertz mobility in polyfluorenes from large-scale atomistic simulations and time-resolved terahertz spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Vukmirović, N.; Ponseca, C.S.; Němec, Hynek; Yartsev, A.; Sundström, V.

    2012-01-01

    Roč. 116, č. 37 (2012), s. 19665-1972 ISSN 1932-7447 Institutional research plan: CEZ:AV0Z10100520 Keywords : charge carrier mobility * time-resolved terahertz spectroscopy * multiscale atomistic calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.814, year: 2012

  11. Heterogeneities in metallic glasses. Atomistic computer simulations on the structure and mechanical properties of copper-zirconium alloys and composites

    International Nuclear Information System (INIS)

    Brink, Tobias

    2017-01-01

    The present thesis deals with molecular dynamics computer simulations of heterogeneities in copper-zirconium metallic glasses, ranging from intrinsic structural fluctuations to crystalline secondary phases. These heterogeneities define, on a microscopic scale, the properties of the glass, and an understanding of their nature and behaviour is required for deriving the proper structure-property relations. In terms of composite systems, we start with the amorphisation of copper nanolayers embedded in a metallic glass matrix. While copper is an fcc metal with a high propensity for crystallisation, amorphisation can in fact occur in such systems for thermodynamic reasons. This is due to interface effects, which are also known from heterogeneous interfaces in crystals or from grain boundary complexions, although in absence of lattice mismatch. In single-phase glasses, intrinsic heterogeneities are often discussed in terms of soft spots or geometrically unfavourable motifs (GUMs), which can be considered to be mechanically weaker, defective regions of the glass. We investigate the relation between these motifs and the boson peak, an anomaly in the vibrational spectrum of all glasses. We demonstrate a relation between the boson peak and soft spots by analysing various amorphous and partially amorphous samples as well as highentropy alloys. Finally, we treat the plastic deformation of glasses, with and without crystalline secondary phases. We propose an explanation for the experimentally observed variations of propagation direction, composition, and density along a shear band. These variations of propagation direction are small in the case of single-phase glasses. A considerably greater influence on shear band propagation can be exerted by precipitates. We systematically investigate composites ranging from low crystalline volume fraction up to systems which resemble a nanocrystalline metal. In this context, we derive a mechanism map for composite systems and observe the

  12. Automatic and Systematic Atomistic Simulations in the MedeA® Software Environment: Application to EU-REACH

    Directory of Open Access Journals (Sweden)

    Rozanska Xavier

    2015-03-01

    Full Text Available This work demonstrates the systematic prediction of thermodynamic properties for batches of thousands of molecules using automated procedures. This is accomplished with newly developed tools and functions within the Material Exploration and Design Analysis (MedeA® software environment, which handle the automatic execution of sequences of tasks for large numbers of molecules including the creation of 3D molecular models from 1D representations, systematic exploration of possible conformers for each molecule, the creation and submission of computational tasks for property calculations on parallel computers, and the post-processing for comparison with available experimental properties. After the description of the different MedeA® functionalities and methods that make it easy to perform such large number of computations, we illustrate the strength and power of the approach with selected examples from molecular mechanics and quantum chemical simulations. Specifically, comparisons of thermochemical data with quantum-based heat capacities and standard energies of formation have been obtained for more than 2 000 compounds, yielding average deviations with experiments of less than 4% with the Design Institute for Physical PRoperties (DIPPR database. The automatic calculation of the density of molecular fluids is demonstrated for 192 systems. The relaxation to minimum-energy structures and the calculation of vibrational frequencies of 5 869 molecules are evaluated automatically using a semi-empirical quantum mechanical approach with a success rate of 99.9%. The present approach is scalable to large number of molecules, thus opening exciting possibilities with the advent of exascale computing.

  13. Heterogeneities in metallic glasses. Atomistic computer simulations on the structure and mechanical properties of copper-zirconium alloys and composites

    Energy Technology Data Exchange (ETDEWEB)

    Brink, Tobias

    2017-07-01

    The present thesis deals with molecular dynamics computer simulations of heterogeneities in copper-zirconium metallic glasses, ranging from intrinsic structural fluctuations to crystalline secondary phases. These heterogeneities define, on a microscopic scale, the properties of the glass, and an understanding of their nature and behaviour is required for deriving the proper structure-property relations. In terms of composite systems, we start with the amorphisation of copper nanolayers embedded in a metallic glass matrix. While copper is an fcc metal with a high propensity for crystallisation, amorphisation can in fact occur in such systems for thermodynamic reasons. This is due to interface effects, which are also known from heterogeneous interfaces in crystals or from grain boundary complexions, although in absence of lattice mismatch. In single-phase glasses, intrinsic heterogeneities are often discussed in terms of soft spots or geometrically unfavourable motifs (GUMs), which can be considered to be mechanically weaker, defective regions of the glass. We investigate the relation between these motifs and the boson peak, an anomaly in the vibrational spectrum of all glasses. We demonstrate a relation between the boson peak and soft spots by analysing various amorphous and partially amorphous samples as well as highentropy alloys. Finally, we treat the plastic deformation of glasses, with and without crystalline secondary phases. We propose an explanation for the experimentally observed variations of propagation direction, composition, and density along a shear band. These variations of propagation direction are small in the case of single-phase glasses. A considerably greater influence on shear band propagation can be exerted by precipitates. We systematically investigate composites ranging from low crystalline volume fraction up to systems which resemble a nanocrystalline metal. In this context, we derive a mechanism map for composite systems and observe the

  14. Atomistic simulation of the mechanical properties of β-SiC based on the first-principles

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Renhui, E-mail: zrh_111@126.com [Research Center of Material and Chemical Engineering, School of Material and Chemical Engineering, Tongren University, Tongren 554300 (China); Leng, Senlin, E-mail: 764546880@qq.com [Research Center of Material and Chemical Engineering, School of Material and Chemical Engineering, Tongren University, Tongren 554300 (China); Yang, Yingchang; Shi, Wei [Research Center of Material and Chemical Engineering, School of Material and Chemical Engineering, Tongren University, Tongren 554300 (China); Lu, Zhibin, E-mail: zblu@licp.cas.cn [Lanzhou Institute of Chemical Physics, Lanzhou 730000 (China)

    2017-05-01

    On the basis of the pseudopotential plane-wave method and the local-density-functional theory, this work studied the energetics and stress-strain relationship of β-SiC, where uniform uniaxial compression and tension were considered along (001), (110) and (111) planes. The calculated results were in consistence with the experimental data. The present work should be conducive to understanding the mechanical property of β-SiC.

  15. Atomistic simulation of ideal shear strength, point defects, and screw dislocations in bcc transition metals: Mo as a prototype

    International Nuclear Information System (INIS)

    Xu, W.; Moriarty, J.A.

    1996-01-01

    Using multi-ion interatomic potentials derived from first-principles generalized pseudopotential theory, we have studied ideal shear strength, point defects, and screw dislocations in the prototype bcc transition metal molybdenum (Mo). Many-body angular forces, which are important to the structural and mechanical properties of such central transition metals with partially filled d bands, are accounted for in the present theory through explicit three- and four-ion potentials. For the ideal shear strength of Mo, our computed results agree well with those predicted by full electronic-structure calculations. For point defects in Mo, our calculated vacancy-formation and activation energies are in excellent agreement with experimental results. The energetics of six self-interstitial configurations have also been investigated. The left-angle 110 right-angle split dumbbell interstitial is found to have the lowest formation energy, in agreement with the configuration found by x-ray diffuse scattering measurements. In ascending order, the sequence of energetically stable interstitials is predicted to be left-angle 110 right-angle split dumbbell, crowdion, left-angle 111 right-angle split dumbbell, tetrahedral site, left-angle 001 right-angle split dumbbell, and octahedral site. In addition, the migration paths for the left-angle 110 right-angle dumbbell self-interstitial have been studied. The migration energies are found to be 3 endash 15 times higher than previous theoretical estimates obtained using simple radial-force Finnis-Sinclair potentials. Finally, the atomic structure and energetics of left-angle 111 right-angle screw dislocations in Mo have been investigated. We have found that the so-called open-quote open-quote easy close-quote close-quote core configuration has a lower formation energy than the open-quote open-quote hard close-quote close-quote one, consistent with previous theoretical studies. (Abstract Truncated)

  16. RTS amplitudes in decananometer MOSFETs: 3-D simulation study

    OpenAIRE

    Asenov, A.; Balasubramaniam, R.; Brown, A.R.; Davies, J.H.

    2003-01-01

    In this paper we study the amplitudes of random telegraph signals (RTS) associated with the trapping of a single electron in defect states at the Si/SiO/sub 2/ interface of sub-100-nm (decananometer) MOSFETs employing three-dimensional (3-D) "atomistic" simulations. Both continuous doping charge and random discrete dopants in the active region of the MOSFETs are considered in the simulations. The dependence of the RTS amplitudes on the position of the trapped charge in the channel and on devi...

  17. An Atomistic Modeling Study of Alloying Element Impurity Element, and Transmutation Products on the cohesion of A Nickel E5 {001} Twist Grain Boundary

    International Nuclear Information System (INIS)

    Young, G.A. Jr.; Najafabadi, R.; Strohmayer, W.; Baldrey, D.G.; Hamm, B.; Harris, J.; Sticht, J.; Wimmer, E.

    2003-01-01

    Atomistic modeling methods were employed to investigate the effects of impurity elements on the metallurgy, irradiation embrittlement, and environmentally assisted cracking of nickel-base alloys exposed to nuclear environments. Calculations were performed via ab initio atomistic modeling methods to ensure the accuracy and reliability of the results. A Griffith-type fracture criterion was used to quantitatively assess the effect of elements or element pairs on the grain boundary cohesive strength. In order of most embrittling to most strengthening, the elements are ranked as: He, Li, S, H, C, Zr, P, Fe, Mn, Nb, Cr, and B. Helium is strongly embrittling (-2.04 eV/atom lowering of the Griffith energy), phosphorus has little effect on the grain boundary (0.1 eV/atom), and boron offers appreciable strengthening (1.03 eV/atom increase in the Griffith energy). Calculations for pairs of elements (H-Li, H-B, H-C, H-P, and H-S) show little interaction on the grain boundary cohesive energy, so that for the conditions studied, linear superposition of elemental effects is a good approximation. These calculations help explain metallurgical effects (e.g. why boron can strengthen grain boundaries), irradiation embrittlement (e.g. how boron transmutation results in grain boundary embrittlement), as well as how grain boundary impurity elements can affect environmentally assisted cracking (i.e. low temperature crack propagation and stress corrosion cracking) of nickel-base alloys

  18. Multiscale Simulations Using Particles

    DEFF Research Database (Denmark)

    Walther, Jens Honore

    vortex methods for problems in continuum fluid dynamics, dissipative particle dynamics for flow at the meso scale, and atomistic molecular dynamics simulations of nanofluidic systems. We employ multiscale techniques to breach the atomistic and continuum scales to study fundamental problems in fluid...... dynamics. Recent work on the thermophoretic motion of water nanodroplets confined inside carbon nanotubes, and multiscale techniques for polar liquids will be discussed in detail at the symposium....

  19. Atomistic Properties of Solids

    CERN Document Server

    Sirdeshmukh, Dinker B; Subhadra, K G

    2011-01-01

    The book deals with atomistic properties of solids which are determined by the crystal structure, interatomic forces and atomic displacements influenced by the effects of temperature, stress and electric fields. The book gives equal importance to experimental details and theory. There are full chapters dedicated to the tensor nature of physical properties, mechanical properties, lattice vibrations, crystal structure determination and ferroelectricity. The other crystalline states like nano-, poly-, liquid- and quasi crystals are discussed. Several new topics like nonlinear optics and the Rietveld method are presented in the book. The book lays emphasis on the role of symmetry in crystal properties. Comprehensiveness is the strength of the book; this allows users at different levels a choice of chapters according to their requirements.

  20. Study of the embedded atom method of atomistic calculations for metals and alloys: Progress report, March 1, 1987-February 28, 1988

    International Nuclear Information System (INIS)

    Johnson, R.A.

    1987-11-01

    The relationships between the physical input and output of the Embedded Atom Method (EAM) used in atomistic calculations for metals and alloys and the model functions and parameters are being investigated. An analytic fcc EAM model has been derived based on short range approximations to the input functions in EAM and has been studied both analytically and numerically for the fcc lattice. This model has been extended to longer ranges and applied to both fcc and hcp metals. The correspondence between models based on density functional theory (EAM), tight binding methods, and effective medium theory has been reported. The reasons for difficulty in applying EAM to bcc metals is under study and a new form of alloy potential which retains general properties of pure metal potentials has been developed. 8 refs

  1. Atomistically informed solute drag in Al–Mg

    International Nuclear Information System (INIS)

    Zhang, F; Curtin, W A

    2008-01-01

    Solute drag in solute-strengthened alloys, caused by diffusion of solute atoms around moving dislocations, controls the stress at deformation rates and temperatures useful for plastic forming processes. In the technologically important Al–Mg alloys, the solute drag stresses predicted by classical theories are much larger than experiments, which is resolved in general by eliminating the singularity of the dislocation core via Peierls–Nabarro-type models. Here, the drag stress versus dislocation velocity is computed numerically using a realistic dislocation core structure obtained from an atomistic model to investigate the role of the core and obtain quantitative stresses for comparison with experiment. The model solves a discrete diffusion equation in a reference frame moving with the dislocation, with input solute enthalpies and diffusion activation barriers in the core computed by or estimated from atomistic studies. At low dislocation velocities, the solute drag stress is controlled by bulk solute diffusion because the core diffusion occurs too quickly. In this regime, the drag stress can be obtained using a Peierls–Nabarro model with a core spreading parameter tuned to best match the atomistic models. At intermediate velocities, both bulk and core diffusion can contribute to the drag, leading to a complex stress–velocity relationship showing two peaks in stress. At high velocities, the drag stress is controlled solely by diffusion within and across the core. Like the continuum models, the drag stress is nearly linear in solute concentration. The Orowan relationship is used to connect dislocation velocity to deformation strain rate. Accounting for the dependence of mobile dislocation density on stress, the simulations are in good agreement with experiments on Al–Mg alloys over a range of concentrations and temperatures

  2. Atomistic simulation study of the interaction of organic adsorbates with fluorapatite surfaces

    CSIR Research Space (South Africa)

    Mkhonto, D

    2006-04-01

    Full Text Available MMM 2006 UL Methodology Block I Block II surface •Region I : ions relaxed •Region II : ions kept at bulk equilibrium position } } Metadise program • Static lattice minimisation technique • Forces between species described by potential model... + - + - + - + - + - - + - + - + - + - + + - + - + - + - + - - + - + - + - + - + + - + - + - + - + - - + - + - + - + - + + - + - + - + - + - - + - + - + - + - + + - + - + - + - + - - + - + - + - + - + + - + - + - + - + - - + - + - + - + - + + - + - + - + - + - - + - + - + - + - + Region II Region I Region I Region II interface...

  3. Atomistics of crack propagation

    International Nuclear Information System (INIS)

    Sieradzki, K.; Dienes, G.J.; Paskin, A.; Massoumzadeh, B.

    1988-01-01

    The molecular dynamic technique is used to investigate static and dynamic aspects of crack extension. The material chosen for this study was the 2D triangular solid with atoms interacting via the Johnson potential. The 2D Johnson solid was chosen for this study since a sharp crack in this material remains stable against dislocation emission up to the critical Griffith load. This behavior allows for a meaningful comparison between the simulation results and continuum energy theorems for crack extension by appropriately defining an effective modulus which accounts for sample size effects and the non-linear elastic behavior of the Johnson solid. Simulation results are presented for the stress fields of moving cracks and these dynamic results are discussed in terms of the dynamic crack propagation theories, of Mott, Eshelby, and Freund

  4. Atomistic characterization of pseudoelasticity and shape memory in NiTi nanopillars

    International Nuclear Information System (INIS)

    Zhong Yuan; Gall, Ken; Zhu Ting

    2012-01-01

    Molecular dynamics simulations are performed to study the atomistic mechanisms governing the pseudoelasticity and shape memory in nickel–titanium (NiTi) nanostructures. For a 〈1 1 0〉 – oriented nanopillar subjected to compressive loading–unloading, we observe either a pseudoelastic or shape memory response, depending on the applied strain and temperature that control the reversibility of phase transformation and deformation twinning. We show that irreversible twinning arises owing to the dislocation pinning of twin boundaries, while hierarchically twinned microstructures facilitate the reversible twinning. The nanoscale size effects are manifested as the load serration, stress plateau and large hysteresis loop in stress–strain curves that result from the high stresses required to drive the nucleation-controlled phase transformation and deformation twinning in nanosized volumes. Our results underscore the importance of atomistically resolved modeling for understanding the phase and deformation reversibilities that dictate the pseudoelasticity and shape memory behavior in nanostructured shape memory alloys.

  5. Coupling Strategies Investigation of Hybrid Atomistic-Continuum Method Based on State Variable Coupling

    Directory of Open Access Journals (Sweden)

    Qian Wang

    2017-01-01

    Full Text Available Different configurations of coupling strategies influence greatly the accuracy and convergence of the simulation results in the hybrid atomistic-continuum method. This study aims to quantitatively investigate this effect and offer the guidance on how to choose the proper configuration of coupling strategies in the hybrid atomistic-continuum method. We first propose a hybrid molecular dynamics- (MD- continuum solver in LAMMPS and OpenFOAM that exchanges state variables between the atomistic region and the continuum region and evaluate different configurations of coupling strategies using the sudden start Couette flow, aiming to find the preferable configuration that delivers better accuracy and efficiency. The major findings are as follows: (1 the C→A region plays the most important role in the overlap region and the “4-layer-1” combination achieves the best precision with a fixed width of the overlap region; (2 the data exchanging operation only needs a few sampling points closer to the occasions of interactions and decreasing the coupling exchange operations can reduce the computational load with acceptable errors; (3 the nonperiodic boundary force model with a smoothing parameter of 0.1 and a finer parameter of 20 can not only achieve the minimum disturbance near the MD-continuum interface but also keep the simulation precision.

  6. On the junction physics of Schottky contact of (10, 10) MX{sub 2} (MoS{sub 2}, WS{sub 2}) nanotube and (10, 10) carbon nanotube (CNT): an atomistic study

    Energy Technology Data Exchange (ETDEWEB)

    Sengupta, Amretashis [Hanse-Wissenschaftskolleg (HWK), Delmenhorst (Germany); Universitaet Bremen, Bremen Center for Computational Materials Science (BCCMS), Bremen (Germany)

    2017-04-15

    Armchair nanotubes of MoS{sub 2} and WS{sub 2} offer a sizeable band gap, with the advantage of a one dimensional (1D) electronic material, but free from edge roughness and thermodynamic instability of nanoribbons. Use of such semiconducting MX{sub 2} (MoS{sub 2}, WS{sub 2}) armchair nanotubes (NTs) in conjunction with metallic carbon nanotubes (CNT) can be useful for nanoelectronics and photonics applications. In this work, atomistic simulations of MoS{sub 2} NT-CNT and WS{sub 2} NT-CNT junctions are carried out to study the physics of such junctions. With density functional theory (DFT) we study the carrier density distribution, effective potential, electron difference density, electron localization function, electrostatic difference potential and projected local density of states of such MX{sub 2} NT-CNT 1D junctions. Thereafter the conductance of such a junction under moderate bias is studied with non-equilibrium Green's function (NEGF) method. From the forward bias characteristics simulated from NEGF, we extract diode parameters of the junction. The electrostatic simulations from DFT show the formation of an inhomogeneous Schottky barrier with a tendency towards charge transfer from metal and chalcogen atoms towards the C atoms. For low bias conditions, the ideality factor was calculated to be 1.1322 for MoS{sub 2} NT-CNT junction and 1.2526 for the WS{sub 2} NT-CNT junction. The Schottky barrier heights displayed significant bias dependent modulation and are calculated to be in the range 0.697-0.664 eV for MoS{sub 2} NT-CNT and 0.669-0.610 eV for the WS{sub 2} NT-CNT, respectively. (orig.)

  7. Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations

    Science.gov (United States)

    Prakash, Meher K.; Barducci, Alessandro; Parrinello, Michele

    2010-01-01

    Abstract One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family. PMID:20643078

  8. Addressing uncertainty in atomistic machine learning

    DEFF Research Database (Denmark)

    Peterson, Andrew A.; Christensen, Rune; Khorshidi, Alireza

    2017-01-01

    Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predi......Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility...... of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We...... suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate...

  9. Adsorption and pathways of single atomistic processes on NbN (0 0 1) and (1 1 1) surfaces: A first-principle study

    International Nuclear Information System (INIS)

    Ren, Yuan; Liu, Xuejie; Tan, Xin; Sun, Shiyang; Wei, Huai; Lu, Feng

    2014-01-01

    Highlights: • We investigate the behaviors of Nb, Si, N atom on NbN(0 0 1) and (1 1 1) surfaces. • The adsorption and diffusion of single atom on NbN(0 0 1) and (1 1 1) were calculated by DFT. • The potential energy surface of single atom on NbN(0 0 1) and (1 1 1) surfaces were investigated. • The diffusion process of single on NbN(0 0 1) and (1 1 1) were calculated by nudged elastic band. - Abstract: The adsorption and pathway processes of atomistic Nb, Si, and N at high-symmetry sites on NbN (0 0 1) and (1 1 1) surfaces were studied using first-principle method, which is based on the density functional theory. This investigation presents some of the results obtained. The potential energy surface (PES) was obtained by calculating the adsorption of Nb, Si, and N atoms on NbN (0 0 1). The most energetic site for the Nb atom adsorbed on NbN(0 0 1) was the site ‘on-top of face–center cubic’ (HL), whereas those for N and Si were both at the site ‘between TopN and HL’ (TopN-HL). The minimum energy paths of the single atom on NbN (0 0 1) surface diffusion were obtained using the PES calculation results. The Nb and Si atoms were diffused from the TopN to the HL position. The N atom was diffused from the TopNb, whereas the TopN–HL to HL position. The diffusion energies of the Nb, Si, and N atoms on the NbN (0 0 1) surface were 0.32, 0.69, and 1.32 eV, respectively. The pathways of the atomistic diffusion involved the diffusion of atoms from the FCC to the HCP site on the NbN (1 1 1) surface. The results showed that the diffusion energy of Si on the Nb layer was smaller than that on the N layer. Si and N can easily form stable structures while bonding on the N layer. Moreover, Si atoms can stabilize the activity of N atoms while promoting the spread of Nb atoms during deposition

  10. Structural and functional analysis of glycoprotein butyrylcholinesterase using atomistic molecular dynamics

    Science.gov (United States)

    Bernardi, Austen; Faller, Roland

    Atomistic molecular dynamics (MD) has proven to be a powerful tool for studying the structure and dynamics of biological systems on nanosecond to microsecond time scales and nanometer length scales. In this work we study the effects of modifying the glycan distribution on the structure and function of full length monomeric butyrylcholinesterase (BChE). BChE exists as a monomer, dimer, or tetramer, and is a therapeutic glycoprotein with nine asparagine glycosylation sites per monomer. Each monomer acts as a stoichiometric scavenger for organophosphorus (OP) nerve agents (e.g. sarin, soman). Glycan distributions are highly heterogeneous and have been shown experimentally to affect certain glycoproteins' stability and reactivity. We performed structural analysis of various biologically relevant glycoforms of BChE using classical atomistic MD. Functional analysis was performed through binding energy simulations using umbrella sampling with BChE and OP cofactors. Additionally, we assess the quality of the glycans' conformational sampling. We found that the glycan distribution has a significant effect on the structure and function of BChE on timescales available to atomistic MD. This project is funded by the DTRA Grant HDTRA1-15-1-0054.

