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.

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)

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.

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...

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.

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.

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.

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

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.

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...

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.

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.

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.

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.

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.

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

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.

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

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.

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

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

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.

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...

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

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.

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

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

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

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/

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...

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,

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,

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.

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...

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.

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.

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.

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

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;

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

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

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.

FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

KAUST Repository

Harmandaris, Vagelis

2017-10-03

The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

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

Thermodynamic and Mechanical Properties of Epon 862 With Curing Agent Detda by Molecular Simulation

National Research Council Canada - National Science Library

Tack, Jeremy L

2006-01-01

Fully atomistic molecular dynamics (MD) simulations were used to predict the properties of EPON 862 cross-linked with curing agent DETDA, a potentially useful epoxy resin for future applications of nanocomposites...

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...

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...

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.

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

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.

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

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.

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.

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...

A Long-Range Electric Field Solver for Molecular Dynamics Based on Atomistic-to-Continuum Modeling.

Science.gov (United States)

Templeton, Jeremy A; Jones, Reese E; Lee, Jonathan W; Zimmerman, Jonathan A; Wong, Bryan M

2011-06-14

Understanding charge transport processes at a molecular level is currently hindered by a lack of appropriate models for incorporating nonperiodic, anisotropic electric fields in molecular dynamics (MD) simulations. In this work, we develop a model for including electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and the algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. Our model represents the electric potential on a FE mesh satisfying a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagate to each atom through modified forces. The method is verified using simulations where analytical solutions are known or comparisons can be made to existing techniques. In addition, a calculation of a salt water solution in a silicon nanochannel is performed to demonstrate the method in a target scientific application in which ions are attracted to charged surfaces in the presence of electric fields and interfering media.

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.

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...

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....

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.

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.

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.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

Science.gov (United States)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of

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

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.

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

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.

Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

2010-01-01

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

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

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.

Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts

Directory of Open Access Journals (Sweden)

Kazuaki Z. Takahashi

2017-01-01

Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

Science.gov (United States)

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

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

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....

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.

Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

Science.gov (United States)

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

2006-01-01

A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

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.

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.

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

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.

Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective.

Science.gov (United States)

Moore, Timothy C; Iacovella, Christopher R; Leonhard, Anne C; Bunge, Annette L; McCabe, Clare

2018-03-29

The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships. However, most simulation studies of SC lipids have focused on preassembled bilayer configurations, which, owing to the slow dynamics of the lipids, may influence the final structure and hence the calculated properties. Self-assembled structures would avoid this dependence on the initial configuration, however, the size and length scales involved make self-assembly impractical to study with atomistic models. Here, we report on the development of coarse-grained models of SC lipids designed to study self-assembly. Building on previous work, we present the interactions between the headgroups of ceramide and free fatty acid developed using the multistate iterative Boltzmann inversion method. Validation of the new interactions is performed with simulations of preassembled bilayers and good agreement between the atomistic and coarse-grained models is found for structural properties. The self-assembly of mixtures of ceramide and free fatty acid is investigated and both bilayer and multilayer structures are found to form. This work therefore represents a necessary step in studying SC lipid systems on multiple time and length scales. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

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

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...

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

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.

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.

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

Multiresolution molecular mechanics: Implementation and efficiency

Energy Technology Data Exchange (ETDEWEB)

Biyikli, Emre; To, Albert C., E-mail: albertto@pitt.edu

2017-01-01

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3–8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

Science.gov (United States)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2012-10-01

Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

Science.gov (United States)

Stalter, S.; Yelash, L.; Emamy, N.; Statt, A.; Hanke, M.; Lukáčová-Medvid'ová, M.; Virnau, P.

2018-03-01

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations.

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...

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

An atomistic fingerprint algorithm for learning ab initio molecular force fields

Science.gov (United States)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

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.

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...

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).

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

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.

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...

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

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Science.gov (United States)

2018-01-01

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

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

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...