  11. Study of the embedded atom method of atomistic calculations for metals and alloys. Final report, March 1, 1986--February 29, 1992

    International Nuclear Information System (INIS)

    Johnson, R.A.

    1992-04-01

    Solids have been studied by atomistic modeling since the earliest availability of computers for scientific research. By the mid sixties, it was understood that models for metals based on reasonably short ranged two-body forces coupled with a global volume dependent contribution to the crystal energy yielded surprisingly good results for bulk calculations, but were unsatisfactory at surfaces. Little progress was made until the early eighties, when Daw and Baskes developed the Embedded-Atom Method (EAM) based on density functional theory and intended primarily for tight-packed transitional metals, and Finnis and Sinclair developed a model based on tight binding theory and intended primarily for bcc transition metals. The underlying mathematical format of both approaches is the same, and provides an extension of the earlier models through a function which in practice provides a measure of local volume dependence. The primary purpose of this research project was to investigate the implications of this mathematical format and to use the resulting insight to correlate the known physical input data with computed results of properties that are difficult to access experimentally. Embedded-Atom Method terminology is used, but this research is applicable as well to the Finnis-Sinclair model

  12. Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal

    International Nuclear Information System (INIS)

    Huang, Liangliang; Gubbins, Keith E.; Seredych, Mykola; Bandosz, Teresa J.; Duin, Adri C. T. van; Lu, Xiaohua

    2013-01-01

    The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H 2 S and H 2 O/H 2 S mixtures on GO materials and compare the results with experiment. We find that H 2 S molecules dissociate on the carbonyl functional groups, and H 2 O, CO 2 , and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H 2 O/H 2 S mixtures, H 2 O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H 2 S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials

  13. Physically representative atomistic modeling of atomic-scale friction

    Science.gov (United States)

    Dong, Yalin

    Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the

  14. In Silico Affinity Profiling of Neuroactive Polyphenols for Post-Traumatic Calpain Inactivation: A Molecular Docking and Atomistic Simulation Sensitivity Analysis

    Directory of Open Access Journals (Sweden)

    Pradeep Kumar

    2014-12-01

    Full Text Available Calcium-activated nonlysosomal neutral proteases, calpains, are believed to be early mediators of neuronal damage associated with neuron death and axonal degeneration after traumatic neural injuries. In this study, a library of biologically active small molecular weight calpain inhibitors was used for model validation and inhibition site recognition. Subsequently, two natural neuroactive polyphenols, curcumin and quercetin, were tested for their sensitivity and activity towards calpain’s proteolytic sequence and compared with the known calpain inhibitors via detailed molecular mechanics (MM, molecular dynamics (MD, and docking simulations. The MM and MD energy profiles (SJA6017 < AK275 < AK295 < PD151746 < quercetin < leupeptin < PD150606 < curcumin < ALLN < ALLM < MDL-28170 < calpeptin and the docking analysis (AK275 < AK295 < PD151746 < ALLN < PD150606 < curcumin < leupeptin < quercetin < calpeptin < SJA6017 < MDL-28170 < ALLM demonstrated that polyphenols conferred comparable calpain inhibition profiling. The modeling paradigm used in this study provides the first detailed account of corroboration of enzyme inhibition efficacy of calpain inhibitors and the respective calpain–calpain inhibitor molecular complexes’ energetic landscape and in addition stimulates the polyphenol bioactive paradigm for post-SCI intervention with implications reaching to experimental in vitro, in cyto, and in vivo studies.

  15. Contribution to the study of mechanical properties of nuclear fuel: atomistic modelling of the deformation of uranium dioxide

    International Nuclear Information System (INIS)

    Fossati, P.

    2012-01-01

    Mechanical properties of nuclear fuel are a complex problem, involving many coupled mechanisms occurring at different length scales. We used Molecular Dynamics models to bring some light on some of these mechanisms at the atomic scale. We devised a procedure to calculate transition pathways between some UO 2 polymorphs, and then carried out dynamics simulations of these transitions. We confirmed the stability of the cotunnite structure at high pressure using various empirical potentials, the fluorite structure being the most stable at room pressure. Moreover, we showed a reconstructive phase transition between the fluorite and cotunnite structures. We also showed the importance of the major deformation axis on the kind of transition that occur under tensile conditions. Depending on the loading direction, a scrutinyite or rutile phase can appear. We then calculated the elastic behaviour of UO 2 using different potentials. The relative agreement between them was used to produce a set of parameters to be used as input in mesoscale models. We also simulated crack propagation in UO 2 single crystals. These simulations showed secondary phases nucleation at crack tips, and hinted at the importance thereof on crack propagation at higher length-scales. We then described some properties of edge dislocations in UO 2 . The core structures were compared for various glide planes. The critical resolved shear stress was calculated for temperatures up to 2000 K. These calculations showed a link between lattice disorder at the dislocations core and the dislocations mobility. (author)

  16. Atomistic modeling of carbon Cottrell atmospheres in bcc iron

    Science.gov (United States)

    Veiga, R. G. A.; Perez, M.; Becquart, C. S.; Domain, C.

    2013-01-01

    Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

  17. Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential

    International Nuclear Information System (INIS)

    Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V; Carloni, Paolo

    2006-01-01

    Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases

  18. Molecular modeling and simulation of atactic polystyrene/amorphous silica nanocomposites

    International Nuclear Information System (INIS)

    Mathioudakis, I; Vogiatzis, G G; Tzoumanekas, C; Theodorou, D N

    2016-01-01

    The local structure, segmental dynamics, topological analysis of entanglement networks and mechanical properties of atactic polystyrene - amorphous silica nanocomposites are studied via molecular simulations using two interconnected levels of representation: (a) A coarse - grained level. Equilibration at all length scales at this level is achieved via connectivity - altering Monte Carlo simulations. (b) An atomistic level. Initial configurations for atomistic Molecular Dynamics (MD) simulations are obtained by reverse mapping well- equilibrated coarse-grained configurations. By analyzing atomistic MD trajectories, the polymer density profile is found to exhibit layering in the vicinity of the nanoparticle surface. The dynamics of polystyrene (in neat and filled melt systems) is characterized in terms of bond orientation. Well-equilibrated coarse-grained long-chain configurations are reduced to entanglement networks via topological analysis with the CReTA algorithm. Atomistic simulation results for the mechanical properties are compared to the experimental measurements and other computational works. (paper)

  19. Atomistic simulation of femtosecond laser pulse interactions with a copper film: Effect of dependency of penetration depth and reflectivity on electron temperature

    Science.gov (United States)

    Amouye Foumani, A.; Niknam, A. R.

    2018-01-01

    The response of copper films to irradiation with laser pulses of fluences in the range of 100-6000 J/m2 is simulated by using a modified combination of a two-temperature model (TTM) and molecular dynamics (MD). In this model, the dependency of the pulse penetration depth and the reflectivity of the target on electron temperature are taken into account. Also, the temperature-dependent electron-phonon coupling factor, electron thermal conductivity, and electron heat capacity are used in the simulations. Based on this model, the dependence of the integral reflectivity on pulse fluence, the changes in the film thickness, and the evolution of density and electron and lattice temperatures are obtained. Moreover, snapshots that show the melting and disintegration processes are presented. The disintegration starts at a fluence of 4200 J/m2, which corresponds with an absorbed fluence of 616 J/m2. The calculated values of integral reflectivity are in good agreement with the experimental data. The inclusion of such temperature-dependent absorption models in the TTM-MD method would facilitate the comparison of experimental data with simulation results.

  20. First Principles Based Reactive Atomistic Simulations to Understand the Effects of Molecular Hypervelocity Impact on Cassini's Ion and Neutral Mass Spectrometer

    Science.gov (United States)

    Jaramillo-Botero, A.; Cheng, M-J; Cvicek, V.; Beegle, Luther W.; Hodyss, R.; Goddard, W. A., III

    2011-01-01

    We report here on the predicted impact of species such as ice-water, CO2, CH4, and NH3, on oxidized titanium, as well as HC species on diamond surfaces. These simulations provide the dynamics of product distributions during and after a hypervelocity impact event, ionization fractions, and dissociation probabilities for the various species of interest as a function of impact velocity (energy). We are using these results to determine the relevance of the fragmentation process to Cassini INMS results, and to quantify its effects on the observed spectra.

  1. Understanding the effects of alpha self-irradiation on the glass structure by coupling spectroscopic studies and atomistic modeling

    International Nuclear Information System (INIS)

    Bureau, G.

    2008-12-01

    Our objective was to assess irradiation effects on nuclear containment glass in order to guarantee glass performance when subjected to high alpha decay doses. Experimental studies and molecular dynamics modeling provided a better understanding of the impact of cumulative alpha decay on the structural behavior of complex nuclear glass formulations and of simplified glass models. A mechanism typical of sodium borosilicate glass was identified in response to nuclear interactions or ballistic collisions. The glass local order is slightly modified by the conversion of a fraction of the boron atoms from coordination number IV to III, releasing charge-compensating alkali ions that become available as network modifiers, and resulting in a slight increase in the number of non bridging oxygen atoms. The medium-range order shifts toward increasing disorder in the glass as indicated by broadening of the angular, radial, and size distributions. A model of accumulated quasi-thermal quenching is proposed to account for these changes, based on the two steps describing the reaction of the glass to the alpha decay recoil nucleus: a cascade generates a ballistic phase that completely destabilizes the glass structure with no short and medium-range order, resulting in the loss of the initial structure; glass reconstruction is controlled only by the 'quenching rate' in the displacement cascade, i.e. by its thermal history and the corresponding relaxation options. From this standpoint the final glass structure is the consequence of the ballistic changes and the regenerative capacity of the glass structure, resulting in a higher fictive-temperature glass corresponding to the structural changes identified in this study. (author)

  2. Chlorine Evolution Reaction on RuO2(110): Ab initio Atomistic Thermodynamics Study - Pourbaix Diagrams

    International Nuclear Information System (INIS)

    Exner, Kai S.; Anton, Josef; Jacob, Timo; Over, Herbert

    2014-01-01

    Graphical abstract: - Highlights: • Using the method Pourbaix diagram we identified the oxygen covered RuO 2 (110) surface as the catalytically active phase under chlorine evolution reaction (CER) conditions. This active phase is compared with the active phase in the Deacon process, the heterogeneous gas phase counterpart of the CER. - Abstract: Constrained ab initio thermodynamics in the form of a Pourbaix diagram can greatly assist kinetic modeling of a particular electrochemical reaction such as the chlorine evolution reaction (CER) over RuO 2 (110). Pourbaix diagrams reveal stable surface structures, as a function of pH and the potential. The present DFT study indicates that the Pourbaix diagram in the CER potential region above 1.36 V and pH values around zero is dominated by a stable surface structure in which all coordinatively undercoordinated Ru sites (Ru cus ) are capped by on-top oxygen (O ot ). This oxygen saturated RuO 2 (110) surface is considered to serve as the catalytically active phase in the CER, quite in contrast to the heterogeneously catalyzed HCl oxidation (Deacon process), for which the active RuO 2 (110) surface is mainly covered by on-top chlorine. The active sites in the CER are suggested to be Ru cus O ot surface complexes, while in the Deacon process both undercoordinated surface Ru and oxygen sites must be available for the activation of HCl molecules

  3. Simulation of ablation and plume dynamics under femtosecond double-pulse laser irradiation of aluminum: Comparison of atomistic and continual approaches

    Energy Technology Data Exchange (ETDEWEB)

    Fokin, Vladimir B.; Povarnitsyn, Mikhail E., E-mail: povar@ihed.ras; Levashov, Pavel R.

    2017-02-28

    Highlights: • We model double-pulse laser ablation of aluminum using microscopic and macroscopic approaches. • Both methods show decrease in depth of crater with increasing delay between pulses. • Both methods reveal the plume temperature growth with the increasing delay. • Good agreement between results is a step towards the development of combined model. - Abstract: We elaborated two numerical methods, two-temperature hydrodynamics and hybrid two-temperature molecular dynamics, which take into account basic mechanisms of a metal target response to ultrashort laser irradiation. The model used for the description of the electronic subsystem is identical for both approaches, while the ionic part is defined by an equation of state in hydrodynamics and by an interatomic potential in molecular dynamics. Since the phase diagram of the equation of state and corresponding potential match reasonably well, the dynamics of laser ablation obtained by both methods is quite similar. This correspondence can be considered as a first step towards the development of a self-consistent combined model. Two important processes are highlighted in simulations of double-pulse ablation: (1) the crater depth decrease as a result of recoil flux formation in the nascent plume when the delay between the pulses increases; (2) the plume reheating by the second pulse that gives rise to two- three-fold growth of the electron temperature with the delay varying from 0 to 200 ps.

  4. An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Matthew W. Thompson

    2017-10-01

    Full Text Available We report a novel atomistic model of carbide-derived carbons (CDCs, which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors.

  5. Finite element analysis of an atomistically derived cohesive model for brittle fracture

    International Nuclear Information System (INIS)

    Lloyd, J T; McDowell, D L; Zimmerman, J A; Jones, R E; Zhou, X W

    2011-01-01

    In order to apply information from molecular dynamics (MD) simulations in problems governed by engineering length and time scales, a coarse graining methodology must be used. In previous work by Zhou et al (2009 Acta Mater. 57 4671–86), a traction-separation cohesive model was developed using results from MD simulations with atomistic-to-continuum measures of stress and displacement. Here, we implement this cohesive model within a combined finite element/cohesive surface element framework (referred to as a finite element approach or FEA), and examine the ability for the atomistically informed FEA to directly reproduce results from MD. We find that FEA shows close agreement of both stress and crack opening displacement profiles at the cohesive interface, although some differences do exist that can be attributed to the stochastic nature of finite temperature MD. The FEA methodology is then used to study slower loading rates that are computationally expensive for MD. We find that the crack growth process initially exhibits a rate-independent relationship between crack length and boundary displacement, followed by a rate-dependent regime where, at a given amount of boundary displacement, a lower applied strain rate produces a longer crack length. Our method is also extended to larger length scales by simulating a compact tension fracture-mechanics specimen with sub-micrometer dimensions. Such a simulation shows a computational speedup of approximately four orders of magnitude over conventional atomistic simulation, while exhibiting the expected fracture-mechanics response. Finally, differences between FEA and MD are explored with respect to ensemble and temperature effects in MD, and their impact on the cohesive model and crack growth behavior. These results enable us to make several recommendations to improve the methodology used to derive cohesive laws from MD simulations. In light of this work, which has critical implications for efforts to derive continuum laws

  6. Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design

    International Nuclear Information System (INIS)

    Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

    2010-01-01

    This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and

  7. Simulation of atomistic processes during silicon oxidation

    OpenAIRE

    Bongiorno, Angelo

    2003-01-01

    Silicon dioxide (SiO2) films grown on silicon monocrystal (Si) substrates form the gate oxides in current Si-based microelectronics devices. The understanding at the atomic scale of both the silicon oxidation process and the properties of the Si(100)-SiO2 interface is of significant importance in state-of-the-art silicon microelectronics manufacturing. These two topics are intimately coupled and are both addressed in this theoretical investigation mainly through first-principles calculations....

  8. AACSD: An atomistic analyzer for crystal structure and defects

    Science.gov (United States)

    Liu, Z. R.; Zhang, R. F.

    2018-01-01

    We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

  9. Compression deformation of WC: atomistic description of hard ceramic material

    Science.gov (United States)

    Feng, Qing; Song, Xiaoyan; Liu, Xuemei; Liang, Shuhua; Wang, Haibin; Nie, Zuoren

    2017-11-01

    The deformation characteristics of WC, as a typical hard ceramic material, were studied on the nanoscale using atomistic simulations for both the single-crystal and polycrystalline forms under uniaxial compression. In particular, the effects of crystallographic orientation, grain boundary coordination and grain size on the origin of deformation were investigated. The deformation behavior of the single-crystal and polycrystalline WC both depend strongly on the orientation towards the loading direction. The grain boundaries play a significant role in the deformation coordination and the potential high fracture toughness of the nanocrystalline WC. In contrast to conventional knowledge of ceramics, maximum strength was obtained at a critical grain size corresponding to the turning point from a Hall-Petch to an inverse Hall-Petch relationship. For this the mechanism of the combined effect of dislocation motion within grains and the coordination of stress concentration at the grain boundaries were proposed. The present work has moved forward our understanding of plastic deformability and the possibility of achieving a high strength of nanocrystalline ceramic materials.

  10. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

    Science.gov (United States)

    Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

    2016-12-01

    The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

  11. Atomistic k ⋅ p theory

    Energy Technology Data Exchange (ETDEWEB)

    Pryor, Craig E., E-mail: craig-pryor@uiowa.edu [Department of Physics and Astronomy, University of Iowa, Iowa City, Iowa 52242 (United States); Pistol, M.-E., E-mail: mats-erik.pistol@ftf.lth.se [NanoLund and Solid State Physics, Lund University, P.O. Box 118, 221 00 Lund (Sweden)

    2015-12-14

    Pseudopotentials, tight-binding models, and k ⋅ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ⋅ p theory. In its usual formulation, k ⋅ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ⋅ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp{sup 3} tight-binding model. We can thus directly derive the parameters in the sp{sup 3} tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III–V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ⋅ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ⋅ p models to be combined in the same system.

  12. Atomistic approach for modeling metal-semiconductor interfaces

    DEFF Research Database (Denmark)

    Stradi, Daniele; Martinez, Umberto; Blom, Anders

    2016-01-01

    realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via the I–V curve. In particular, it will be demonstrated how doping — and bias — modifies the Schottky barrier, and how finite size models (the slab approach) are unable to describe these interfaces......We present a general framework for simulating interfaces using an atomistic approach based on density functional theory and non-equilibrium Green's functions. The method includes all the relevant ingredients, such as doping and an accurate value of the semiconductor band gap, required to model...

  13. Self-evolving atomistic kinetic Monte Carlo: fundamentals and applications

    International Nuclear Information System (INIS)

    Xu Haixuan; Osetsky, Yuri N; Stoller, Roger E

    2012-01-01

    The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed and applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.

  14. Conducting Simulation Studies in Psychometrics

    Science.gov (United States)

    Feinberg, Richard A.; Rubright, Jonathan D.

    2016-01-01

    Simulation studies are fundamental to psychometric discourse and play a crucial role in operational and academic research. Yet, resources for psychometricians interested in conducting simulations are scarce. This Instructional Topics in Educational Measurement Series (ITEMS) module is meant to address this deficiency by providing a comprehensive…

  15. Simulation in International Studies

    Science.gov (United States)

    Boyer, Mark A.

    2011-01-01

    Social scientists have long worked to replicate real-world phenomena in their research and teaching environments. Unlike our biophysical science colleagues, we are faced with an area of study that is not governed by the laws of physics and other more predictable relationships. As a result, social scientists, and international studies scholars more…

  16. Crystalline cellulose elastic modulus predicted by atomistic models of uniform deformation and nanoscale indentation

    Science.gov (United States)

    Xiawa Wu; Robert J. Moon; Ashlie Martini

    2013-01-01

    The elastic modulus of cellulose Iß in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive...

  17. Atomistically-informed dislocation dynamics in FCC crystals

    International Nuclear Information System (INIS)

    Martinez, E.; Marian, J.; Arsenlis, A.; Victoria, M.; Martinez, E.; Victoria, M.; Perlado, J.M.

    2008-01-01

    Full text of publication follows. We will present a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions, and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our fundings to the plastic behaviour of' monocrystalline fcc metals. (authors)

  18. Modelling phase separation in Fe-Cr system using different atomistic kinetic Monte Carlo techniques

    International Nuclear Information System (INIS)

    Castin, N.; Bonny, G.; Terentyev, D.; Lavrentiev, M.Yu.; Nguyen-Manh, D.

    2011-01-01

    Atomistic kinetic Monte Carlo (AKMC) simulations were performed to study α-α' phase separation in Fe-Cr alloys. Two different energy models and two approaches to estimate the local vacancy migration barriers were used. The energy models considered are a two-band model Fe-Cr potential and a cluster expansion, both fitted to ab initio data. The classical Kang-Weinberg decomposition, based on the total energy change of the system, and an Artificial Neural Network (ANN), employed as a regression tool were used to predict the local vacancy migration barriers 'on the fly'. The results are compared with experimental thermal annealing data and differences between the applied AKMC approaches are discussed. The ability of the ANN regression method to accurately predict migration barriers not present in the training list is also addressed by performing cross-check calculations using the nudged elastic band method.

  19. Atomistic modeling of L10 FePt: path to HAMR 5Tb/in2

    Science.gov (United States)

    Chen, Tianran; Benakli, Mourad; Rea, Chris

    2015-03-01

    Heat assisted magnetic recording (HAMR) is a promising approach for increasing the storage density of hard disk drives. To increase data density, information must be written in small grains, which requires materials with high anisotropy energy such as L10 FePt. On the other hand, high anisotropy implies high coercivity, making it difficult to write the data with existing recording heads. This issue can be overcome by the technique of HAMR, where a laser is used to heat the recording medium to reduce its coercivity while retaining good thermal stability at room temperature due to the large anisotropy energy. One of the keys to the success of HAMR is the precise control of writing process. In this talk, I will propose a Monte Carlo simulation, based on an atomistic model, that would allow us to study the magnetic properties of L10 FePt and dynamics of spin reversal for the writing process in HAMR.

  20. Robust mode space approach for atomistic modeling of realistically large nanowire transistors

    Science.gov (United States)

    Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

    2018-01-01

    Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.

  1. Temperature dependence of creep compliance of highly cross-linked epoxy: A molecular simulation study

    International Nuclear Information System (INIS)

    Khabaz, Fardin; Khare, Ketan S.; Khare, Rajesh

    2014-01-01

    We have used molecular dynamics (MD) simulations to study the effect of temperature on the creep compliance of neat cross-linked epoxy. Experimental studies of mechanical behavior of cross-linked epoxy in literature commonly report creep compliance values, whereas molecular simulations of these systems have primarily focused on the Young’s modulus. In this work, in order to obtain a more direct comparison between experiments and simulations, atomistically detailed models of the cross-linked epoxy are used to study their creep compliance as a function of temperature using MD simulations. The creep tests are performed by applying a constant tensile stress and monitoring the resulting strain in the system. Our results show that simulated values of creep compliance increase with an increase in both time and temperature. We believe that such calculations of the creep compliance, along with the use of time temperature superposition, hold great promise in connecting the molecular insight obtained from molecular simulation at small length- and time-scales with the experimental behavior of such materials. To the best of our knowledge, this work is the first reported effort that investigates the creep compliance behavior of cross-linked epoxy using MD simulations

  2. Modelling of radiation induced segregation in austenitic Fe alloys at the atomistic level

    International Nuclear Information System (INIS)

    Piochaud, Jean-Baptiste

    2013-01-01

    In pressurized water reactors, under irradiation internal structures are subject of irradiation assisted stress corrosion cracking which is influenced by radiation induced segregation (RIS). In this work RIS of 316 stainless steels is modelled considering a model ternary Fe-10Ni-20Cr alloy. For this purpose we have built an Fe-Ni-Cr pair interaction model to simulate RIS at the atomistic level using an atomistic kinetic Monte Carlo approach. The pair interactions have been deduced from density functional theory (DFT) data available in the pure fcc systems but also from DFT calculations we have performed in the Fe-10Ni-20Cr target alloy. Point defect formation energies were calculated and found to depend strongly on the local environment of the defect. As a consequence, a rather good estimation of these energies can be obtained from the knowledge of the number and respective positions of the Ni and Cr atoms in the vicinity of the defect. This work shows that a model based only on interaction parameters between elements positioned in perfect lattice sites (solute atoms and vacancy) cannot capture alone both the thermodynamic and the kinetic aspect of RIS. A more accurate of estimating the barriers encountered by the diffusing species is required than the one used in our model, which has to depend on the saddle point environment. This study therefore shows thus the need to estimate point defect migration energies using the DFT approach to calibrate a model that can be used in the framework of atomic kinetic Monte Carlo simulations. We also found that the reproduction by our pair interaction model of DFT data for the self-interstitial atoms was found to be incompatible with the modelling of RIS under electron irradiation. (author)

  3. Atomistic approach to predict the glass-forming ability in Zr–Cu–Al ternary metallic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Yu, C.Y. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, X.J. [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Zheng, G.P. [Department of Mechanical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong (China); Niu, X.R. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, C.T., E-mail: chainliu@cityu.edu.hk [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China)

    2015-04-05

    Highlights: • An atomistic approach has been developed to predict the glass forming ability (GFA) in Zr–Cu–Al ternary alloy system. • Both of the thermodynamic and structure-dependent kinetic effects to glass formation have been taken into account. • The first-principles calculation and molecular dynamics simulation have been performed. • The approach predicts the best glass former in the model Zr–Cu–Al alloy system. • The predicted GFA is consistent with various experimental results. - Abstract: Prediction of composition-dependent glass-forming ability (GFA) remains to be a key scientific challenge in the metallic-glass community, especially in multi-component alloy systems. In the present study, we apply an atomistic approach to predict the trend of GFA effectively in the Zr–Cu–Al ternary alloy system from alloy compositions alone. This approach is derived from the first-principles calculations based on the density-functional theory and molecular dynamic (MD) simulations. By considering of both the thermodynamic and atomic-structure induced kinetic effects, the predicted GFA trend from this approach shows an excellent agreement with experimental data available in this alloy system, manifesting its capability of seeking metallic glasses with superior GFA in ternary alloy systems.

  4. Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

    Science.gov (United States)

    Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

    2017-01-01

    We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

  5. Investigation of the removing process of cathode material in micro-EDM using an atomistic-continuum model

    International Nuclear Information System (INIS)

    Guo, Jianwen; Zhang, Guojun; Huang, Yu; Ming, Wuyi; Liu, Min; Huang, Hao

    2014-01-01

    Highlights: • An atomistic-continuum computational simulation model for single-discharge micro-EDM process of Cu cathode is constructed. • Cathode material is removed mainly in the form of single atoms or small clusters in micro-EDM. • Electric action leads to the formation of peaks on the surface of crater. • Removing process of cathode material under the hybrid action combining the thermal action and the electric action is studied, and the strength of either action needed for material to remove is much reduced. - Abstract: In micro-electrical discharge machining (micro-EDM), the discharge duration is ultra-short, and both the electric action and the thermal action by the discharge channel play important roles in the removing process of cathode material. However, in most researches on the machining mechanism of micro-EDM, only the thermal action is concerned. In this article, a combined atomistic-continuum modeling method in which the two-temperature model and the molecular dynamics simulation model are integrated is used to construct the simulation model for cathode in single-discharge micro-EDM process. With this simulation model, removing processes of Cu cathode material in micro-EDM under pure thermal action, pure electric action and the combination of them are investigated in a simulative way. By analyzing evolutions of temperature, stress and micro-structure of material as well as the dynamical behaviors of material in the removing process, mechanisms of the cathode material removal and crater formation are revealed. In addition, the removing process of cathode material under the combination of pure thermal action and pure electric action is compared with those under the two pure actions respectively to analyze the interactive effect between the thermal action and the electric action

  6. Atomistic and holistic understanding in physics

    International Nuclear Information System (INIS)

    Bohm, A.

    1992-01-01

    Understanding means always reduction to the simpler. In the atomistic understanding the reduction is to the simpler objects. One asks the question: what does it consist of? For instance, one asks: What does the molecule consist of? and the answer is: The molecule consists of electrons and nuclei. Or: what does the nucleus consist of? And the answer is: The nucleus consists of protons and neutrons. The parts in the atomistic understanding are the constituents. In the holistic understanding, the reduction is to the simpler functions, the simpler motions. One asks the question: What does it do? What does the molecule do? What does the nucleus do? And the answer is: The molecule rotates and oscillates. The nucleus rotates and oscillates

  7. Single asperity nanocontacts: Comparison between molecular dynamics simulations and continuum mechanics models

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    Abstract Using classical molecular dynamics, atomic scale simulations of normal contact between a nominally flat substrate and different atomistic and non-atomistic spherical particles were performed to investigate the applicability of classical contact theories at the nanoscale, and further

  8. Atomistic modeling of BN nanofillers for mechanical and thermal properties: a review.

    Science.gov (United States)

    Kumar, Rajesh; Parashar, Avinash

    2016-01-07

    Due to their exceptional mechanical properties, thermal conductivity and a wide band gap (5-6 eV), boron nitride nanotubes and nanosheets have promising applications in the field of engineering and biomedical science. Accurate modeling of failure or fracture in a nanomaterial inherently involves coupling of atomic domains of cracks and voids as well as a deformation mechanism originating from grain boundaries. This review highlights the recent progress made in the atomistic modeling of boron nitride nanofillers. Continuous improvements in computational power have made it possible to study the structural properties of these nanofillers at the atomistic scale.

  9. Atomistic insights into the nanosecond long amorphization and crystallization cycle of nanoscale G e2S b2T e5 : An ab initio molecular dynamics study

    Science.gov (United States)

    Branicio, Paulo S.; Bai, Kewu; Ramanarayan, H.; Wu, David T.; Sullivan, Michael B.; Srolovitz, David J.

    2018-04-01

    The complete process of amorphization and crystallization of the phase-change material G e2S b2T e5 is investigated using nanosecond ab initio molecular dynamics simulations. Varying the quench rate during the amorphization phase of the cycle results in the generation of a variety of structures from entirely crystallized (-0.45 K/ps) to entirely amorphized (-16 K/ps). The 1.5-ns annealing simulations indicate that the crystallization process depends strongly on both the annealing temperature and the initial amorphous structure. The presence of crystal precursors (square rings) in the amorphous matrix enhances nucleation/crystallization kinetics. The simulation data are used to construct a combined continuous-cooling-transformation (CCT) and temperature-time-transformation (TTT) diagram. The nose of the CCT-TTT diagram corresponds to the minimum time for the onset of homogenous crystallization and is located at 600 K and 70 ps. That corresponds to a critical cooling rate for amorphization of -4.5 K/ps. The results, in excellent agreement with experimental observations, suggest that a strategy that utilizes multiple quench rates and annealing temperatures may be used to effectively optimize the reversible switching speed and enable fast and energy-efficient phase-change memories.

  10. Theoretical modeling of zircon's crystal morphology according to data of atomistic calculations

    Science.gov (United States)

    Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

    2017-04-01

    Zircon is an essential mineral that is used in the U-Pb dating. Moreover, zircon is highly resistant to radioactive exposure. It is of great interest in solving both fundamental and applied problems associated with the isolation of high-level radioactive waste. There is significant progress in forecasting of the most energetically favorable crystal structures at the present time. Unfortunately, the theoretical forecast of crystal morphology at high technological level is under-explored nowadays, though the estimation of crystal equilibrium habit is extremely important in studying the physical and chemical properties of new materials. For the first time, the thesis about relation of the equilibrium shape of a crystal with its crystal structure was put forward in the works by O.Brave. According to it, the idealized habit is determined in the simplest case by a correspondence with the reticular densities Rhkl of individual faces. This approach, along with all subsequent corrections, does not take into account the nature of atoms and the specific features of the chemical bond in crystals. The atomistic calculations of crystal surfaces are commonly performed using the energetic characteristics of faces, namely, the surface energy (Esurf), which is a measure of the thermodynamic stability of the crystal face. The stable crystal faces are characterized by small positive values of Esurf. As we know from our previous research (Gromalova et al.,2015) one of the constitutive factors affecting the value of the surface energy in calculations is a choice of potentials model. In this regard, we studied several sets of parameters of atomistic interatomic potentials optimized previously. As the first test model («Zircon 1») were used sets of interatomic potentials of interaction Zr-O, Si-O and O-O in the form of Buckingham potentials. To improve playback properties of zircon additionally used Morse potential for a couple of Zr-Si, as well as the three-particle angular harmonic

  11. Atomistic modeling of nanowires, small-scale fatigue damage in cast magnesium, and materials for MEMS

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Martin L. [Univ. of Colorado, Boulder, CO (United States); Talmage, Mellisa J. [Univ. of Colorado, Boulder, CO (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); West, Neil [Univ. of Colorado, Boulder, CO (United States); Gullett, Philip Michael [Mississippi State Univ., Mississippi State, MS (United States); Miller, David C. [Univ. of Colorado, Boulder, CO (United States); Spark, Kevin [Univ. of Colorado, Boulder, CO (United States); Diao, Jiankuai [Univ. of Colorado, Boulder, CO (United States); Horstemeyer, Mark F. [Mississippi State Univ., Mississippi State, MS (United States); Zimmerman, Jonathan A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gall, K. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2006-10-01

    Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project

  12. Chernobyl reactor transient simulation study

    International Nuclear Information System (INIS)

    Gaber, F.A.; El Messiry, A.M.

    1988-01-01

    This paper deals with the Chernobyl nuclear power station transient simulation study. The Chernobyl (RBMK) reactor is a graphite moderated pressure tube type reactor. It is cooled by circulating light water that boils in the upper parts of vertical pressure tubes to produce steam. At equilibrium fuel irradiation, the RBMK reactor has a positive void reactivity coefficient. However, the fuel temperature coefficient is negative and the net effect of a power change depends upon the power level. Under normal operating conditions the net effect (power coefficient) is negative at full power and becomes positive under certain transient conditions. A series of dynamic performance transient analysis for RBMK reactor, pressurized water reactor (PWR) and fast breeder reactor (FBR) have been performed using digital simulator codes, the purpose of this transient study is to show that an accident of Chernobyl's severity does not occur in PWR or FBR nuclear power reactors. This appears from the study of the inherent, stability of RBMK, PWR and FBR under certain transient conditions. This inherent stability is related to the effect of the feed back reactivity. The power distribution stability in the graphite RBMK reactor is difficult to maintain throughout its entire life, so the reactor has an inherent instability. PWR has larger negative temperature coefficient of reactivity, therefore, the PWR by itself has a large amount of natural stability, so PWR is inherently safe. FBR has positive sodium expansion coefficient, therefore it has insufficient stability it has been concluded that PWR has safe operation than FBR and RBMK reactors

  13. Atomistic calculation of size effects on elastic coefficients in nanometre-sized tungsten layers and wires

    International Nuclear Information System (INIS)

    Villain, P.; Beauchamp, P.; Badawi, K.F.; Goudeau, P.; Renault, P.-O.

    2004-01-01

    Equilibrium state and elastic coefficients of nanometre-sized single crystal tungsten layers and wires are investigated by atomistic simulations. The variations of the equilibrium distances as a function of the layer thickness or wire cross-section are mainly due to elastic effects of surface tension forces. A strong decrease of the Young's modulus is observed when the transverse dimensions are reduced below 2-3 nm

  14. Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.

    Directory of Open Access Journals (Sweden)

    Yunqiang Bian

    2014-04-01

    Full Text Available In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and K(+ ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes.

  15. Atomistic minimal model for estimating profile of electrodeposited nanopatterns

    Science.gov (United States)

    Asgharpour Hassankiadeh, Somayeh; Sadeghi, Ali

    2018-06-01

    We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip.

  16. Experimentally driven atomistic model of 1,2 polybutadiene

    Energy Technology Data Exchange (ETDEWEB)

    Gkourmpis, Thomas, E-mail: thomas.gkourmpis@borealisgroup.com [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Mitchell, Geoffrey R. [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Centre for Rapid and Sustainable Product Development, Institute Polytechnic Leiria, Marinha Grande (Portugal)

    2014-02-07

    We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

  17. Atomistic Galois insertions for flow sensitive integrity

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis

    2017-01-01

    Several program verification techniques assist in showing that software adheres to the required security policies. Such policies may be sensitive to the flow of execution and the verification may be supported by combinations of type systems and Hoare logics. However, this requires user assistance...... and to obtain full automation we shall explore the over-approximating nature of static analysis. We demonstrate that the use of atomistic Galois insertions constitutes a stable framework in which to obtain sound and fully automatic enforcement of flow sensitive integrity. The framework is illustrated...

  18. A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

    Science.gov (United States)

    Suzuki, Yuichi; Nagaoka, Masataka

    2017-05-28

    Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

  19. Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

    Science.gov (United States)

    Hong, Bingbing

    Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic

  20. Irradiation-induced void evolution in iron: A phase-field approach with atomistic derived parameters

    International Nuclear Information System (INIS)

    Wang Yuan-Yuan; Ding Jian-Hua; Huang Shao-Song; Zhao Ji-Jun; Liu Wen-Bo; Ke Xiao-Qin; Wang Yun-Zhi; Zhang Chi

    2017-01-01

    A series of material parameters are derived from atomistic simulations and implemented into a phase field (PF) model to simulate void evolution in body-centered cubic (bcc) iron subjected to different irradiation doses at different temperatures. The simulation results show good agreement with experimental observations — the porosity as a function of temperature varies in a bell-shaped manner and the void density monotonically decreases with increasing temperatures; both porosity and void density increase with increasing irradiation dose at the same temperature. Analysis reveals that the evolution of void number and size is determined by the interplay among the production, diffusion and recombination of vacancy and interstitial. (paper)

  1. Atomistic modelling of diffusional phase transformations with elastic strain

    International Nuclear Information System (INIS)

    Mason, D R; Rudd, R E; Sutton, A P

    2004-01-01

    Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Atomic interactions are modelled by Finnis-Sinclair potentials constructed for these simulations. Vacancy diffusion is modelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of k B T. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r 3 , it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice

  2. Atomistic modeling of metal surfaces under electric fields: direct coupling of electric fields to a molecular dynamics algorithm

    CERN Document Server

    Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

    2011-01-01

    The effect of electric fields on metal surfaces is fairly well studied, resulting in numerous analytical models developed to understand the mechanisms of ionization of surface atoms observed at very high electric fields, as well as the general behavior of a metal surface in this condition. However, the derivation of analytical models does not include explicitly the structural properties of metals, missing the link between the instantaneous effects owing to the applied field and the consequent response observed in the metal surface as a result of an extended application of an electric field. In the present work, we have developed a concurrent electrodynamic–molecular dynamic model for the dynamical simulation of an electric-field effect and subsequent modification of a metal surface in the framework of an atomistic molecular dynamics (MD) approach. The partial charge induced on the surface atoms by the electric field is assessed by applying the classical Gauss law. The electric forces acting on the partially...

  3. Theory and simulation studies of effective interactions, phase behavior and morphology in polymer nanocomposites.

    Science.gov (United States)

    Ganesan, Venkat; Jayaraman, Arthi

    2014-01-07

    Polymer nanocomposites are a class of materials that consist of a polymer matrix filled with inorganic/organic nanoscale additives that enhance the inherent macroscopic (mechanical, optical and electronic) properties of the polymer matrix. Over the past few decades such materials have received tremendous attention from experimentalists, theoreticians, and computational scientists. These studies have revealed that the macroscopic properties of polymer nanocomposites depend strongly on the (microscopic) morphology of the constituent nanoscale additives in the polymer matrix. As a consequence, intense research efforts have been directed to understand the relationships between interactions, morphology, and the phase behavior of polymer nanocomposites. Theory and simulations have proven to be useful tools in this regard due to their ability to link molecular level features of the polymer and nanoparticle additives to the resulting morphology within the composite. In this article we review recent theory and simulation studies, presenting briefly the methodological developments underlying PRISM theories, density functional theory, self-consistent field theory approaches, and atomistic and coarse-grained molecular simulations. We first discuss the studies on polymer nanocomposites with bare or un-functionalized nanoparticles as additives, followed by a review of recent work on composites containing polymer grafted or functionalized nanoparticles as additives. We conclude each section with a brief outlook on some potential future directions.

  4. Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

    International Nuclear Information System (INIS)

    Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

    2014-01-01

    We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example

  5. Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

    Science.gov (United States)

    Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

    2016-01-01

    Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

  6. Atomistic modelling study of lanthanide incorporation in the crystal lattice of an apatite; Etude par modelisation atomistique de l'incorporation de lanthanides dans le reseau cristallin d'une apatite phosphocalcique

    Energy Technology Data Exchange (ETDEWEB)

    Louis-Achille, V

    1999-07-01

    Studies of natural and synthetic apatites allow to propose such crystals as matrix for nuclear waste storage. The neodymium substituted britholite, Ca{sub 9}Nd(PO{sub 4}){sub 5}(SiO{sub 4})F{sub 2}. is a model for the trivalent actinide storage Neodymium can be substituted in two types of sites. The aim of this thesis is to compare the chemical nature of this two sites in fluoro-apatite Ca{sub 9}(PO{sub 4}){sub 6}F{sub 2} and then in britholite, using ab initio atomistic modeling. Two approaches are used: one considers the infinite crystals and the second considers clusters. The calculations of the electronic structure for both were performed using Kohn and Sham density functional theory in the local approximation. For solids, pseudopotentials were used, and wave functions are expanded in plane waves. For clusters, a frozen core approximation was used, and the wave functions are expanded in a linear combination of Slater type atomic orbitals. The pseudopotential is semi-relativistic for neodymium, and the Hamiltonian is scalar relativistic for the clusters. The validation of the solid approach is performed using two test cases: YPO{sub 4} and ScPO{sub 4}. Two numerical tools were developed to compute electronic deformation density map, and calculate partial density of stases. A full optimisation of the lattice parameters with a relaxation of the atomic coordinates leads to correct structural and thermodynamic properties for the fluoro-apatite, compared to experience. The electronic deformation density maps do not show any significant differences. between the two calcium sites. but Mulliken analysis on the solid and on the clusters point out the more ionic behavior of the calcium in site 2. A neodymium substituted britholite is then studied. Neodymium location only induces local modifications in; the crystalline structure and few changes in the formation enthalpy. The electronic study points out an increase of the covalent character the bonding involving neodymium

  7. Assessing the fracture strength of geological and related materials via an atomistically based J-integral

    Science.gov (United States)

    Jones, R. E.; Criscenti, L. J.; Rimsza, J.