Computational modeling of the behavior of nuclear materials (2). Molecular simulations for nuclear materials. Current situation and future perspective

International Nuclear Information System (INIS)

Okita, Taira; Itakura, Mitsuhiro

2017-01-01

Molecular simulations for nuclear materials aim to reproduce atomistic-scale phenomena induced by irradiation and infer the change in material properties. In the present work, recent progress in this field is presented. In particular, the following three topics are explained: (1) Quantification of lattice defects formation process induced by fast neutron collision. (2) Identification of dislocation-channeling mechanism induced by interactions between defect clusters and dislocations. (3) Modeling of the three dimensional movement of defect clusters using molecular dynamics and kinetic Monte Carlo simulations. (author)

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.

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.

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.

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

DEFF Research Database (Denmark)

Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

2008-01-01

. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

Enhancing protein adsorption simulations by using accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Christian Mücksch

Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

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.

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

Molecular Dynamics Simulation of High Density DNA Arrays

Directory of Open Access Journals (Sweden)

Rudolf Podgornik

2018-01-01

Full Text Available Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and

Physically representative atomistic modeling of atomic-scale friction

Science.gov (United States)

Dong, Yalin

interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

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

Molecular dynamics simulations of liquid crystals at interfaces

International Nuclear Information System (INIS)

Shield, Mark

2002-01-01

Molecular dynamics simulations of an atomistic model of 4-n-octyl-4'-cyanobiphenyl (8CB) were performed for thin films of 8CB on solid substrates (a pseudopotential representation of the molecular topography of the (100) crystal surface of polyethylene (PE), a highly ordered atomistic model of a pseudo-crystalline PE surface and an atomistic model of a partially orientated film of PE), free standing thin films of 8CB and 8CB droplets in a hexagonal pit. The systems showed strong homeotropic anchoring at the free volume interface and planar anchoring at the solid interface whose strength was dependent upon the surface present. The free volume interface also demonstrated weak signs of smectic wetting of the bulk. Simulations of thin free standing films of liquid crystals showed the ordered nature of the liquid crystals at the two free volume interfaces can be adopted by the region of liquid crystal molecules between the homeotropic layer at each interface only if there is a certain number of liquid crystal molecules present. The perpendicular anchoring imposed by the free volume interface and the solid interface for the thin films on the solid substrates resulted in some evidence for the liquid crystal director undergoing a continual rotation at low temperatures and a definite discontinuous change at higher temperatures. The liquid crystal alignment imparted by these substrates was found to depend upon the topography of the surface and not the direction of the polymer chains in the substrate. The liquid crystal was found to order via an epitaxy-like mechanism. The perpendicular anchoring results in a drop in the order - disorder transition temperature for the molecules in the region between the homeotropic layer at the free volume interface and the planar layers at the solid interface. An increase in the size of this region does not alter the transition temperature. The shape of the liquid crystal molecules is dependent upon the degree of order and thus the nematic

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

Energy Technology Data Exchange (ETDEWEB)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt (Germany)

2014-12-14

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

International Nuclear Information System (INIS)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der

2014-01-01

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics

Molecular dynamics simulation of a binary mixture near the lower critical point

Energy Technology Data Exchange (ETDEWEB)

Pousaneh, Faezeh; Edholm, Olle, E-mail: oed@kth.se [Theoretical Biological Physics, Department of Theoretical Physics, Royal Institute of Technology (KTH), AlbaNova University Center, SE-106 91 Stockholm (Sweden); Maciołek, Anna [Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw (Poland); Max-Planck-Institut für Intelligente Systeme, Heisenbergstrasse 3, D-70569 Stuttgart (Germany)

2016-07-07

2,6-lutidine molecules mix with water at high and low temperatures but in a wide intermediate temperature range a 2,6-lutidine/water mixture exhibits a miscibility gap. We constructed and validated an atomistic model for 2,6-lutidine and performed molecular dynamics simulations of 2,6-lutidine/water mixture at different temperatures. We determined the part of demixing curve with the lower critical point. The lower critical point extracted from our data is located close to the experimental one. The estimates for critical exponents obtained from our simulations are in a good agreement with the values corresponding to the 3D Ising universality class.