    2016-12-01

    Predicting fracture initiation and propagation in low-permeability geomaterials is a critical yet un- solved problem crucial to assessing shale caprocks at carbon dioxide sequestration sites, and controlling fracturing for gas and oil extraction. Experiments indicate that chemical reactions at fluid-geomaterial interfaces play a major role in subcritical crack growth by weakening the material and altering crack nu- cleation and growth rates. Engineering the subsurface fracture environment, however, has been hindered by a lack of understanding of the mechanisms relating chemical environment to mechanical outcome, and a lack of capability directly linking atomistic insight to macroscale observables. We have developed a fundamental atomic-level understanding of the chemical-mechanical mecha- nisms that control subcritical cracks through coarse-graining data from reactive molecular simulations. Previous studies of fracture at the atomic level have typically been limited to producing stress-strain curves, quantifying either the system-level stress or energy at which fracture propagation occurs. As such, these curves are neither characteristic of nor insightful regarding fracture features local to the crack tip. In contrast, configurational forces, such as the J-integral, are specific to the crack in that they measure the energy available to move the crack and truly quantify fracture resistance. By development and use of field estimators consistent with the continuum conservation properties we are able to connect the data produced by atomistic simulation to the continuum-level theory of fracture mechanics and thus inform engineering decisions. In order to trust this connection we have performed theoretical consistency tests and validation with experimental data. Although we have targeted geomaterials, this capability can have direct impact on other unsolved technological problems such as predicting the corrosion and embrittlement of metals and ceramics. Sandia National

  8. Atomistic study on the interaction of nitrogen and Mg lattice and the nitride formation in nanocrystalline Mg alloys synthesized using cryomilling process

    International Nuclear Information System (INIS)

    Nezafati, Marjan; Giri, Anit; Hofmeister, Clara; Cho, Kyu; Schneider, Matthew M.; Zhou, Le; Sohn, Yongho; Kim, Chang-Soo

    2016-01-01

    Cryomilling is a broadly applied technique to synthesize nanostructured alloys and composites through powder metallurgy (PM) processing. Understanding the interactions between liquid nitrogen and the nanostructured metal powder is important as it can potentially impact the mechanical performance of these materials. In this study, we performed a series of ab initio density functional theory (DFT) computations to examine the interactions of liquid nitrogen and Mg-based matrices and the formation of Mg-nitrides. The diffusion energy barriers of nitrogen in the Mg and/or Mg-Al alloys were systematically quantified by calculating the transition state (TS) for the displacement of nitrogen between two neighboring equivalent positions. The TS calculation results indicate that diffusion of N atoms is much easier than that of N 2  molecule in the Mg matrix. It is predicted that at least ∼0.4 eV is required to overcome the diffusion energy barrier in the Mg matrix. We also quantified the formation energy of Mg nitride in the matrix. The presence of Mg nitride was demonstrated experimentally using transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS). In conjunction with the DFT computations and TEM/EELS analysis, we performed analytical calculations for the strain energy introduced during cryomilling to examine the impacts of processing parameters.

  9. An Atomistic View on Human Hemoglobin Carbon Monoxide Migration Processes

    Science.gov (United States)

    Lucas, M. Fátima; Guallar, Víctor

    2012-01-01

    A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing the ligand migration processes. First, the methodology was tested on myoglobin's CO migration, and the results were compared with the wealth of theoretical and experimental studies. Then, we explored both hemoglobin tense and relaxed states and identified the differences between the α-and β-subunits. Our results indicate that the proximal site, equivalent to the Xe1 cavity in myoglobin, is never visited. Furthermore, strategically positioned residues alter the diffusion processes within hemoglobin's subunits and suggest that multiple pathways exist, especially diversified in the α-globins. A significant dependency of the ligand dynamics on the tertiary structure is also observed. PMID:22385860

  10. Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer and R. Potestio

    Science.gov (United States)

    Klein, R.

    2015-09-01

    Kreis et al. (Eur. Phys. J. Special Topics, this issue, 2015, doi: 10.1140/epjst/e2015-02412-1) discuss the option of minimizing the complexity of the coarse-grained model in adaptive resolution molecular dynamics simulations (AdResS) by adopting a collisionless ideal gas model for this purpose. Here we discuss the technical detail of how an ideal gas model is implemented, the effective role in the simulation that is left to the coarse-grained model when it is drastically simplified as suggested, and relations between the force and potential interpolations adopted in different variants of AdResS.

  11. The Development of Models to Optimize Selection of Nuclear Fuels through Atomic-Level Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Prof. Simon Phillpot; Prof. Susan B. Sinnott; Prof. Hans Seifert; Prog. James Tulenko

    2009-01-26

    Demonstrated that FRAPCON can be modified to accept data generated from first principles studies, and that the result obtained from the modified FRAPCON make sense in terms of the inputs. Determined the temperature dependence of the thermal conductivity of single crystal UO2 from atomistic simulation.

  12. The Development of Models to Optimize Selection of Nuclear Fuels through Atomic-Level Simulation

    International Nuclear Information System (INIS)

    Phillpot, Simon; Sinnott, Susan B.; Seifert, Hans; Tulenko, James

    2009-01-01

    Demonstrated that FRAPCON can be modified to accept data generated from first principles studies, and that the result obtained from the modified FRAPCON make sense in terms of the inputs. Determined the temperature dependence of the thermal conductivity of single crystal UO2 from atomistic simulation

  13. Simulating chemical systems : MPI and GPU parallelization of novel SD algorithms

    NARCIS (Netherlands)

    Goga, N.

    Molecular dynamics is used for simulating chemical systems with the goal of studying a large range of phenomena starting from cell structures to the design of new materials, drugs, etc. A very important component of molecular dynamics is the use of well-suited atomistic and molecular modelling of

  14. Study of swelling by simulation

    International Nuclear Information System (INIS)

    Gilbon, D.; Le Naour, L.; Didout, G.

    1983-06-01

    Fuel cans and hexagonal tubes containing the pins must withstand high irradiation doses (220 or even 275 dpa) with a low swelling. Qualification of a new alloy for claddings requires several years of irradiation on a reactor. For a fast first selection simulation by 1MeV electron or heavy ions enhance radiation damages. Principles of these techniques are recalled and some examples mainly with steel 316 are given. Results are compared with results obtained in reactor to determine simulation limits. The method is not valid in the case of a structural instability of the irradiated material in a reactor [fr

  15. Inter-ribbon tunneling in graphene: An atomistic Bardeen approach

    Energy Technology Data Exchange (ETDEWEB)

    Van de Put, Maarten L., E-mail: maarten.vandeput@uantwerpen.be; Magnus, Wim [Department of Physics, Universiteit Antwerpen, B-2020 Antwerpen (Belgium); imec, B-3001 Heverlee (Belgium); Vandenberghe, William G.; Fischetti, Massimo V. [Department of Material Science, University of Texas at Dallas, Texas 75080 (United States); Sorée, Bart [Department of Physics, Universiteit Antwerpen, B-2020 Antwerpen (Belgium); imec, B-3001 Heverlee (Belgium); Department of Electrical Engineering, KU Leuven, B-3001 Leuven (Belgium)

    2016-06-07

    A weakly coupled system of two crossed graphene nanoribbons exhibits direct tunneling due to the overlap of the wavefunctions of both ribbons. We apply the Bardeen transfer Hamiltonian formalism, using atomistic band structure calculations to account for the effect of the atomic structure on the tunneling process. The strong quantum-size confinement of the nanoribbons is mirrored by the one-dimensional character of the electronic structure, resulting in properties that differ significantly from the case of inter-layer tunneling, where tunneling occurs between bulk two-dimensional graphene sheets. The current-voltage characteristics of the inter-ribbon tunneling structures exhibit resonance, as well as stepwise increases in current. Both features are caused by the energetic alignment of one-dimensional peaks in the density-of-states of the ribbons. Resonant tunneling occurs if the sign of the curvature of the coupled energy bands is equal, whereas a step-like increase in the current occurs if the signs are opposite. Changing the doping modulates the onset-voltage of the effects as well as their magnitude. Doping through electrostatic gating makes these structures promising for application towards steep slope switching devices. Using the atomistic empirical pseudopotentials based Bardeen transfer Hamiltonian method, inter-ribbon tunneling can be studied for the whole range of two-dimensional materials, such as transition metal dichalcogenides. The effects of resonance and of step-like increases in the current we observe in graphene ribbons are also expected in ribbons made from these alternative two-dimensional materials, because these effects are manifestations of the one-dimensional character of the density-of-states.

  16. Simulation of the optical coating deposition

    Science.gov (United States)

    Grigoriev, Fedor; Sulimov, Vladimir; Tikhonravov, Alexander

    2018-04-01

    A brief review of the mathematical methods of thin-film growth simulation and results of their applications is presented. Both full-atomistic and multi-scale approaches that were used in the studies of thin-film deposition are considered. The results of the structural parameter simulation including density profiles, roughness, porosity, point defect concentration, and others are discussed. The application of the quantum level methods to the simulation of the thin-film electronic and optical properties is considered. Special attention is paid to the simulation of the silicon dioxide thin films.

  17. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Directory of Open Access Journals (Sweden)

    Thomas M. Vlasic

    2016-08-01

    Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  18. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Energy Technology Data Exchange (ETDEWEB)

    Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D., E-mail: alejandro.rey@mcgill.ca [Department of Chemical Engineering, McGill University, Montreal H3A 0C5 (Canada)

    2016-08-15

    This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  19. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Science.gov (United States)

    Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

    2016-08-01

    This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  20. An adhesive contact mechanics formulation based on atomistically induced surface traction

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Houfu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States); Ren, Bo [Livermore Software Technology Corporation, 7374 Las Positas Road, Livermore, CA 94551 (United States); Li, Shaofan, E-mail: shaofan@berkeley.edu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)

    2015-12-01

    In this work, we have developed a novel multiscale computational contact formulation based on the generalized Derjuguin approximation for continua that are characterized by atomistically enriched constitutive relations in order to study macroscopic interaction between arbitrarily shaped deformable continua. The proposed adhesive contact formulation makes use of the microscopic interaction forces between individual particles in the interacting bodies. In particular, the double-layer volume integral describing the contact interaction (energy, force vector, matrix) is converted into a double-layer surface integral through a mathematically consistent approach that employs the divergence theorem and a special partitioning technique. The proposed contact model is formulated in the nonlinear continuum mechanics framework and implemented using the standard finite element method. With no large penalty constant, the stiffness matrix of the system will in general be well-conditioned, which is of great significance for quasi-static analysis. Three numerical examples are presented to illustrate the capability of the proposed method. Results indicate that with the same mesh configuration, the finite element computation based on the surface integral approach is faster and more accurate than the volume integral based approach. In addition, the proposed approach is energy preserving even in a very long dynamic simulation.

  1. Atomistic modeling trap-assisted tunneling in hole tunnel field effect transistors

    Science.gov (United States)

    Long, Pengyu; Huang, Jun Z.; Povolotskyi, Michael; Sarangapani, Prasad; Valencia-Zapata, Gustavo A.; Kubis, Tillmann; Rodwell, Mark J. W.; Klimeck, Gerhard

    2018-05-01

    Tunnel Field Effect Transistors (FETs) have the potential to achieve steep Subthreshold Swing (S.S.) below 60 mV/dec, but their S.S. could be limited by trap-assisted tunneling (TAT) due to interface traps. In this paper, the effect of trap energy and location on OFF-current (IOFF) of tunnel FETs is evaluated systematically using an atomistic trap level representation in a full quantum transport simulation. Trap energy levels close to band edges cause the highest leakage. Wave function penetration into the surrounding oxide increases the TAT current. To estimate the effects of multiple traps, we assume that the traps themselves do not interact with each other and as a whole do not modify the electrostatic potential dramatically. Within that model limitation, this numerical metrology study points to the critical importance of TAT in the IOFF in tunnel FETs. The model shows that for Dit higher than 1012/(cm2 eV) IO F F is critically increased with a degraded IO N/IO F F ratio of the tunnel FET. In order to have an IO N/IO F F ratio higher than 104, the acceptable Dit near Ev should be controlled to no larger than 1012/(cm2 eV) .

  2. On Atomistic Models for Molecular Oxygen

    DEFF Research Database (Denmark)

    Javanainen, Matti; Vattulainen, Ilpo; Monticelli, Luca

    2017-01-01

    Molecular oxygen (O2) is key to all life on earth, as it is constantly cycled via photosynthesis and cellular respiration. Substantial scientific effort has been devoted to understanding every part of this cycle. Classical molecular dynamics (MD) simulations have been used to study some of the key...... processes involved in cellular respiration: O2 permeation through alveolar monolayers and cellular membranes, its binding to hemoglobin during transport in the bloodstream, as well as its transport along optimal pathways toward its reduction sites in proteins. Moreover, MD simulations can help interpret...

  3. Operations planning simulation: Model study

    Science.gov (United States)

    1974-01-01

    The use of simulation modeling for the identification of system sensitivities to internal and external forces and variables is discussed. The technique provides a means of exploring alternate system procedures and processes, so that these alternatives may be considered on a mutually comparative basis permitting the selection of a mode or modes of operation which have potential advantages to the system user and the operator. These advantages are measurements is system efficiency are: (1) the ability to meet specific schedules for operations, mission or mission readiness requirements or performance standards and (2) to accomplish the objectives within cost effective limits.

  4. Effect of Pore Geometry on Gas Adsorption: Grand Canonical Monte Carlo Simulation Studies

    International Nuclear Information System (INIS)

    Lee, Eon Ji; Chang, Rak Woo; Han, Ji Hyung; Chung, Taek Dong

    2012-01-01

    In this study, we investigated the pure geometrical effect of porous materials in gas adsorption using the grand canonical Monte Carlo simulations of primitive gas-pore models with various pore geometries such as planar, cylindrical, and random pore geometries. Although the model does not possess atomistic level details of porous materials, our simulation results provided many insightful information in the effect of pore geometry on the adsorption behavior of gas molecules. First, the surface curvature of porous materials plays a significant role in the amount of adsorbed gas molecules: the concave surface such as in cylindrical pores induces more attraction between gas molecules and pore, which results in the enhanced gas adsorption. On the contrary, the convex surface of random pores gives the opposite effect. Second, this geometrical effect shows a nonmonotonic dependence on the gas-pore interaction strength and length. Third, as the external gas pressure is increased, the change in the gas adsorption due to pore geometry is reduced. Finally, the pore geometry also affects the collision dynamics of gas molecules. Since our model is based on primitive description of fluid molecules, our conclusion can be applied to any fluidic systems including reactant-electrode systems

  5. Dual-energy mammography: simulation studies

    International Nuclear Information System (INIS)

    Bliznakova, K; Kolitsi, Z; Pallikarakis, N

    2006-01-01

    This paper presents a mammography simulator and demonstrates its applicability in feasibility studies in dual-energy (DE) subtraction mammography. This mammography simulator is an evolution of a previously presented x-ray imaging simulation system, which has been extended with new functionalities that are specific for DE simulations. The new features include incident exposure and dose calculations, the implementation of a DE subtraction algorithm as well as amendments to the detector and source modelling. The system was then verified by simulating experiments and comparing their results against published data. The simulator was used to carry out a feasibility study of the applicability of DE techniques in mammography, and more precisely to examine whether this modality could result in better visualization and detection of microcalcifications. Investigations were carried out using a 3D breast software phantom of average thickness, monoenergetic and polyenergetic beam spectra and various detector configurations. Dual-shot techniques were simulated. Results showed the advantage of using monoenergetic in comparison with polyenergetic beams. Optimization studies with monochromatic sources were carried out to obtain the optimal low and high incident energies, based on the assessment of the figure of merit of the simulated microcalcifications in the subtracted images. The results of the simulation study with the optimal energies demonstrated that the use of the DE technique can improve visualization and increase detectability, allowing identification of microcalcifications of sizes as small as 200 μm. The quantitative results are also verified by means of a visual inspection of the synthetic images

  6. Structural elucidation of transmembrane domain zero (TMD0) of EcdL: A multidrug resistance-associated protein (MRP) family of ATP-binding cassette transporter protein revealed by atomistic simulation.

    Science.gov (United States)

    Bera, Krishnendu; Rani, Priyanka; Kishor, Gaurav; Agarwal, Shikha; Kumar, Antresh; Singh, Durg Vijay

    2017-09-20

    ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known. We hypothesized that the transportation of echonocandinB is mediated via EcdL protein. Henceforth, it is pertinent to know the topological arrangement of TMD0, with other domains of protein and its possible role in transportation of echinocandinB. Absence of effective template for TMD0 domain lead us to model by I-TASSER, further structure has been refined by multiple template modelling using homologous templates of remaining domains (TMD1, NBD1, TMD2, NBD2). The modelled structure has been validated for packing, folding and stereochemical properties. MD simulation for 0.1 μs has been carried out in the biphasic environment for refinement of modelled protein. Non-redundant structures have been excavated by clustering of MD trajectory. The structural alignment of modelled structure has shown Z-score -37.9; 31.6, 31.5 with RMSD; 2.4, 4.2, 4.8 with ABC transporters; PDB ID 4F4C, 4M1 M, 4M2T, respectively, reflecting the correctness of structure. EchinocandinB has been docked to the modelled as well as to the clustered structures, which reveals interaction of echinocandinB with TMD0 and other TM helices in the translocation path build of TMDs.

  7. Atomistic nucleation sites of Pt nanoparticles on N-doped carbon nanotubes.

    Science.gov (United States)

    Sun, Chia-Liang; Pao, Chih-Wen; Tsai, Huang-Ming; Chiou, Jau-Wern; Ray, Sekhar C; Wang, Houng-Wei; Hayashi, Michitoshi; Chen, Li-Chyong; Lin, Hong-Ji; Lee, Jyh-Fu; Chang, Li; Tsai, Min-Hsiung; Chen, Kuei-Hsien; Pong, Way-Faung

    2013-08-07

    The atomistic nucleation sites of Pt nanoparticles (Pt NPs) on N-doped carbon nanotubes (N-CNTs) were investigated using C and N K-edge and Pt L3-edge X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure (EXAFS) spectroscopy. Transmission electron microscopy and XANES/EXAFS results revealed that the self-organized Pt NPs on N-CNTs are uniformly distributed because of the relatively high binding energies of the adsorbed Pt atoms at the imperfect sites. During the atomistic nucleation process of Pt NPs on N-CNTs, stable Pt-C and Pt-N bonds are presumably formed, and charge transfer occurs at the surface/interface of the N-CNTs. The findings in this study were consistent with density functional theory calculations performed using cluster models for the undoped, substitutional-N-doped and pyridine-like-N-doped CNTs.

  8. Cationic Dimyristoylphosphatidylcholine and Dioleoyloxytrimethylammonium Propane Lipid Bilayers: Atomistic Insight for Structure and Dynamics

    DEFF Research Database (Denmark)

    Zhao, W.; Gurtovenko, A. A.; Vattulainen, I.

    2012-01-01

    We performed atomistic molecular dynamics simulations of lipid bilayers consisting of a mixture of cationic dioleoyloxytrimethylammonium propane (DOTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) lipids at different DOTAP fractions. Our primary focus was the specific effects...... of unsaturated lipid chains on structural and dynamic properties of mixed cationic bilayers. The bilayer area, as well as the ordering of lipid tails, shows a pronounced nonmonotonic behavior when TAP lipid fraction increases. The minimum in area (maximum in ordering) was observed for a bilayer with TAP fraction...... lipids, which were found to form PC-PC and PC-TAP pairs, and the formation of lipid clusters....

  9. Atomistic switch of giant magnetoresistance and spin thermopower in graphene-like nanoribbons

    Science.gov (United States)

    Zhai, Ming-Xing; Wang, Xue-Feng

    2016-01-01

    We demonstrate that the giant magnetoresistance can be switched off (on) in even- (odd-) width zigzag graphene-like nanoribbons by an atomistic gate potential or edge disorder inside the domain wall in the antiparallel (ap) magnetic configuration. A strong magneto-thermopower effect is also predicted that the spin thermopower can be greatly enhanced in the ap configuration while the charge thermopower remains low. The results extracted from the tight-binding model agree well with those obtained by first-principles simulations for edge doped graphene nanoribbons. Analytical expressions in the simplest case are obtained to facilitate qualitative analyses in general contexts. PMID:27857156

  10. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

    DEFF Research Database (Denmark)

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia

    2016-01-01

    -oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-. D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-. D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers[U+05F3] compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed...

  11. Comparison of atomistic and elasticity approaches for carbon diffusion near line defects in {alpha}-iron

    Energy Technology Data Exchange (ETDEWEB)

    Veiga, R.G.A., E-mail: rgaveiga@gmail.com [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Perez, M. [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Becquart, C.S. [Unite Materiaux et Transformations (UMET), Ecole Nationale Superieure de Chimie de Lille, UMR CNRS 8207, Bat. C6, F59655 Villeneuve d' Ascq Cedex (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Clouet, E. [Service de Recherches de Metallurgie Physique, CEA/Saclay, 91191 Gif-sur-Yvette (France); Domain, C. [EDF, Recherche et Developpement, Materiaux et Mecanique des Composants, Les Renardieres, F77250 Moret sur Loing (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France)

    2011-10-15

    Energy barriers for carbon migration in the neighborhood of line defects in body-centered cubic iron have been obtained by atomistic simulations. For this purpose, molecular statics with an Fe-C interatomic potential, based on the embedded atom method, has been employed. Results of these simulations have been compared to the predictions of anisotropic elasticity theory. The agreement is better for a carbon atom sitting on an octahedral site (energy minimum) than one on a tetrahedral site (saddle point). Absolute differences in the energy barriers obtained by the two methods are usually below 5 meV at distances larger than 1.5 nm from a screw dislocation and 2 nm (up to 4 nm in the glide plane) from the edge dislocation. Atomistic kinetic Monte Carlo simulations performed at T = 300 K and additional analysis based on the activation energies obtained by both methods show that they are in good qualitative agreement, despite some important quantitative discrepancies due to the large absolute errors found near the dislocation cores.

  12. Applicability of mode-coupling theory to polyisobutylene: a molecular dynamics simulation study.

    Science.gov (United States)

    Khairy, Y; Alvarez, F; Arbe, A; Colmenero, J

    2013-10-01

    The applicability of Mode Coupling Theory (MCT) to the glass-forming polymer polyisobutylene (PIB) has been explored by using fully atomistic molecular dynamics simulations. MCT predictions for the so-called asymptotic regime have been successfully tested on the dynamic structure factor and the self-correlation function of PIB main-chain carbons calculated from the simulated cell. The factorization theorem and the time-temperature superposition principle are satisfied. A consistent fitting procedure of the simulation data to the MCT asymptotic power-laws predicted for the α-relaxation regime has delivered the dynamic exponents of the theory-in particular, the exponent parameter λ-the critical non-ergodicity parameters, and the critical temperature T(c). The obtained values of λ and T(c) agree, within the uncertainties involved in both studies, with those deduced from depolarized light scattering experiments [A. Kisliuk et al., J. Polym. Sci. Part B: Polym. Phys. 38, 2785 (2000)]. Both, λ and T(c)/T(g) values found for PIB are unusually large with respect to those commonly obtained in low molecular weight systems. Moreover, the high T(c)/T(g) value is compatible with a certain correlation of this parameter with the fragility in Angell's classification. Conversely, the value of λ is close to that reported for real polymers, simulated "realistic" polymers and simple polymer models with intramolecular barriers. In the framework of the MCT, such finding should be the signature of two different mechanisms for the glass-transition in real polymers: intermolecular packing and intramolecular barriers combined with chain connectivity.

  13. Crop micrometeorology : a simulation study

    NARCIS (Netherlands)

    Goudriaan, J.

    1977-01-01

    This monograph presents the results of a detailed study in micrometeorology; one of the sciences that play an important role in production ecology. The purpose is to explain the microweather as a function of the properties of plant and soil, and of the weather conditions prevalent at some

  14. Superlubricity mechanism of diamond-like carbon with glycerol. Coupling of experimental and simulation studies

    International Nuclear Information System (INIS)

    Bouchet, M I De Barros; Matta, C; Le-Mogne, Th; Martin, J Michel; Zhang, Q; III, W Goddard; Kano, M; Mabuchi, Y; Ye, J

    2007-01-01

    We report a unique tribological system that produces superlubricity under boundary lubrication conditions with extremely little wear. This system is a thin coating of hydrogen-free amorphous Diamond-Like-Carbon (denoted as ta-C) at 353 K in a ta-C/ta-C friction pair lubricated with pure glycerol. To understand the mechanism of friction vanishing we performed ToF-SIMS experiments using deuterated glycerol and 13 C glycerol. This was complemented by first-principles-based computer simulations using the ReaxFF reactive force field to create an atomistic model of ta-C. These simulations show that DLC with the experimental density of 3.24 g/cc leads to an atomistic structure consisting of a 3D percolating network of tetrahedral (sp 3 ) carbons accounting for 71.5% of the total, in excellent agreement with the 70% deduced from our Auger spectroscopy and XANES experiments. The simulations show that the remaining carbons (with sp 2 and sp 1 character) attach in short chains of length 1 to 7. In sliding simulations including glycerol molecules, the surface atoms react readily to form a very smooth carbon surface containing OH-terminated groups. This agrees with our SIMS experiments. The simulations find that the OH atoms are mostly bound to surface sp 1 atoms leading to very flexible elastic response to sliding. Both simulations and experiments suggest that the origin of the superlubricity arises from the formation of this OH-terminated surface

  15. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

    International Nuclear Information System (INIS)

    Shi, Jade; Schwantes, Christian; Bilsel, Osman

    2017-01-01

    The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

  16. Fully Atomistic Understanding of the Electronic and Optical Properties of a Prototypical Doped Charge-Transfer Interface

    DEFF Research Database (Denmark)

    Brivio, Gian Paolo; Baby, Anu; Gruenewald, Marco

    2017-01-01

    The current study generates profound atomistic insights into doping-induced changes of the optical and electronic properties of the prototypical PTCDA/Ag(111) interface. For doping K atoms are used, as KxPTCDA/Ag(111) has the distinct advantage of forming well-defined stoichiometric phases...

  17. Multiscale Simulation of Thermo-mechanical Processes in Irradiated Fission-reactor Materials

    International Nuclear Information System (INIS)

    Phillpot, Simon R.

    2012-01-01

    The work funded from this project has been published in six papers, with two more in draft form, with submission planned for the near future. The papers are: (1) Kinetically-Evolving Irradiation-Induced Point-Defect Clusters in UO 2 by Molecular-Dynamics Simulation; (2) Kinetically driven point-defect clustering in irradiated MgO by molecular-dynamics simulation; (3) Grain-Boundary Source/Sink Behavior for Point Defect: An Atomistic Simulation Study; (4) Energetics of intrinsic point defects in uranium dioxide from electronic structure calculations; (5) Thermodynamics of fission products in UO 2±x ; and (6) Atomistic study of grain boundary sink strength under prolonged electron irradiation. The other two pieces of work that are currently being written-up for publication are: (1) Effect of Pores and He Bubbles on the Thermal Transport Properties of UO2 by Molecular Dynamics Simulation; and (2) Segregation of Ruthenium to Edge Dislocations in Uranium Dioxide.

  18. A Bond-Order Potential for Atomistic Simulations in Iron

    National Research Council Canada - National Science Library

    Rice, Betsy

    2000-01-01

    .... With a total of 15 fitted parameters, the potential reproduces with only minor deviations to the elastic moduli, the volume-pressure equation of states in the BCC phase, the energies in face-centered cubic (FCC...

  19. Atomistic simulations of jog migration on extended screw dislocations

    DEFF Research Database (Denmark)

    Vegge, T.; Leffers, T.; Pedersen, O.B.

    2001-01-01

    on the Effective Medium Theory, The minimum energy path through configuration space and the corresponding transition state energy are obtained using the Nudged Elastic Band path technique. We find very similar migration properties for elementary jogs on the (110){110} octahedral slip systems and the (110){110} non...

  20. Dislocation motion in tungsten: Atomistic input to discrete dislocation simulations

    Czech Academy of Sciences Publication Activity Database

    Srivastava, K.; Gröger, Roman; Weygand, D.; Gumbsch, P.

    2013-01-01

    Roč. 47, AUG (2013), s. 126-142 ISSN 0749-6419 R&D Projects: GA ČR GAP204/10/0255; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081723 Keywords : body -centered cubic * non-Schmid effects * anomalous slip * discrete dislocation dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism; BM - Solid Matter Physics ; Magnetism (UFM-A) Impact factor: 5.971, year: 2013

  1. Fluorinated Phosphorene: Electrochemical Synthesis, Atomistic Fluorination, and Enhanced Stability.

    Science.gov (United States)

    Tang, Xian; Liang, Weiyuan; Zhao, Jinlai; Li, Zhongjun; Qiu, Meng; Fan, Taojian; Luo, Crystal Shaojuan; Zhou, Ye; Li, Yu; Guo, Zhinan; Fan, Dianyuan; Zhang, Han

    2017-12-01

    Phosphorene has attracted great interest due to its unique electronic and optoelectronic properties owing to its tunable direct and moderate band-gap in association with high carrier mobility. However, its intrinsic instability in air seriously hinders its practical applications, and problems of technical complexity and in-process degradation exist in currently proposed stabilization strategies. A facile pathway in obtaining and stabilizing phosphorene through a one-step, ionic liquid-assisted electrochemical exfoliation and synchronous fluorination process is reported in this study. This strategy enables fluorinated phosphorene (FP) to be discovered and large-scale, highly selective few-layer FP (3-6 atomic layers) to be obtained. The synthesized FP is found to exhibit unique morphological and optical characteristics. Possible atomistic fluorination configurations of FP are revealed by core-level binding energy shift calculations in combination with spectroscopic measurements, and the results indicate that electrolyte concentration significantly modulates the fluorination configurations. Furthermore, FP is found to exhibit enhanced air stability thanks to the antioxidation and antihydration effects of the introduced fluorine adatoms, and demonstrate excellent photothermal stability during a week of air exposure. These findings pave the way toward real applications of phosphorene-based nanophotonics. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Multi-scale modelling of ions in solution: from atomistic descriptions to chemical engineering

    International Nuclear Information System (INIS)

    Molina, J.J.

    2011-01-01

    Ions in solution play a fundamental role in many physical, chemical, and biological processes. The PUREX process used in the nuclear industry to the treatment of spent nuclear fuels is considered as an example. For industrial applications these systems are usually described using simple analytical models which are fitted to reproduce the available experimental data. In this work, we propose a multi-scale coarse graining procedure to derive such models from atomistic descriptions. First, parameters for classical force-fields of ions in solution are extracted from ab-initio calculations. Effective (McMillan-Mayer) ion-ion potentials are then derived from radial distribution functions measured in classical molecular dynamics simulations, allowing us to define an implicit solvent model of electrolytes. Finally, perturbation calculations are performed to define the best possible representation for these systems, in terms of charged hard-sphere models. Our final model is analytical and contains no free 'fitting' parameters. It shows good agreement with the exact results obtained from Monte-Carlo simulations for the thermodynamic and structural properties. Development of a similar model for the electrolyte viscosity, from information derived from atomistic descriptions, is also introduced. (author)

  3. Atomistic Modeling of Ion Conduction through the Voltage-Sensing Domain of the Shaker K+ Ion Channel.

    Science.gov (United States)

    Wood, Mona L; Freites, J Alfredo; Tombola, Francesco; Tobias, Douglas J

    2017-04-20

    Voltage-sensing domains (VSDs) sense changes in the membrane electrostatic potential and, through conformational changes, regulate a specific function. The VSDs of wild-type voltage-dependent K + , Na + , and Ca 2+ channels do not conduct ions, but they can become ion-permeable through pathological mutations in the VSD. Relatively little is known about the underlying mechanisms of conduction through VSDs. The most detailed studies have been performed on Shaker K + channel variants in which ion conduction through the VSD is manifested in electrophysiology experiments as a voltage-dependent inward current, the so-called omega current, which appears when the VSDs are in their resting state conformation. Only monovalent cations appear to permeate the Shaker VSD via a pathway that is believed to be, at least in part, the same as that followed by the S4 basic side chains during voltage-dependent activation. We performed μs-time scale atomistic molecular dynamics simulations of a cation-conducting variant of the Shaker VSD under applied electric fields in an experimentally validated resting-state conformation, embedded in a lipid bilayer surrounded by solutions containing guanidinium chloride or potassium chloride. Our simulations provide insights into the Shaker VSD permeation pathway, the protein-ion interactions that control permeation kinetics, and the mechanism of voltage-dependent activation of voltage-gated ion channels.

  4. Preliminary simulation study of doppler reflectometry

    International Nuclear Information System (INIS)

    Ishii, Yuta; Hojo, Hitoshi; Yoshikawa, Masashi; Ichimura, Makoto; Haraguchi, Yusuke; Imai, Tsuyoshi; Mase, Atsushi

    2010-01-01

    A preliminary simulation study of Doppler reflectometry is performed. The simulations solve Maxwell's equations by a finite difference time domain (FDTD) code method in two dimensions. A moving corrugated metal target is used as a plasma cutoff layer to study the basic features of Doppler reflectometry. We examined the effects of the full width at half maximum (FWHM) of the electromagnetic waves and the corrugation depth of the metal target. Furthermore, the effect of a nonuniform plasma is studied using this FDTD analysis. The Doppler shift and velocity are compared with those obtained from FDTD analysis of a uniform plasma. (author)

  5. General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium Green's function

    DEFF Research Database (Denmark)

    Stradi, Daniele; Martinez, Umberto; Blom, Anders

    2016-01-01

    Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce...... an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-Vbias curve simulations. We apply...... interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid...

  6. Digital Simulation Games for Social Studies Classrooms

    Science.gov (United States)

    Devlin-Scherer, Roberta; Sardone, Nancy B.

    2010-01-01

    Data from ten teacher candidates studying teaching methods were analyzed to determine perceptions toward digital simulation games in the area of social studies. This research can be used as a conceptual model of how current teacher candidates react to new methods of instruction and determine how education programs might change existing curricula…

  7. A study on the plasticity of soda-lime silica glass via molecular dynamics simulations

    Science.gov (United States)

    Urata, Shingo; Sato, Yosuke

    2017-11-01

    Molecular dynamics (MD) simulations were applied to construct a plasticity model, which enables one to simulate deformations of soda-lime silica glass (SLSG) by using continuum methods. To model the plasticity, stress induced by uniaxial and a variety of biaxial deformations was measured by MD simulations. We found that the surfaces of yield and maximum stresses, which are evaluated from the equivalent stress-strain curves, are reasonably represented by the Mohr-Coulomb ellipsoid. Comparing a finite element model using the constructed plasticity model to a large scale atomistic model on a nanoindentation simulation of SLSG reveals that the empirical method is accurate enough to evaluate the SLSG mechanical responses. Furthermore, the effect of ion-exchange on the SLSG plasticity was examined by using MD simulations. As a result, it was demonstrated that the effects of the initial compressive stress on the yield and maximum stresses are anisotropic contrary to our expectations.

  8. Simulator Studies of the Deep Stall

    Science.gov (United States)

    White, Maurice D.; Cooper, George E.

    1965-01-01

    Simulator studies of the deep-stall problem encountered with modern airplanes are discussed. The results indicate that the basic deep-stall tendencies produced by aerodynamic characteristics are augmented by operational considerations. Because of control difficulties to be anticipated in the deep stall, it is desirable that adequate safeguards be provided against inadvertent penetrations.

  9. Preliminary simulation studies of accelerator cavity loading

    International Nuclear Information System (INIS)

    Faehl, R.J.

    1980-06-01

    Two-dimensional simulations of loading effects in a 350 MHz accelerator cavity have been performed. Electron currents of 1-10 kA have been accelerated in 5 MV/m fields. Higher order cavity modes induced by the beam may lead to emittance growth. Operation in an autoaccelerator mode has been studied

  10. Driving Simulator Development and Performance Study

    OpenAIRE

    Juto, Erik

    2010-01-01

    The driving simulator is a vital tool for much of the research performed at theSwedish National Road and Transport Institute (VTI). Currently VTI posses three driving simulators, two high fidelity simulators developed and constructed by VTI, and a medium fidelity simulator from the German company Dr.-Ing. Reiner Foerst GmbH. The two high fidelity simulators run the same simulation software, developed at VTI. The medium fidelity simulator runs a proprietary simulation software. At VTI there is...

  11. Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties

    DEFF Research Database (Denmark)

    Voroshylova, I. V.; Chaban, V. V.

    2014-01-01

    Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....

  12. Optimal kernel shape and bandwidth for atomistic support of continuum stress

    International Nuclear Information System (INIS)

    Ulz, Manfred H; Moran, Sean J

    2013-01-01

    The treatment of atomistic scale interactions via molecular dynamics simulations has recently found favour for multiscale modelling within engineering. The estimation of stress at a continuum point on the atomistic scale requires a pre-defined kernel function. This kernel function derives the stress at a continuum point by averaging the contribution from atoms within a region surrounding the continuum point. This averaging volume, and therefore the associated stress at a continuum point, is highly dependent on the bandwidth and shape of the kernel. In this paper we propose an effective and entirely data-driven strategy for simultaneously computing the optimal shape and bandwidth for the kernel. We thoroughly evaluate our proposed approach on copper using three classical elasticity problems. Our evaluation yields three key findings: firstly, our technique can provide a physically meaningful estimation of kernel bandwidth; secondly, we show that a uniform kernel is preferred, thereby justifying the default selection of this kernel shape in future work; and thirdly, we can reliably estimate both of these attributes in a data-driven manner, obtaining values that lead to an accurate estimation of the stress at a continuum point. (paper)

  13. Computational Method for Atomistic-Continuum Homogenization

    National Research Council Canada - National Science Library

    Chung, Peter

    2002-01-01

    ...." Physical Review Letters. vol. 61, no. 25, pp. 2879-2882, 19 December 1988; Brenner, D. W. "Empirical Potential for Hydrocarbons for Use in Simulating the Chemical Vapor Deposition of Diamond Films...

  14. Control algorithm for multiscale flow simulations of water

    DEFF Research Database (Denmark)

    Kotsalis, E. M.; Walther, Jens Honore; Kaxiras, E.

    2009-01-01

    We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions...

  15. Thermodynamic Database for the Terrestrial and Planetary Mantle Studies: Where we stand, and some future directions involving experimental studies, numerical protocol for EoS and atomistic calculations (Invited)

    Science.gov (United States)

    Ganguly, J.; Tirone, M.; Sorcar, N.

    2013-12-01

    problem of appropriate combination of binary mixing properties in a multicomponent system, and present simplified a-x formalisms for complex multi-site solutions the full-blown treatment of which requires a body of experimental data that are unlikely to be available in the near future. It appears that Cp and the coefficients of thermal expansion and compression of solids could be calculated quite well form density functional theory (DFT) (e.g. 7), so that the future development of databases should not only consider the available DFT data, but also have active involvement in such studies 'to fill the gap' when reliable data are not available. While the current trend in geodynamic modeling is to use thermodynamic properties in tabulated form, more realistic simulations, which we would try to illustrate by examples, would require real-time thermodynamic calculations for evolving bulk compositions; hence the development of a robust yet simple thermodynamic formulation becomes essential. 1. Fabrichnaya et al. (2004), Springer-verlag; 2. Stixrude and Lithgow-Bertelloni, Geophys. J. Int. (2011) 184, 1180-1213. 3. Holland et al. ( 2013) J. Petrol. 4. Report, Geomaterials Genome Project, March 19-23, 2013, Miami, Florida, NSF Geoinformatics program. 5. Ferreira et al. (1988) Phys Rev B, 37, 10547-10570; 6. Ganguly et al. (1993) Amer Min 78, 583-593 7. Ottonello et a. (2009) PCM 36, 87-106

  16. Long time scale simulation of a grain boundary in copper

    DEFF Research Database (Denmark)

    Pedersen, A.; Henkelman, G.; Schiøtz, Jakob

    2009-01-01

    A general, twisted and tilted, grain boundary in copper has been simulated using the adaptive kinetic Monte Carlo method to study the atomistic structure of the non-crystalline region and the mechanism of annealing events that occur at low temperature. The simulated time interval spanned 67 mu s...... was also observed. In the final low-energy configurations, the thickness of the region separating the crystalline grains corresponds to just one atomic layer, in good agreement with reported experimental observations. The simulated system consists of 1307 atoms and atomic interactions were described using...

  17. An atomistic methodology of energy release rate for graphene at nanoscale

    International Nuclear Information System (INIS)

    Zhang, Zhen; Lee, James D.; Wang, Xianqiao

    2014-01-01

    Graphene is a single layer of carbon atoms packed into a honeycomb architecture, serving as a fundamental building block for electric devices. Understanding the fracture mechanism of graphene under various conditions is crucial for tailoring the electrical and mechanical properties of graphene-based devices at atomic scale. Although most of the fracture mechanics concepts, such as stress intensity factors, are not applicable in molecular dynamics simulation, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at nanoscale. This work introduces an atomistic simulation methodology, based on the energy release rate, as a tool to unveil the fracture mechanism of graphene at nanoscale. This methodology can be easily extended to any atomistic material system. We have investigated both opening mode and mixed mode at different temperatures. Simulation results show that the critical energy release rate of graphene is independent of initial crack length at low temperature. Graphene with inclined pre-crack possesses higher fracture strength and fracture deformation but smaller critical energy release rate compared with the graphene with vertical pre-crack. Owing to its anisotropy, graphene with armchair chirality always has greater critical energy release rate than graphene with zigzag chirality. The increase of temperature leads to the reduction of fracture strength, fracture deformation, and the critical energy release rate of graphene. Also, higher temperature brings higher randomness of energy release rate of graphene under a variety of predefined crack lengths. The energy release rate is independent of the strain rate as long as the strain rate is small enough

  18. Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures

    Science.gov (United States)

    Yan, Xin; Gouissem, Afif; Guduru, Pradeep R.; Sharma, Pradeep

    2017-10-01

    Amorphous lithium-silicon (a-Li-Si), especially in nanostructure form, is an attractive high-capacity anode material for next-generation Li-ion batteries. During cycles of charging and discharging, a-Li-Si undergoes substantive inelastic deformation and exhibits microcracking. The mechanical response to repeated lithiation-delithiation eventually results in the loss of electrical contact and consequent decrease of capacity, thus underscoring the importance of studying the plasticity of a-Li-Si nanostructures. In recent years, a variety of phenomenological continuum theories have been introduced that purport to model plasticity and the electro-chemo-mechanical behavior of a-Li-Si. Unfortunately, the micromechanisms and atomistic considerations underlying plasticity in Li-Si material are not yet fully understood and this impedes the development of physics-based constitutive models. Conventional molecular dynamics, although extensively used to study this material, is grossly inadequate to resolve this matter. As is well known, conventional molecular dynamics simulations can only address phenomena with characteristic time scales of (at most) a microsecond. Accordingly, in such simulations, the mechanical behavior is deduced under conditions of very high strain rates (usually, 108s-1 or even higher). This limitation severely impacts a realistic assessment of rate-dependent effects. In this work, we attempt to circumvent the time-scale bottleneck of conventional molecular dynamics and provide novel insights into the mechanisms underpinning plastic deformation of Li-Si nanostructures. We utilize an approach that allows imposition of slow strain rates and involves the employment of a new and recently developed potential energy surface sampling method—the so-called autonomous basin climbing—to identify the local minima in the potential energy surface. Combined with other techniques, such as nudged elastic band, kinetic Monte Carlo and transition state theory, we assess

  19. SCT: a suite of programs for comparing atomistic models with small-angle scattering data.

    Science.gov (United States)

    Wright, David W; Perkins, Stephen J

    2015-06-01

    Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.

  20. Adhesive contact: from atomistic model to continuum model

    International Nuclear Information System (INIS)

    Fan Kang-Qi; Jia Jian-Yuan; Zhu Ying-Min; Zhang Xiu-Yan

    2011-01-01

    Two types of Lennard-Jones potential are widely used in modeling adhesive contacts. However, the relationships between the parameters of the two types of Lennard-Jones potential are not well defined. This paper employs a self-consistent method to derive the Lennard-Jones surface force law from the interatomic Lennard-Jones potential with emphasis on the relationships between the parameters. The effect of using correct parameters in the adhesion models is demonstrated in single sphere-flat contact via continuum models and an atomistic model. Furthermore, the adhesion hysteresis behaviour is investigated, and the S-shaped force-distance relation is revealed by the atomistic model. It shows that the adhesion hysteresis loop is generated by the jump-to-contact and jump-off-contact, which are illustrated by the S-shaped force-distance curve. (atomic and molecular physics)

  1. Atomic scale numerical simulation study of elementary mechanisms of plasticity in aluminium and copper

    International Nuclear Information System (INIS)

    Aslanides, Antoine

    1998-01-01

    This study deals with elementary mechanisms of plasticity, such as the dissociation of a perfect edge dislocation into Shockley partials, the annihilation of dislocation dipoles and the interaction between a dislocation and an interface (free surface and grain boundary). Dislocation core effects are expected to influence crucially these interactions. A deeper understanding of these situations is thus achieved by resorting to an atomistic numerical approach, the application of the elastic theory of dislocations being no longer justified. Two FCC metals are considered: aluminium and copper, with respectively a small and a large dissociation width. An empirical potential for aluminium was designed to study the perfect as well as the dissociated states of the dislocation. The results are compared to the ones obtained with the interaction model for copper, for both the edge and the screw characters. The obtained core radius value ensures the continuity between the atomic and the elastic treatments. The calculations concerning edge dislocation dipole configurations show that there exists a critical distance between the glide planes of the two constitutive dislocations under which a spontaneous recombination occurs. We then compute the variation of the excess energy associated to the gradual approach of an edge dislocation toward the free surface of a crystal. An estimation of the energy required for the introduction of a dislocation in a thin film is obtained. The study of the interaction between a dislocation and a tilt grain boundary shows that the dislocation is absorbed in the interface, the stress required for its extraction being rather large. Finally, by proceeding to the simulation of a tensile test, we demonstrate that the surface steps constitute favoured sites for the nucleation of the dislocations. (author) [fr

  2. NATO Advanced Study Institute on Advances in the Computer Simulations of Liquid Crystals

    CERN Document Server

    Zannoni, Claudio

    2000-01-01

    Computer simulations provide an essential set of tools for understanding the macroscopic properties of liquid crystals and of their phase transitions in terms of molecular models. While simulations of liquid crystals are based on the same general Monte Carlo and molecular dynamics techniques as are used for other fluids, they present a number of specific problems and peculiarities connected to the intrinsic properties of these mesophases. The field of computer simulations of anisotropic fluids is interdisciplinary and is evolving very rapidly. The present volume covers a variety of techniques and model systems, from lattices to hard particle and Gay-Berne to atomistic, for thermotropics, lyotropics, and some biologically interesting liquid crystals. Contributions are written by an excellent panel of international lecturers and provides a timely account of the techniques and problems in the field.

  3. Dislocation climb models from atomistic scheme to dislocation dynamics

    OpenAIRE

    Niu, Xiaohua; Luo, Tao; Lu, Jianfeng; Xiang, Yang

    2016-01-01

    We develop a mesoscopic dislocation dynamics model for vacancy-assisted dislocation climb by upscalings from a stochastic model on the atomistic scale. Our models incorporate microscopic mechanisms of (i) bulk diffusion of vacancies, (ii) vacancy exchange dynamics between bulk and dislocation core, (iii) vacancy pipe diffusion along the dislocation core, and (iv) vacancy attachment-detachment kinetics at jogs leading to the motion of jogs. Our mesoscopic model consists of the vacancy bulk dif...

  4. Mobile-ip Aeronautical Network Simulation Study

    Science.gov (United States)

    Ivancic, William D.; Tran, Diepchi T.

    2001-01-01

    NASA is interested in applying mobile Internet protocol (mobile-ip) technologies to its space and aeronautics programs. In particular, mobile-ip will play a major role in the Advanced Aeronautic Transportation Technology (AATT), the Weather Information Communication (WINCOMM), and the Small Aircraft Transportation System (SATS) aeronautics programs. This report presents the results of a simulation study of mobile-ip for an aeronautical network. The study was performed to determine the performance of the transmission control protocol (TCP) in a mobile-ip environment and to gain an understanding of how long delays, handoffs, and noisy channels affect mobile-ip performance.

  5. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

    Science.gov (United States)

    Prior, C; Danilāne, L; Oganesyan, V S

    2018-05-16

    We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

  6. DWPF Simulant CPC Studies For SB8

    Energy Technology Data Exchange (ETDEWEB)

    Newell, J. D.

    2013-09-25

    Prior to processing a Sludge Batch (SB) in the Defense Waste Processing Facility (DWPF), flowsheet studies using simulants are performed. Typically, the flowsheet studies are conducted based on projected composition(s). The results from the flowsheet testing are used to 1) guide decisions during sludge batch preparation, 2) serve as a preliminary evaluation of potential processing issues, and 3) provide a basis to support the Shielded Cells qualification runs performed at the Savannah River National Laboratory (SRNL). SB8 was initially projected to be a combination of the Tank 40 heel (Sludge Batch 7b), Tank 13, Tank 12, and the Tank 51 heel. In order to accelerate preparation of SB8, the decision was made to delay the oxalate-rich material from Tank 12 to a future sludge batch. SB8 simulant studies without Tank 12 were reported in a separate report.1 The data presented in this report will be useful when processing future sludge batches containing Tank 12. The wash endpoint target for SB8 was set at a significantly higher sodium concentration to allow acceptable glass compositions at the targeted waste loading. Four non-coupled tests were conducted using simulant representing Tank 40 at 110-146% of the Koopman Minimum Acid requirement. Hydrogen was generated during high acid stoichiometry (146% acid) SRAT testing up to 31% of the DWPF hydrogen limit. SME hydrogen generation reached 48% of of the DWPF limit for the high acid run. Two non-coupled tests were conducted using simulant representing Tank 51 at 110-146% of the Koopman Minimum Acid requirement. Hydrogen was generated during high acid stoichiometry SRAT testing up to 16% of the DWPF limit. SME hydrogen generation reached 49% of the DWPF limit for hydrogen in the SME for the high acid run. Simulant processing was successful using previously established antifoam addition strategy. Foaming during formic acid addition was not observed in any of the runs. Nitrite was destroyed in all runs and no N2O was detected

  7. A simulation study on garment manufacturing process

    Science.gov (United States)

    Liong, Choong-Yeun; Rahim, Nur Azreen Abdul

    2015-02-01

    Garment industry is an important industry and continues to evolve in order to meet the consumers' high demands. Therefore, elements of innovation and improvement are important. In this work, research studies were conducted at a local company in order to model the sewing process of clothes manufacturing by using simulation modeling. Clothes manufacturing at the company involves 14 main processes, which are connecting the pattern, center sewing and side neating, pockets sewing, backside-sewing, attaching the front and back, sleeves preparation, attaching the sleeves and over lock, collar preparation, collar sewing, bottomedge sewing, buttonholing sewing, removing excess thread, marking button, and button cross sewing. Those fourteen processes are operated by six tailors only. The last four sets of processes are done by a single tailor. Data collection was conducted by on site observation and the probability distribution of processing time for each of the processes is determined by using @Risk's Bestfit. Then a simulation model is developed using Arena Software based on the data collected. Animated simulation model is developed in order to facilitate understanding and verifying that the model represents the actual system. With such model, what if analysis and different scenarios of operations can be experimented with virtually. The animation and improvement models will be presented in further work.

  8. Atomistic modeling of defect evolution in Si for amorphizing and subamorphizing implants

    International Nuclear Information System (INIS)

    Lopez, Pedro; Pelaz, Lourdes; Marques, Luis A.; Santos, Ivan; Aboy, Maria; Barbolla, Juan

    2004-01-01

    Solid phase epitaxial regrowth of pre-amorphizing implants has received significant attention as a method to achieve high dopant activation with minimal diffusion at low implant temperatures and suppress channelling. Therefore, a good understanding of the amorphization and regrowth mechanisms is required in process simulators. We present an atomistic amorphization and recrystallization model that uses the interstitial-vacancy (I-V) pair as a building block to describe the amorphous phase. I-V pairs are locally characterized by the number of neighbouring I-V pairs. This feature captures the damage generation and the dynamical annealing during ion implantation, and also explains the annealing behaviour of amorphous layers and amorphous pockets

  9. Modelling radiation-induced phase changes in binary FeCu and ternary FeCuNi alloys using an artificial intelligence-based atomistic kinetic Monte Carlo approach

    International Nuclear Information System (INIS)

    Castin, N.; Malerba, L.; Bonny, G.; Pascuet, M.I.; Hou, M.

    2009-01-01

    We apply a novel atomistic kinetic Monte Carlo model, which includes local chemistry and relaxation effects when assessing the migration energy barriers of point defects, to the study of the microchemical evolution driven by vacancy diffusion in FeCu and FeCuNi alloys. These alloys are of importance for nuclear applications because Cu precipitation, enhanced by the presence of Ni, is one of the main causes of hardening and embrittlement in reactor pressure vessel steels used in existing nuclear power plants. Local chemistry and relaxation effects are introduced using artificial intelligence techniques, namely a conveniently trained artificial neural network, to calculate the migration energy barriers of vacancies as functions of the local atomic configuration. We prove, through a number of results, that the use of the neural network is fully equivalent to calculating the migration energy barriers on-the-fly, using computationally expensive methods such as nudged elastic bands with an interatomic potential. The use of the neural network makes the computational cost affordable, so that simulations of the same type as those hitherto carried out using heuristic formulas for the assessment of the energy barriers can now be performed, at the same computational cost, using more rigorously calculated barriers. This method opens the way to properly treating more complex problems, such as the case of self-interstitial cluster formation, in an atomistic kinetic Monte Carlo framework.

  10. Modelling radiation-induced phase changes in binary FeCu and ternary FeCuNi alloys using an artificial intelligence-based atomistic kinetic Monte Carlo approach

    Science.gov (United States)

    Castin, N.; Malerba, L.; Bonny, G.; Pascuet, M. I.; Hou, M.

    2009-09-01

    We apply a novel atomistic kinetic Monte Carlo model, which includes local chemistry and relaxation effects when assessing the migration energy barriers of point defects, to the study of the microchemical evolution driven by vacancy diffusion in FeCu and FeCuNi alloys. These alloys are of importance for nuclear applications because Cu precipitation, enhanced by the presence of Ni, is one of the main causes of hardening and embrittlement in reactor pressure vessel steels used in existing nuclear power plants. Local chemistry and relaxation effects are introduced using artificial intelligence techniques, namely a conveniently trained artificial neural network, to calculate the migration energy barriers of vacancies as functions of the local atomic configuration. We prove, through a number of results, that the use of the neural network is fully equivalent to calculating the migration energy barriers on-the-fly, using computationally expensive methods such as nudged elastic bands with an interatomic potential. The use of the neural network makes the computational cost affordable, so that simulations of the same type as those hitherto carried out using heuristic formulas for the assessment of the energy barriers can now be performed, at the same computational cost, using more rigorously calculated barriers. This method opens the way to properly treating more complex problems, such as the case of self-interstitial cluster formation, in an atomistic kinetic Monte Carlo framework.

  11. Modelling radiation-induced phase changes in binary FeCu and ternary FeCuNi alloys using an artificial intelligence-based atomistic kinetic Monte Carlo approach

    Energy Technology Data Exchange (ETDEWEB)

    Castin, N. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium); Physique des Solides Irradies et des Nanostructures (PSIN), Universite Libre de Bruxelles (ULB), Boulevard du Triomphe CP234, 1050 Brussels (Belgium); Malerba, L. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium)], E-mail: lmalerba@sckcen.be; Bonny, G. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium); Laboratory of Theoretical Physics, Universiteit Gent, Proeftuinstraat 86, B-9000 Gent (Belgium); Pascuet, M.I. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium); CAC-CNEA, Departamento de Materiales, Avda. Gral. Paz 1499, 1650 San Martin, Pcia. Buenos Aires (Argentina); CONICET, Avda. Rivadavia 1917, 1033 Buenos Aires (Argentina); Hou, M. [Physique des Solides Irradies et des Nanostructures (PSIN), Universite Libre de Bruxelles (ULB), Boulevard du Triomphe CP234, 1050 Brussels (Belgium)

    2009-09-15

    We apply a novel atomistic kinetic Monte Carlo model, which includes local chemistry and relaxation effects when assessing the migration energy barriers of point defects, to the study of the microchemical evolution driven by vacancy diffusion in FeCu and FeCuNi alloys. These alloys are of importance for nuclear applications because Cu precipitation, enhanced by the presence of Ni, is one of the main causes of hardening and embrittlement in reactor pressure vessel steels used in existing nuclear power plants. Local chemistry and relaxation effects are introduced using artificial intelligence techniques, namely a conveniently trained artificial neural network, to calculate the migration energy barriers of vacancies as functions of the local atomic configuration. We prove, through a number of results, that the use of the neural network is fully equivalent to calculating the migration energy barriers on-the-fly, using computationally expensive methods such as nudged elastic bands with an interatomic potential. The use of the neural network makes the computational cost affordable, so that simulations of the same type as those hitherto carried out using heuristic formulas for the assessment of the energy barriers can now be performed, at the same computational cost, using more rigorously calculated barriers. This method opens the way to properly treating more complex problems, such as the case of self-interstitial cluster formation, in an atomistic kinetic Monte Carlo framework.

  12. Simulation Studies of LCST-like Phase Transitions in Elastin-like Polypeptides (ELPs) and Conjugates of ELP with Rigid Macromolecules

    Science.gov (United States)

    Condon, Joshua; Martin, Tyler; Jayaraman, Arthi

    We use atomistic (AA) and coarse-grained (CG) molecular dynamics simulations to elucidate the thermodynamic driving forces governing lower critical solution temperature (LCST)-like phase transition exhibited by elastin-like peptides (ELPs) and conjugates of ELP with other macromolecules. In the AA simulations, we study ELP oligomers in explicit water, and mark the transition as the temperature at which they undergo a change in ``hydration'' state. While AA simulations are restricted to small systems of short ELPs and do not capture the chain aggregation observed in experiments of ELPs, they guide the phenomenological CG model development by highlighting the solvent induced polymer-polymer effective interactions with changing temperature. In the CG simulations, we capture the LCST polymer aggregation by increasing polymer-polymer effective attractive interactions in an implicit solvent. We examine the impact of conjugating a block of LCST polymer to another rigid unresponsive macromolecular block on the LCST-like transition. We find that when multiple LCST polymers are conjugated to a rigid polymer block, increased crowding of the LCST polymers shifts the onset of chain aggregation to smaller effective polymer-polymer attraction compared to the free LCST polymers. These simulation results provide guidance on the design of conjugated bio-mimetic thermoresponsive materials, and shape the fundamental understanding of the impact of polymer crowding on phase behavior in thermoresponsive LCST polymer systems.

  13. Molecular simulations of beta-amyloid protein near hydrated lipids (PECASE).

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Aidan Patrick; Han, Kunwoo (Texas A& M University, College Station, TX); Ford, David M. (Texas A& M University, College Station, TX)

    2005-12-01

    We performed molecular dynamics simulations of beta-amyloid (A{beta}) protein and A{beta} fragment(31-42) in bulk water and near hydrated lipids to study the mechanism of neurotoxicity associated with the aggregation of the protein. We constructed full atomistic models using Cerius2 and ran simulations using LAMMPS. MD simulations with different conformations and positions of the protein fragment were performed. Thermodynamic properties were compared with previous literature and the results were analyzed. Longer simulations and data analyses based on the free energy profiles along the distance between the protein and the interface are ongoing.

  14. One-dimensional plasma simulation studies

    International Nuclear Information System (INIS)

    Friberg, Ari; Virtamo, Jorma

    1976-01-01

    Some basic plasma phenomena are studied by a one-dimensional electrostatic simulation code. A brief description of the code and its application to a test problem is given. The experiments carried out include Landau damping of an excited wave, particle retardation by smoothed field and beam-plasma instability. In each case, the set-up of the experiment is described and the results are compared with theoretical predictions. In the theoretical discussions, the oscillatory behaviour found in the Landau damping experiment is explained, an explicit formula for the particle retardation rate is derived and a rudimentary picture of the beam-plasma instability in terms of quasilinear theory is given. (author)

  15. Feasible and realiable ab initio atomistic modeling for nuclear waste management

    Energy Technology Data Exchange (ETDEWEB)

    Beridze, George

    2016-07-01

    The studies in this PhD dissertation focus on finding a computationally feasible ab initio methodology which would make the reliable first principle atomistic modeling of nuclear materials possible. Here we tested the performance of the different DFT functionals and the DFT-based methods that explicitly account for the electronic correlations, such as the DFT+U approach, for prediction of structural and thermochemical properties of lanthanide- and actinide-bearing materials. In the previous studies, the value of the Hubbard U parameter, required by the DFT+U method, was often guessed or empirically derived. We applied and extensively tested the recently developed ab initio methods such as the constrained local density approximation (cLDA) and the constrained random phase approximation (cRPA), to compute the Hubbard U parameter values from first principles, thus making the DFT+U method a real it ab initio parameter free approach. Our successful benchmarking studies of the parameter-free DFT+U method, for prediction of the structures and the reaction enthalpies of actinide- and lanthanide-bearing molecular compounds and solids indicate, that the linear response method (cLDA) provides a very good, and consistent with the cRPA prediction, estimate of the Hubbard U parameter. In particular, we found that the Hubbard U parameter value, which describes the strength of the on-site Coulomb repulsion between f-electrons, depends strongly on the oxidation state of the f-element, its local bonding environment and crystalline structure of the materials, which has never been considered in such detail before. We have shown, that the applied computational approach substantially, if not dramatically, reduces the error of the predicted reaction enthalpies making the accuracy of the prediction comparable with the uncertainty of the computational unfeasible, higher order methods of quantum chemistry, and experiments. The derived methodology resulted in various, already published

  16. Feasible and realiable ab initio atomistic modeling for nuclear waste management

    International Nuclear Information System (INIS)

    Beridze, George

    2016-01-01

    The studies in this PhD dissertation focus on finding a computationally feasible ab initio methodology which would make the reliable first principle atomistic modeling of nuclear materials possible. Here we tested the performance of the different DFT functionals and the DFT-based methods that explicitly account for the electronic correlations, such as the DFT+U approach, for prediction of structural and thermochemical properties of lanthanide- and actinide-bearing materials. In the previous studies, the value of the Hubbard U parameter, required by the DFT+U method, was often guessed or empirically derived. We applied and extensively tested the recently developed ab initio methods such as the constrained local density approximation (cLDA) and the constrained random phase approximation (cRPA), to compute the Hubbard U parameter values from first principles, thus making the DFT+U method a real it ab initio parameter free approach. Our successful benchmarking studies of the parameter-free DFT+U method, for prediction of the structures and the reaction enthalpies of actinide- and lanthanide-bearing molecular compounds and solids indicate, that the linear response method (cLDA) provides a very good, and consistent with the cRPA prediction, estimate of the Hubbard U parameter. In particular, we found that the Hubbard U parameter value, which describes the strength of the on-site Coulomb repulsion between f-electrons, depends strongly on the oxidation state of the f-element, its local bonding environment and crystalline structure of the materials, which has never been considered in such detail before. We have shown, that the applied computational approach substantially, if not dramatically, reduces the error of the predicted reaction enthalpies making the accuracy of the prediction comparable with the uncertainty of the computational unfeasible, higher order methods of quantum chemistry, and experiments. The derived methodology resulted in various, already published

  17. Molecular dynamics simulation of self-driven solid state amorphization at Ni/Zr interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, M.G. [Ecole Polytechnique, 91 - Palaiseau (France). Lab. des Solides Irradies]|[Massachusetts Inst. of Tech., Cambridge (United States). Dept. of Materials Science and Engineering; Pontikis, V. [Ecole Polytechnique, 91 - Palaiseau (France). Lab. des Solides Irradies

    1996-08-01

    We present results of an atomistic simulation study of a Ni/Zr heterophase interface. Our model is consistent with experiments and shows that the semi-coherent boundary is stable at finite temperatures and mixing does not occur. The introduction of free surfaces intercepting the hetero-interface allows for composition fluctuations to take place and trigger the mixing process. Interdiffusion proceeds and produces a disordered structure which propagates into the volume at the expense of the ordered phase. (orig.)

  18. Atomistic theory of excitonic fine structure in InAs/InP nanowire quantum dot molecules

    Science.gov (United States)

    Świderski, M.; Zieliński, M.

    2017-03-01

    Nanowire quantum dots have peculiar electronic and optical properties. In this work we use atomistic tight binding to study excitonic spectra of artificial molecules formed by a double nanowire quantum dot. We demonstrate a key role of atomistic symmetry and nanowire substrate orientation rather than cylindrical shape symmetry of a nanowire and a molecule. In particular for [001 ] nanowire orientation we observe a nonvanishing bright exciton splitting for a quasimolecule formed by two cylindrical quantum dots of different heights. This effect is due to interdot coupling that effectively reduces the overall symmetry, whereas single uncoupled [001 ] quantum dots have zero fine structure splitting. We found that the same double quantum dot system grown on [111 ] nanowire reveals no excitonic fine structure for all considered quantum dot distances and individual quantum dot heights. Further we demonstrate a pronounced, by several orders of magnitude, increase of the dark exciton optical activity in a quantum dot molecule as compared to a single quantum dot. For [111 ] systems we also show spontaneous localization of single particle states in one of nominally identical quantum dots forming a molecule, which is mediated by strain and origins from the lack of the vertical inversion symmetry in [111 ] nanostructures of overall C3 v symmetry. Finally, we study lowering of symmetry due to alloy randomness that triggers nonzero excitonic fine structure and the dark exciton optical activity in realistic nanowire quantum dot molecules of intermixed composition.

  19. Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

    Directory of Open Access Journals (Sweden)

    Helgi Adalsteinsson

    2008-01-01

    Full Text Available Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-level dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.

  20. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

    Science.gov (United States)

    Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

    2017-09-14

    In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

  1. The challenges of understanding glycolipid functions: An open outlook based on molecular simulations

    DEFF Research Database (Denmark)

    Manna, M.; Rog, T.; Vattulainen, I.

    2014-01-01

    and molecular simulations can be used to shed light on the role of glycolipids in membrane structure and dynamics, receptor function, and other phenomena related to emergence of diseases such as Parkinson's. The cases we discuss highlight the challenge to understand how glycolipids function in cell membranes......, and the significant added value that one would gain by bridging molecular simulations with experiments. This article is part of a Special Issue entitled Tools to study lipid functions. (C) 2014 Elsevier B.V. All rights reserved.......Glycolipids are the most complex lipid type in cell membranes, characterized by a great diversity of different structures and functions. The underlying atomistic/molecular interactions and mechanisms associated with these functions are not well understood. Here we discuss how atomistic...

  2. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    Science.gov (United States)

    Shekhar, Adarsh

    Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

  3. DWPF simulant CPC studies for SB8

    Energy Technology Data Exchange (ETDEWEB)

    Koopman, D. C.; Zamecnik, J. R.

    2013-06-25

    The Savannah River National Laboratory (SRNL) accepted a technical task request (TTR) from Waste Solidification Engineering to perform simulant tests to support the qualification of Sludge Batch 8 (SB8) and to develop the flowsheet for SB8 in the Defense Waste Processing Facility (DWPF). These efforts pertained to the DWPF Chemical Process Cell (CPC). Separate studies were conducted for frit development and glass properties (including REDOX). The SRNL CPC effort had two primary phases divided by the decision to drop Tank 12 from the SB8 constituents. This report focuses on the second phase with SB8 compositions that do not contain the Tank 12 piece. A separate report will document the initial phase of SB8 testing that included Tank 12. The second phase of SB8 studies consisted of two sets of CPC studies. The first study involved CPC testing of an SB8 simulant for Tank 51 to support the CPC demonstration of the washed Tank 51 qualification sample in the SRNL Shielded Cells facility. SB8-Tank 51 was a high iron-low aluminum waste with fairly high mercury and moderate noble metal concentrations. Tank 51 was ultimately washed to about 1.5 M sodium which is the highest wash endpoint since SB3-Tank 51. This study included three simulations of the DWPF Sludge Receipt and Adjustment Tank (SRAT) cycle and Slurry Mix Evaporator (SME) cycle with the sludge-only flowsheet at nominal DWPF processing conditions and three different acid stoichiometries. These runs produced a set of recommendations that were used to guide the successful SRNL qualification SRAT/SME demonstration with actual Tank 51 washed waste. The second study involved five SRAT/SME runs with SB8-Tank 40 simulant. Four of the runs were designed to define the acid requirements for sludge-only processing in DWPF with respect to nitrite destruction and hydrogen generation. The fifth run was an intermediate acid stoichiometry demonstration of the coupled flowsheet for SB8. These runs produced a set of processing

  4. DWPF simulant CPC studies for SB8

    International Nuclear Information System (INIS)

    Koopman, D. C.; Zamecnik, J. R.

    2013-01-01

    The Savannah River National Laboratory (SRNL) accepted a technical task request (TTR) from Waste Solidification Engineering to perform simulant tests to support the qualification of Sludge Batch 8 (SB8) and to develop the flowsheet for SB8 in the Defense Waste Processing Facility (DWPF). These efforts pertained to the DWPF Chemical Process Cell (CPC). Separate studies were conducted for frit development and glass properties (including REDOX). The SRNL CPC effort had two primary phases divided by the decision to drop Tank 12 from the SB8 constituents. This report focuses on the second phase with SB8 compositions that do not contain the Tank 12 piece. A separate report will document the initial phase of SB8 testing that included Tank 12. The second phase of SB8 studies consisted of two sets of CPC studies. The first study involved CPC testing of an SB8 simulant for Tank 51 to support the CPC demonstration of the washed Tank 51 qualification sample in the SRNL Shielded Cells facility. SB8-Tank 51 was a high iron-low aluminum waste with fairly high mercury and moderate noble metal concentrations. Tank 51 was ultimately washed to about 1.5 M sodium which is the highest wash endpoint since SB3-Tank 51. This study included three simulations of the DWPF Sludge Receipt and Adjustment Tank (SRAT) cycle and Slurry Mix Evaporator (SME) cycle with the sludge-only flowsheet at nominal DWPF processing conditions and three different acid stoichiometries. These runs produced a set of recommendations that were used to guide the successful SRNL qualification SRAT/SME demonstration with actual Tank 51 washed waste. The second study involved five SRAT/SME runs with SB8-Tank 40 simulant. Four of the runs were designed to define the acid requirements for sludge-only processing in DWPF with respect to nitrite destruction and hydrogen generation. The fifth run was an intermediate acid stoichiometry demonstration of the coupled flowsheet for SB8. These runs produced a set of processing

  5. Protocols for atomistic modeling of water uptake into zeolite crystals for thermal storage and other applications

    International Nuclear Information System (INIS)

    Fasano, Matteo; Borri, Daniele; Chiavazzo, Eliodoro; Asinari, Pietro

    2016-01-01

    Highlights: • Numerical protocols for modeling water adsorption and infiltration into zeolite. • A priori screening of new materials for heat storage and desalination is possible. • Water uptake isotherms for bridging atomistic and engineering scales. - Abstract: We report numerical protocols for describing the water uptake process into microporous materials, with special emphasis on zeolite crystals. A better understanding and more predictive tools of the latter process are critical for a number of modern engineering applications, ranging from the optimization of loss free and compact thermal storage plants up to more efficient separation processes. Water sorption (and desorption) is indeed the key physical phenomenon to consider when designing several heat storage cycles, whereas water infiltration is to be studied when concerned with sieving through microporous materials for manufacturing selective membranes (e.g. water desalination by reverse osmosis). Despite the two quite different applications above, in this article we make an effort for illustrating a comprehensive numerical framework for predicting the engineering performances of microporous materials, based on detailed atomistic models. Thanks to the nowadays spectacular progresses in synthesizing an ever increasing number of new materials with desired properties such as zeolite with various concentrations of hydrophilic defects, we believe that the reported tools can possibly guide engineers in choosing and optimizing innovative materials for (thermal) engineering applications in the near future.

  6. Atomistic nature in band-to-band tunneling in two-dimensional silicon pn tunnel diodes

    International Nuclear Information System (INIS)

    Tabe, Michiharu; Tan, Hoang Nhat; Mizuno, Takeshi; Muruganathan, Manoharan; Anh, Le The; Mizuta, Hiroshi; Nuryadi, Ratno; Moraru, Daniel

    2016-01-01

    We study low-temperature transport properties of two-dimensional (2D) Si tunnel diodes, or Si Esaki diodes, with a lateral layout. In ordinary Si Esaki diodes, interband tunneling current is severely limited because of the law of momentum conservation, while nanoscale Esaki diodes may behave differently due to the dopants in the narrow depletion region, by atomistic effects which release such current limitation. In thin-Si lateral highly doped pn diodes, we find clear signatures of interband tunneling between 2D-subbands involving phonon assistance. More importantly, the tunneling current is sharply enhanced in a narrow voltage range by resonance via a pair of a donor- and an acceptor-atom in the pn junction region. Such atomistic behavior is recognized as a general feature showing up only in nanoscale tunnel diodes. In particular, a donor-acceptor pair with deeper ground-state energies is likely to be responsible for such a sharply enhanced current peak, tunable by external biases.

  7. Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

    Science.gov (United States)

    Lee, Hui Sun; Qi, Yifei; Im, Wonpil

    2015-03-09

    N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

  8. Prediction of irradiation induced microstructures in the AgCu model alloy using a multiscale method coupling atomistic and phase field modelling

    OpenAIRE

    Demange, Gilles; Pontikis, Vassilis; Lunéville, Laurence; Simeone, David

    2016-01-01

    In this work, a multiscale approach based on phase field was developed to simulate the microstructure's evolution under irradiation in binary systems, from atomic to microstructural scale. For that purpose, an efficient numerical scheme was developed. In the case of AgCu alloy under Krypton ions irradiation, phenomenological parameters were computed using atomistic methods, as a function of the temperature and the irradiation flux. As a result, we predicted the influence of the irradiation fl...

  9. The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

    Science.gov (United States)

    Limmer, David T.; Chandler, David

    2013-06-01

    This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys. 135, 134503 (2011), 10.1063/1.3643333 and preprint arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light.

  10. The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

    International Nuclear Information System (INIS)

    Limmer, David T.; Chandler, David

    2013-01-01

    This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys.135, 134503 (2011) and preprint http://arxiv.org/abs/arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light

  11. The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

    Energy Technology Data Exchange (ETDEWEB)

    Limmer, David T.; Chandler, David, E-mail: chandler@berkeley.edu [Department of Chemistry, University of California, Berkeley, California 94720 (United States)

    2013-06-07

    This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys.135, 134503 (2011) and preprint http://arxiv.org/abs/arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light.

  12. The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II.

    Science.gov (United States)

    Limmer, David T; Chandler, David

    2013-06-07

    This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys. 135, 134503 (2011) and preprint arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light.

  13. Atomistic-level non-equilibrium model for chemically reactive systems based on steepest-entropy-ascent quantum thermodynamics

    International Nuclear Information System (INIS)

    Li, Guanchen; Al-Abbasi, Omar; Von Spakovsky, Michael R

    2014-01-01

    This paper outlines an atomistic-level framework for modeling the non-equilibrium behavior of chemically reactive systems. The framework called steepest- entropy-ascent quantum thermodynamics (SEA-QT) is based on the paradigm of intrinsic quantum thermodynamic (IQT), which is a theory that unifies quantum mechanics and thermodynamics into a single discipline with wide applications to the study of non-equilibrium phenomena at the atomistic level. SEA-QT is a novel approach for describing the state of chemically reactive systems as well as the kinetic and dynamic features of the reaction process without any assumptions of near-equilibrium states or weak-interactions with a reservoir or bath. Entropy generation is the basis of the dissipation which takes place internal to the system and is, thus, the driving force of the chemical reaction(s). The SEA-QT non-equilibrium model is able to provide detailed information during the reaction process, providing a picture of the changes occurring in key thermodynamic properties (e.g., the instantaneous species concentrations, entropy and entropy generation, reaction coordinate, chemical affinities, reaction rate, etc). As an illustration, the SEA-QT framework is applied to an atomistic-level chemically reactive system governed by the reaction mechanism F + H 2 ↔ FH + H

  14. Heat load material studies: Simulated tokamak disruptions

    International Nuclear Information System (INIS)

    Gahl, J.M.; McDonald, J.M.; Zakharov, A.; Tserevitinov, S.; Barabash, V.; Guseva, M.

    1991-01-01

    It is clear that an improved understanding of the effects of tokamak disruptions on plasma facing component materials is needed for the ITER program. very large energy fluxes are predicted to be deposited in ITER and could be very damaging to the machine. During 1991, Sandia National Laboratories and the University of New Mexico conducted cooperative tokamak disruption simulation experiments at several Soviet facilities. These facilities were located at the Efremov Institute in Leningrad, the Kurchatov Atomic Energy Institute (Troisk and Moscow) and the Institute for Physical Chemistry of the Soviet Adademy of Sciences in Moscow. Erosion of graphite from plasma stream impact is seen to be much less than that observed with laser or electron beams with similar energy fluxes. This, along with other data obtained, seem to suggest that the ''vapor shielding'' effect is a very important phenomenon in the study of graphite erosion during tokamak disruption

  15. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  16. A new simulation model for electrochemical metal deposition

    International Nuclear Information System (INIS)

    Schmickler, W.; Poetting, K.; Mariscal, M.

    2006-01-01

    A new atomistic simulation model for electrochemical systems is presented. It combines microcanonical molecular dynamics for the electrode with stochastic dynamics for the solution, and allows the simulation of electrochemical deposition and dissolution for specific electrode potentials. As first applications the deposition of silver and platinum on Au(1 1 1) have been studied; both flat surfaces and surfaces with islands have been considered. The two systems behave quite differently: Ag on Au(1 1 1) grows layer by layer, while Pt forms a surface alloy on Au(1 1 1), which is followed by three-dimensional growth

  17. Short- and medium-range order in a Zr73Pt27 glass: Experimental and simulation studies

    International Nuclear Information System (INIS)

    Wang, S.Y.; Wang, C.Z.; Li, M.Z.; Huang, L.; Ott, R.T.; Kramer, M.J.; Sordelet, D.J.; Ho, K.M.

    2008-01-01

    The structure of a Zr 73 Pt 27 metallic glass, which forms a Zr 5 Pt 3 (Mn 5 Si 3 -type) phase having local atomic clusters with distorted icosahedral coordination during the primary crystallization, has been investigated by means of x-ray diffraction and combining ab initio molecular-dynamics (MD) and reverse Monte Carlo (RMC) simulations. The ab initio MD simulation provides an accurate description of short-range structural and chemical ordering in the glass. A three-dimensional atomistic model of 18?000 atoms for the glass structure has been generated by the RMC method utilizing both the structure factor S(k) from x-ray diffraction experiment and the partial pair-correlation functions from ab initio MD simulation. Honeycutt and Andersen index and Voronoi cell analyses, respectively, were used to characterize the short- and medium-range order in the atomistic structure models generated by ab initio MD and RMC simulations. The ab initio results show that an icosahedral type of short-range order is predominant in the glass state. Furthermore, analysis of the atomic model from the constrained RMC simulations reveals that the icosahedral-like clusters are packed in arrangements having higher-order correlations, thus establishing medium-range topological order up to two or three cluster shells.

  18. Quench Simulation Studies: Program documentation of SPQR

    CERN Document Server

    Sonnemann, F

    2001-01-01

    Quench experiments are being performed on prototypes of the superconducting magnets and busbars to determine the adequate design and protection. Many tests can only be understood correctly with the help of quench simulations that model the thermo-hydraulic and electrodynamic processes during a quench. In some cases simulations are the only method to scale the experimental results of prototype measurements to match the situation of quenching superconducting elements in the LHC. This note introduces the theoretical quench model and the use of the simulation program SPQR (Simulation Program for Quench Research), which has been developed to compute the quench process in superconducting magnets and busbars. The model approximates the heat balance equation with the finite difference method including the temperature dependence of the material parameters. SPQR allows the simulation of longitudinal quench propagation along a superconducting cable, the transverse propagation between adjacent conductors, heat transfer i...

  19. Simulation study of pixel detector charge digitization

    Science.gov (United States)

    Wang, Fuyue; Nachman, Benjamin; Sciveres, Maurice; Lawrence Berkeley National Laboratory Team

    2017-01-01

    Reconstruction of tracks from nearly overlapping particles, called Tracking in Dense Environments (TIDE), is an increasingly important component of many physics analyses at the Large Hadron Collider as signatures involving highly boosted jets are investigated. TIDE makes use of the charge distribution inside a pixel cluster to resolve tracks that share one of more of their pixel detector hits. In practice, the pixel charge is discretized using the Time-over-Threshold (ToT) technique. More charge information is better for discrimination, but more challenging for designing and operating the detector. A model of the silicon pixels has been developed in order to study the impact of the precision of the digitized charge distribution on distinguishing multi-particle clusters. The output of the GEANT4-based simulation is used to train neutral networks that predict the multiplicity and location of particles depositing energy inside one cluster of pixels. By studying the multi-particle cluster identification efficiency and position resolution, we quantify the trade-off between the number of ToT bits and low-level tracking inputs. As both ATLAS and CMS are designing upgraded detectors, this work provides guidance for the pixel module designs to meet TIDE needs. Work funded by the China Scholarship Council and the Office of High Energy Physics of the U.S. Department of Energy under contract DE-AC02-05CH11231.

  20. Deep Space Storm Shelter Simulation Study

    Science.gov (United States)

    Dugan, Kathryn; Phojanamongkolkij, Nipa; Cerro, Jeffrey; Simon, Matthew

    2015-01-01

    Missions outside of Earth's magnetic field are impeded by the presence of radiation from galactic cosmic rays and solar particle events. To overcome this issue, NASA's Advanced Exploration Systems Radiation Works Storm Shelter (RadWorks) has been studying different radiation protective habitats to shield against the onset of solar particle event radiation. These habitats have the capability of protecting occupants by utilizing available materials such as food, water, brine, human waste, trash, and non-consumables to build short-term shelters. Protection comes from building a barrier with the materials that dampens the impact of the radiation on astronauts. The goal of this study is to develop a discrete event simulation, modeling a solar particle event and the building of a protective shelter. The main hallway location within a larger habitat similar to the International Space Station (ISS) is analyzed. The outputs from this model are: 1) the total area covered on the shelter by the different materials, 2) the amount of radiation the crew members receive, and 3) the amount of time for setting up the habitat during specific points in a mission given an event occurs.

  1. Simulation study of the high intensity S-Band photoinjector

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Xiongwei; Nakajima, Kazuhisa [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan)

    2001-10-01

    In this paper, we report the results of simulation study of the high intensity S-Band photoinjector. The aim of the simulation study is to transport high bunch charge with low emittance evolution. The simulation result shows that 7nC bunch with rms emittance 22.3 {pi} mm mrad can be outputted at the exit of photoinjector. (author)

  2. Simulation study of the high intensity S-Band photoinjector

    International Nuclear Information System (INIS)

    Zhu, Xiongwei; Nakajima, Kazuhisa

    2001-01-01

    In this paper, we report the results of simulation study of the high intensity S-Band photoinjector. The aim of the simulation study is to transport high bunch charge with low emittance evolution. The simulation result shows that 7nC bunch with rms emittance 22.3 π mm mrad can be outputted at the exit of photoinjector. (author)

  3. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

    International Nuclear Information System (INIS)

    Vögele, Martin; Holm, Christian; Smiatek, Jens

    2015-01-01

    We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models

  4. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

    Energy Technology Data Exchange (ETDEWEB)

    Vögele, Martin [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany); Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M. (Germany); Holm, Christian; Smiatek, Jens, E-mail: smiatek@icp.uni-stuttgart.de [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany)

    2015-12-28

    We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.

  5. Conducting Simulation Studies in the R Programming Environment.

    Science.gov (United States)

    Hallgren, Kevin A

    2013-10-12

    Simulation studies allow researchers to answer specific questions about data analysis, statistical power, and best-practices for obtaining accurate results in empirical research. Despite the benefits that simulation research can provide, many researchers are unfamiliar with available tools for conducting their own simulation studies. The use of simulation studies need not be restricted to researchers with advanced skills in statistics and computer programming, and such methods can be implemented by researchers with a variety of abilities and interests. The present paper provides an introduction to methods used for running simulation studies using the R statistical programming environment and is written for individuals with minimal experience running simulation studies or using R. The paper describes the rationale and benefits of using simulations and introduces R functions relevant for many simulation studies. Three examples illustrate different applications for simulation studies, including (a) the use of simulations to answer a novel question about statistical analysis, (b) the use of simulations to estimate statistical power, and (c) the use of simulations to obtain confidence intervals of parameter estimates through bootstrapping. Results and fully annotated syntax from these examples are provided.

  6. Unpacking students' atomistic uderstanding of stoichiometry

    Science.gov (United States)

    Baluyut, John Ysrael

    Despite the use by instructors of particulate nature of matter (PNOM) diagrams in the general chemistry classroom, misconceptions on stoichiometry continue to prevail among students tasked with conceptual problems on concepts of limiting and excess reagents, and reaction yields. This dissertation set out to explore students' understanding of stoichiometry at the microscopic level as they solved problems that using PNOM diagrams. In particular, the study investigated how students coordinated symbolic and microscopic representations to demonstrate their knowledge of stoichiometric concepts, quantified the prevalence and explained the nature of stoichiometric misconceptions in terms of dual processing and dual coding theories, and used eye tracking to identify visual behaviors that accompanied cognitive processes students used to solve conceptual stoichiometry problems with PNOM diagrams. Interviews with students asked to draw diagrams for specific stoichiometric situations showed dual processing systems were in play. Many students were found to have used these processing systems in a heuristic-analytic sequence. Heuristics, such as the factor-label method and the least amount misconception, were often used by students to select information for further processing in an attempt to reduce the cognitive load of the subsequent analytic stage of the solution process. Diagrams drawn by students were used then to develop an instrument administered over a much larger sample of the general chemistry student population. The robustness of the dual processing theory was manifested by response patterns observed with large proportions of the student samples. These response patterns suggest that many students seemed to rely on heuristics to respond to a specific item for one of two diagrams given for the same chemical context, and then used a more analytic approach in dealing with the same item for the other diagram. It was also found that many students incorrectly treated items

  7. Learning with a strategic management simulation game: A case study

    OpenAIRE

    Loon, Mark; Evans, Jason; Kerridge, Clive

    2015-01-01

    The use of simulation games as a pedagogic method is well established though its effective use is context-driven. This study adds to the increasing growing body of empirical evidence of the effectiveness of simulation games but more importantly emphasises why by explaining the instructional design implemented reflecting best practices. This multi-method study finds evidence that student learning was enhanced through the use of simulation games, reflected in the two key themes; simulation game...

  8. Simulation studies of GST phase change alloys

    Science.gov (United States)

    Martyna, Glenn

    2008-03-01

    In order to help drive post-Moore's Law technology development, switching processes involving novel materials, in particular, GeSbTe (GST) alloys are being investigated for use in memory and eFuse applications. An anneal/quench thermal process crystallizes/amorphosizes a GST alloy which then has a low/high resistance and thereby forms a readable/writeable bit; for example, a ``one'' might be the low resistance, conducting crystalline state and a ``zero'' might be the high resistance, glassy state. There are many open questions about the precise nature of the structural transitions and the coupling to electronic structure changes. Computational and experimental studies of the effect of pressure on the GST materials were initiated in order to probe the physics behind the thermal switching process. A new pathway to reversible phase change involving pressure-induced structural metal insulator transitions was discovered. In a binary GS system, a room-temperature, direct, pressure-induced transformation from the high resistance amorphous phase to the low resistance crystalline phase was observed experimentally while the reverse process under tensile load was demonstrated via ab initio MD simulations performed on IBM's Blue Gene/L enabled by massively parallel software. Pressure induced transformations of the ternary material GST-225 (Ge2Sb2Te5) were, also, examined In the talk, the behavior of the two systems will be compared and insight into the nature of the phase change given.

  9. Plasma simulation studies using multilevel physics models

    International Nuclear Information System (INIS)

    Park, W.; Belova, E.V.; Fu, G.Y.; Tang, X.Z.; Strauss, H.R.; Sugiyama, L.E.

    1999-01-01

    The question of how to proceed toward ever more realistic plasma simulation studies using ever increasing computing power is addressed. The answer presented here is the M3D (Multilevel 3D) project, which has developed a code package with a hierarchy of physics levels that resolve increasingly complete subsets of phase-spaces and are thus increasingly more realistic. The rationale for the multilevel physics models is given. Each physics level is described and examples of its application are given. The existing physics levels are fluid models (3D configuration space), namely magnetohydrodynamic (MHD) and two-fluids; and hybrid models, namely gyrokinetic-energetic-particle/MHD (5D energetic particle phase-space), gyrokinetic-particle-ion/fluid-electron (5D ion phase-space), and full-kinetic-particle-ion/fluid-electron level (6D ion phase-space). Resolving electron phase-space (5D or 6D) remains a future project. Phase-space-fluid models are not used in favor of δf particle models. A practical and accurate nonlinear fluid closure for noncollisional plasmas seems not likely in the near future. copyright 1999 American Institute of Physics

  10. Plasma simulation studies using multilevel physics models

    International Nuclear Information System (INIS)

    Park, W.; Belova, E.V.; Fu, G.Y.

    2000-01-01

    The question of how to proceed toward ever more realistic plasma simulation studies using ever increasing computing power is addressed. The answer presented here is the M3D (Multilevel 3D) project, which has developed a code package with a hierarchy of physics levels that resolve increasingly complete subsets of phase-spaces and are thus increasingly more realistic. The rationale for the multilevel physics models is given. Each physics level is described and examples of its application are given. The existing physics levels are fluid models (3D configuration space), namely magnetohydrodynamic (MHD) and two-fluids; and hybrid models, namely gyrokinetic-energetic-particle/MHD (5D energetic particle phase-space), gyrokinetic-particle-ion/fluid-electron (5D ion phase-space), and full-kinetic-particle-ion/fluid-electron level (6D ion phase-space). Resolving electron phase-space (5D or 6D) remains a future project. Phase-space-fluid models are not used in favor of delta f particle models. A practical and accurate nonlinear fluid closure for noncollisional plasmas seems not likely in the near future

  11. Computer Simulation Studies of Trishomocubane Heptapeptide of ...

    African Journals Online (AJOL)

    NICO

    Trishomocubane, molecular dynamics, Amber, CLASICO, β-turn, α-helical. 1. Introduction .... MD simulations of Ac-Ala3-Tris-Ala3-NHMe explicitly in MEOH. 3. Results and .... worthwhile to group all conformations into clusters according to.

  12. White book Escrime. Climatic simulation studies

    International Nuclear Information System (INIS)

    Terray, L.; Braconnot, P.

    2007-01-01

    The ESCRIME project aims to manage the analysis realized on the climatic simulations on the framework of the fourth report of the GIEC (group of intergovernmental experts on the climate evolution), in particularly the simulations based on french models. This white book is constituted by 8 chapters: the global scenario, the climatic sensibility, the variation modes, the regionalization and the extremes, the hydrological cycle, the polar regions and the cryo-sphere, the carbon cycle, detection and attributions. (A.L.B.)

  13. Development of a Cardiovascular Simulator for Studying Pulse Diagnosis Mechanisms

    Directory of Open Access Journals (Sweden)

    Min Jang

    2017-01-01

    Full Text Available This research was undertaken to develop a cardiovascular simulator for use in the study of pulse diagnosis. The physical (i.e., pulse wave transmission and reflection and physiological (i.e., systolic and diastolic pressure, pulse pressure, and mean pressure characteristics of the radial pulse wave were reproduced by our simulator. The simulator consisted of an arterial component and a pulse-generating component. Computer simulation was used to simplify the arterial component while maintaining the elastic modulus and artery size. To improve the reflected wave characteristics, a palmar arch was incorporated within the simulator. The simulated radial pulse showed good agreement with clinical data.

  14. Deductive multiscale simulation using order parameters

    Science.gov (United States)

    Ortoleva, Peter J.

    2017-05-16

    Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

  15. A simulation study of CS2 solutions in two related ionic liquids with dications and monocations

    Science.gov (United States)

    Lynden-Bell, R. M.; Quitevis, E. L.

    2018-05-01

    Atomistic simulations of solutions of CS2 in an ionic liquid, [C8(C1im)2 ] [NTf2]2, with a divalent cation and in the corresponding ionic liquid with a monovalent cation, [C4C1im][NTf2], were carried out. The low-frequency librational density of states of the CS2 was of particular interest in view of recent optical heterodyne-detected Raman-induced Kerr effect spectroscopy (OHD-RIKES). Compared to the monocation ionic liquid, the maximum shifts to higher frequencies in the dication ionic liquid under ambient conditions, but was found to be significantly pressure-dependent. CS2 molecules lie above and below the plane of the imidazolium rings and found to be close to the butyl tails of the monocation. The diffusion rates and embedding energies of solvent ions and CS2 in the two ionic liquids were measured.

  16. Grain-Boundary Resistance in Copper Interconnects: From an Atomistic Model to a Neural Network

    Science.gov (United States)

    Valencia, Daniel; Wilson, Evan; Jiang, Zhengping; Valencia-Zapata, Gustavo A.; Wang, Kuang-Chung; Klimeck, Gerhard; Povolotskyi, Michael

    2018-04-01

    Orientation effects on the specific resistance of copper grain boundaries are studied systematically with two different atomistic tight-binding methods. A methodology is developed to model the specific resistance of grain boundaries in the ballistic limit using the embedded atom model, tight- binding methods, and nonequilibrium Green's functions. The methodology is validated against first-principles calculations for thin films with a single coincident grain boundary, with 6.4% deviation in the specific resistance. A statistical ensemble of 600 large, random structures with grains is studied. For structures with three grains, it is found that the distribution of specific resistances is close to normal. Finally, a compact model for grain-boundary-specific resistance is constructed based on a neural network.

  17. Temperature Dependence of the OH- + CH3I Reaction Kinetics. Experimental and Simulation Studies and Atomic-Level Dynamics (Postprint)

    Science.gov (United States)

    2013-11-25

    reaction time, the core of the flow was sampled through a small orifice in a rounded nose cone, while the bulk of the gas was pumped by an oil free...with direct dynamics simulations,6’ 10’ 11’ 13- 17 have provided an atomistic understanding of the dynamics of gas phase x- + CH3Y reactions. In...OH- was mass selected using a quadrupole mass filter, injected into the flow tube through a Venturi inlet, and carried downstream by a helium

  18. A prospective study to determine the need for physical simulation following virtual simulation

    International Nuclear Information System (INIS)

    Valicenti, R.K.; Waterman, F.M.; Corn, B.W.; Sweet, J.; Curran, W.J.

    1996-01-01

    Purpose: Virtual simulation is CT based planning utilizing computed digitally reconstructed radiographs (DRRs) in a manner similar to conventional fluoroscopic simulation. However, conventional or physical simulation is still widely used to assure precise implementation of the devised plan. To evaluate the need for performing physical simulation, we prospectively studied patients undergoing virtual simulation who either had or did not have a subsequent physical simulation. Materials and Methods: From July, 1995 to February, 1996, 48 patients underwent conformal 4-field radiation therapy for prostate cancer using a commercial grade spiral CT simulator. All patients were immobilized in a foam body cast and positioned by using a fiducial laser marking system. Following prostate and seminal vesicle definition on a slice-by-slice basis, virtual simulation was performed. The isocenter defined by this process was marked on both the patient and the immobilization device before leaving the CT simulator room. The isocenter position of the devised plan was evaluated by three verification methods: physical simulation, first day treatment port filming, and port filming immediately following physical simulation. Simulator radiographs and port films were compared against DRRs for x, y, and z deviations of the isocenter. These deviations were used as a measure of the implementation precision achieved by each verification method. Results: Thirty-seven patients underwent physical simulation and first day port filming. Eleven had first day treatment verification films only and never had a physical simulation. A total of 79 simulator radiographs and 126 first day treatment port films were reviewed. The tabulation of all deviations is as follows: There was significantly more setup error (≥ 5 mm) observed when the devised treatment was implemented in the treatment room as opposed to the physical simulator. The physical simulator did not lead to a significant reduction in setup error

  19. Simulation studies on high-gradient experiments

    International Nuclear Information System (INIS)

    Yamaguchi, S.

    1992-12-01

    Computer simulation of the characteristics of the dark current emitted from a 0.6 m long S-band accelerating structure has been made. The energy spectra and the dependence of the dark current on the structure length were simulated. By adjusting the secondary electron emission (SEE) coefficients, the simulated energy spectra qualitatively reproduced the observed ones. It was shown that the dark current increases exponentially with the structure length. The measured value of the multiplication factor of the dark current per unit cell can be explained if the SEE coefficient is set to 1.2. The critical gradient for dark current capture E cri has been calculated for two structures of 180 cells. They are E cri [MV/m] = 13.1 f and 8.75 f for a/λ = 0.089 and 0.16, respectively, where f is the frequency in GHz, a the iris diameter and λ the wave length

  20. Conducting Simulation Studies in the R Programming Environment

    Directory of Open Access Journals (Sweden)

    Kevin A. Hallgren

    2013-10-01

    Full Text Available Simulation studies allow researchers to answer specific questions about data analysis, statistical power, and best-practices for obtainingaccurate results in empirical research. Despite the benefits that simulation research can provide, many researchers are unfamiliar with available tools for conducting their own simulation studies. The use of simulation studies need not be restricted toresearchers with advanced skills in statistics and computer programming, and such methods can be implemented by researchers with a variety of abilities and interests. The present paper provides an introduction to methods used for running simulationstudies using the R statistical programming environment and is written for individuals with minimal experience running simulation studies or using R. The paper describes the rationale and benefits of using simulations and introduces R functions relevant for many simulation studies. Three examples illustrate different applications for simulation studies, including (a the use of simulations to answer a novel question about statistical analysis, (b the use of simulations to estimate statistical power, and (c the use of simulations to obtain confidence intervals of parameter estimates throughbootstrapping. Results and fully annotated syntax from these examples are provided.

  1. Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

    International Nuclear Information System (INIS)

    Stimson, Lorna M.

    2003-01-01

    Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a single dendrimer molecule in the gas phase at the atomistic level, semi-atomistic molecular dynamics of a single molecule in liquid crystalline solvents and a coarse-grained molecular dynamics study of the dendrimer in the bulk. The coarse-grained model has been developed and parameterized using the results of the atomistic and semi-atomistic work. The single molecule studies showed that the liquid crystalline dendrimer was able to change its structure by conformational changes in the flexible chains that link the mesogenic groups to the core. Structural change was seen under the application of a mean field ordering potential in the gas phase, and in the presence of liquid crystalline solvents. No liquid crystalline phases were observed for the bulk phase studies of the coarse-grained model. However, when the length of the mesogenic units was increased there was some evidence for microphase separation in these systems. (author)

  2. A study on the thermal expansion characteristics of simulated spent fuel and simulated DUPIC fuel

    International Nuclear Information System (INIS)

    Kang, Kweon Ho; Ryu, H. J.; Kim, H. S.; Song, K. C.; Yang, M. S.

    2001-10-01

    Thermal expansions of simulated spent PWR fuel and simulated DUPIC fuel were studied using a dilatometer in the temperature range from 298 to 1900 K. The densities of simulated spent PWR fuel and simulated DUPIC fuel used in the measurement were 10.28 g/cm3 (95.35 % of TD) and 10.26 g/cm3 (95.14 % of TD), respectively. Their linear thermal expansions of simulated fuels are higher than that of UO2, and the difference between these fuels and UO2 increases progressively as temperature increases. However, the difference between simulated spent PWR fuel and simulated DUPIC fuel can hardly be observed. For the temperature range from 298 to 1900 K, the values of the average linear thermal expansion coefficients for simulated spent PWR fuel and simulated DUPIC fuel are 1.391 10-5 and 1.393 10-5 K-1, respectively. As temperature increases to 1900 K, the relative densities of simulated spent PWR fuel and simulated DUPIC fuel decrease to 93.81 and 93.76 % of initial densities at 298 K, respectively

  3. An atomistic analysis of the interface mobility in a massive transformation

    International Nuclear Information System (INIS)

    Bos, C.; Sommer, F.; Mittemeijer, E.J.

    2005-01-01

    A new multi-lattice kinetic Monte Carlo method has been used for an atomistic study on the interpretation of the interface mobility parameter for a massive face-centred cubic (fcc) to body-centred cubic (bcc) transformation in a single element system. For lateral growth of bcc in a system with an fcc(111)//bcc(110) and fcc[112-bar ]//bcc[001-bar ] interface orientation the overall activation energy for the interface mobility parameter is governed by energetically unfavourable atomic jumps. The atoms on the fcc lattice often cannot jump directly to bcc lattice sites because neighbouring atoms block the empty bcc sites. By single unfavourable jumps and by groups of unfavourable jumps a path from fcc to bcc is created. The necessity of these unfavourable jumps leads to an overall activation energy considerably larger than the activation energy barrier for a single atomic jump

  4. An atomistic vision of the Mass Action Law: Prediction of carbon/oxygen defects in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Brenet, G.; Timerkaeva, D.; Caliste, D.; Pochet, P. [CEA, INAC-SP2M, Atomistic Simulation Laboratory, F-38000 Grenoble (France); Univ. Grenoble Alpes, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Sgourou, E. N.; Londos, C. A. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece)

    2015-09-28

    We introduce an atomistic description of the kinetic Mass Action Law to predict concentrations of defects and complexes. We demonstrate in this paper that this approach accurately predicts carbon/oxygen related defect concentrations in silicon upon annealing. The model requires binding and migration energies of the impurities and complexes, here obtained from density functional theory (DFT) calculations. Vacancy-oxygen complex kinetics are studied as a model system during both isochronal and isothermal annealing. Results are in good agreement with experimental data, confirming the success of the methodology. More importantly, it gives access to the sequence of chain reactions by which oxygen and carbon related complexes are created in silicon. Beside the case of silicon, the understanding of such intricate reactions is a key to develop point defect engineering strategies to control defects and thus semiconductors properties.

  5. Phonon dispersion and thermal conductivity of nanocrystal superlattices using three-dimensional atomistic models

    International Nuclear Information System (INIS)

    Zanjani, Mehdi B.; Lukes, Jennifer R.

    2014-01-01

    A computational study of thermal conductivity and phonon dispersion of gold nanocrystal superlattices is presented. Phonon dispersion curves, reported here for the first time from combined molecular dynamics and lattice dynamics calculations, show multiple phononic band gaps and consist of many more dispersion branches than simple atomic crystals. Fully atomistic three dimensional molecular dynamics calculations of thermal conductivity using the Green Kubo method are also performed for the first time on these materials. Thermal conductivity is observed to increase for increasing nanocrystal core size and decrease for increasing surface ligand density. Our calculations predict values in the range 0.1–1 W/m K that are consistent with reported experimental results

  6. Making coarse grained polymer simulations quantitatively predictive for statics and dynamics

    Science.gov (United States)

    Kremer, Kurt

    2010-03-01

    By combining input from short simulation runs of rather small systems with all atomistic details together with properly adapted coarse grained models we are able quantitatively predict static and especially dynamical properties of both pure polymer melts of long fully entangled but also of systems with low molecular weight additives. Comparisons to rather different experiments such as diffusion constant measurements or NMR relaxation experiments show a remarkable quantitative agreement without any adjustable parameter. Reintroduction of chemical details into the coarse grained trajectories allows the study of long time trajectories in all atomistic detail providing the opportunity for rather different means of data analysis. References: V. Harmandaris, K. Kremer, Macromolecules, in press (2009) V. Harmandaris et al, Macromolecules, 40, 7026 (2007) B. Hess, S. Leon, N. van der Vegt, K. Kremer, Soft Matter 2, 409 (2006) D. Fritz et al, Soft Matter 5, 4556 (2009)

  7. Simulated x-ray scattering of protein solutions using explicit-solvent models

    International Nuclear Information System (INIS)

    Park, Sanghyun; Bardhan, Jaydeep P.; Makowski, Lee; Roux, Benoit

    2009-01-01

    X-ray solution scattering shows new promise for the study of protein structures, complementing crystallography and nuclear magnetic resonance. In order to realize the full potential of solution scattering, it is necessary to not only improve experimental techniques but also develop accurate and efficient computational schemes to relate atomistic models to measurements. Previous computational methods, based on continuum models of water, have been unable to calculate scattering patterns accurately, especially in the wide-angle regime which contains most of the information on the secondary, tertiary, and quaternary structures. Here we present a novel formulation based on the atomistic description of water, in which scattering patterns are calculated from atomic coordinates of protein and water. Without any empirical adjustments, this method produces scattering patterns of unprecedented accuracy in the length scale between 5 and 100 A, as we demonstrate by comparing simulated and observed scattering patterns for myoglobin and lysozyme.

  8. A molecular dynamics simulation study of chloroform

    Science.gov (United States)

    Tironi, Ilario G.; van Gunsteren, Wilfred F.

    Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

  9. Computer Simulation Studies of Trishomocubane Heptapeptide of ...

    African Journals Online (AJOL)

    As part of an extension on the cage peptide chemistry, the present work involves an assessment of the conformational profile of trishomocubane heptapeptide of the type Ac-Ala3-Tris-Ala3-NHMe using molecular dynamics (MD) simulations. All MD protocols were explored within the framework of a molecular mechanics ...

  10. Assessing phylogenetic accuracy : a simulation study

    NARCIS (Netherlands)

    Heijerman, T.

    1995-01-01

    A simulation model of phylogeny, called GENESIS, was developed to evaluate and to estimate the qualities of various numerical taxonomic procedures. The model produces sets of imaginary species with known character state distributions and with known phylogenies. The model can be made to

  11. Anharmonic phonon-phonon scattering modeling of three-dimensional atomistic transport: An efficient quantum treatment

    Science.gov (United States)

    Lee, Y.; Bescond, M.; Logoteta, D.; Cavassilas, N.; Lannoo, M.; Luisier, M.

    2018-05-01

    We propose an efficient method to quantum mechanically treat anharmonic interactions in the atomistic nonequilibrium Green's function simulation of phonon transport. We demonstrate that the so-called lowest-order approximation, implemented through a rescaling technique and analytically continued by means of the Padé approximants, can be used to accurately model third-order anharmonic effects. Although the paper focuses on a specific self-energy, the method is applicable to a very wide class of physical interactions. We apply this approach to the simulation of anharmonic phonon transport in realistic Si and Ge nanowires with uniform or discontinuous cross sections. The effect of increasing the temperature above 300 K is also investigated. In all the considered cases, we are able to obtain a good agreement with the routinely adopted self-consistent Born approximation, at a remarkably lower computational cost. In the more complicated case of high temperatures (≫300 K), we find that the first-order Richardson extrapolation applied to the sequence of the Padé approximants N -1 /N results in a significant acceleration of the convergence.

  12. Spontaneous Formation of A Nanotube From A Square Ag Nanowire: An Atomistic View

    Science.gov (United States)

    Konuk Onat, Mine; Durukanoglu, Sondan

    2012-02-01

    We have performed molecular static calculations to investigate the recently observed phenomenon of the spontaneous formation of a nanotube from a regular, square Ag nanowire[1]. In the simulations, atoms are allowed to interact via the model potential obtained from the modified embedded atom method. Our simulations predict that this particular type of structural phase transformation is controlled by the nature of applied strain, length of the wire and initial cross-sectional shape. For such a perfect structural transformation, the axially oriented fcc nanowire needs (1) to be formed by stacking A and B layers of an fcc crystal, both possessing the geometry of two interpenetrating one-lattice-parameter-wide squares, containing four atoms each, (2) to have an optimum length of eight layers, and (3) to be exposed to a combination of low and high stress along the length direction. The results further offer insights into atomistic nature of this specific structural transformation into a nanotube with the smallest possible cross-section. [1] M.J. Lagos et al., Nature Nanotech. 4, 149 (2009).

  13. Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting.

    Science.gov (United States)

    Goel, Saurav; Luo, Xichun; Reuben, Robert L; Rashid, Waleed Bin

    2011-11-11

    Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear.

  14. Quantum dynamical simulations of local field enhancement in metal nanoparticles.

    Science.gov (United States)

    Negre, Christian F A; Perassi, Eduardo M; Coronado, Eduardo A; Sánchez, Cristián G

    2013-03-27

    Field enhancements (Γ) around small Ag nanoparticles (NPs) are calculated using a quantum dynamical simulation formalism and the results are compared with electrodynamic simulations using the discrete dipole approximation (DDA) in order to address the important issue of the intrinsic atomistic structure of NPs. Quite remarkably, in both quantum and classical approaches the highest values of Γ are located in the same regions around single NPs. However, by introducing a complete atomistic description of the metallic NPs in optical simulations, a different pattern of the Γ distribution is obtained. Knowing the correct pattern of the Γ distribution around NPs is crucial for understanding the spectroscopic features of molecules inside hot spots. The enhancement produced by surface plasmon coupling is studied by using both approaches in NP dimers for different inter-particle distances. The results show that the trend of the variation of Γ versus inter-particle distance is different for classical and quantum simulations. This difference is explained in terms of a charge transfer mechanism that cannot be obtained with classical electrodynamics. Finally, time dependent distribution of the enhancement factor is simulated by introducing a time dependent field perturbation into the Hamiltonian, allowing an assessment of the localized surface plasmon resonance quantum dynamics.

  15. Partnering to Establish and Study Simulation in International Nursing Education.

    Science.gov (United States)

    Garner, Shelby L; Killingsworth, Erin; Raj, Leena

    The purpose of this article was to describe an international partnership to establish and study simulation in India. A pilot study was performed to determine interrater reliability among faculty new to simulation when evaluating nursing student competency performance. Interrater reliability was below the ideal agreement level. Findings in this study underscore the need to obtain baseline interrater reliability data before integrating competency evaluation into a simulation program.

  16. Emergence of linear elasticity from the atomistic description of matter

    Energy Technology Data Exchange (ETDEWEB)

    Cakir, Abdullah, E-mail: acakir@ntu.edu.sg [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Pica Ciamarra, Massimo [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Dipartimento di Scienze Fisiche, CNR–SPIN, Università di Napoli Federico II, I-80126 Napoli (Italy)

    2016-08-07

    We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

  17. Diffusion in energy materials: Governing dynamics from atomistic modelling

    Science.gov (United States)

    Parfitt, D.; Kordatos, A.; Filippatos, P. P.; Chroneos, A.

    2017-09-01

    Understanding diffusion in energy materials is critical to optimising the performance of solid oxide fuel cells (SOFCs) and batteries both of which are of great technological interest as they offer high efficiency for cleaner energy conversion and storage. In the present review, we highlight the insights offered by atomistic modelling of the ionic diffusion mechanisms in SOFCs and batteries and how the growing predictive capability of high-throughput modelling, together with our new ability to control compositions and microstructures, will produce advanced materials that are designed rather than chosen for a given application. The first part of the review focuses on the oxygen diffusion mechanisms in cathode and electrolyte materials for SOFCs and in particular, doped ceria and perovskite-related phases with anisotropic structures. The second part focuses on disordered oxides and two-dimensional materials as these are very promising systems for battery applications.

  18. Emergence of linear elasticity from the atomistic description of matter

    International Nuclear Information System (INIS)

    Cakir, Abdullah; Pica Ciamarra, Massimo

    2016-01-01

    We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

  19. Atomistic modeling of ion beam induced amorphization in silicon

    International Nuclear Information System (INIS)

    Pelaz, Lourdes; Marques, Luis A.; Lopez, Pedro; Santos, Ivan; Aboy, Maria; Barbolla, Juan

    2005-01-01

    Ion beam induced amorphization in Si has attracted significant interest since the beginning of the use of ion implantation for the fabrication of Si devices. Nowadays, a renewed interest in the modeling of amorphiza