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.

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.

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.

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.

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.

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.

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

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....

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.

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

Continuum simulations of water flow past fullerene molecules

DEFF Research Database (Denmark)

Popadic, A.; Praprotnik, M.; Koumoutsakos, P.

2015-01-01

We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow...

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.

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)

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.

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.

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

Constraint methods that accelerate free-energy simulations of biomolecules.

Science.gov (United States)

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

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.

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.

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)

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.

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.

Long-range force and moment calculations in multiresolution simulations of molecular systems

International Nuclear Information System (INIS)

Poursina, Mohammad; Anderson, Kurt S.

2012-01-01

Multiresolution simulations of molecular systems such as DNAs, RNAs, and proteins are implemented using models with different resolutions ranging from a fully atomistic model to coarse-grained molecules, or even to continuum level system descriptions. For such simulations, pairwise force calculation is a serious bottleneck which can impose a prohibitive amount of computational load on the simulation if not performed wisely. Herein, we approximate the resultant force due to long-range particle-body and body-body interactions applicable to multiresolution simulations. Since the resultant force does not necessarily act through the center of mass of the body, it creates a moment about the mass center. Although this potentially important torque is neglected in many coarse-grained models which only use particle dynamics to formulate the dynamics of the system, it should be calculated and used when coarse-grained simulations are performed in a multibody scheme. Herein, the approximation for this moment due to far-field particle-body and body-body interactions is also provided.

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.

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.)

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.

Molecular dynamics simulation of radiation damage cascades in diamond

Energy Technology Data Exchange (ETDEWEB)

Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)

2015-06-28

Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

Understanding the mechanisms of amorphous creep through molecular simulation.

Science.gov (United States)

Cao, Penghui; Short, Michael P; Yip, Sidney

2017-12-26

Molecular processes of creep in metallic glass thin films are simulated at experimental timescales using a metadynamics-based atomistic method. Space-time evolutions of the atomic strains and nonaffine atom displacements are analyzed to reveal details of the atomic-level deformation and flow processes of amorphous creep in response to stress and thermal activations. From the simulation results, resolved spatially on the nanoscale and temporally over time increments of fractions of a second, we derive a mechanistic explanation of the well-known variation of creep rate with stress. We also construct a deformation map delineating the predominant regimes of diffusional creep at low stress and high temperature and deformational creep at high stress. Our findings validate the relevance of two original models of the mechanisms of amorphous plasticity: one focusing on atomic diffusion via free volume and the other focusing on stress-induced shear deformation. These processes are found to be nonlinearly coupled through dynamically heterogeneous fluctuations that characterize the slow dynamics of systems out of equilibrium.

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.

Solubility of gases and solvents in silicon polymers: molecular simulation and equation of state modeling

DEFF Research Database (Denmark)

Economou, Ioannis; Makrodimitri, Zoi A.; Kontogeorgis, Georgios

2007-01-01

of gas and solvent solubilities using the test particle insertion method of Widom. Polymer chains are modelled using recently developed realistic atomistic force fields. Calculations are performed at various temperatures and ambient pressure. A crossover in the temperature dependence of solubility......) and also the phase equilibria of these mixtures over a wide composition range. In all cases, the agreement between model predictions/correlations and literature experimental data, when available, is excellent.......The solubility of n-alkanes, perfluoroalkanes, noble gases and light gases in four elastomer polymers containing silicon is examined based on molecular simulation and macroscopic equation of state modelling. Polymer melt samples generated from molecular dynamics ( MD) are used for the calculation...

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

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

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)

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.

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.

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.

Effect of gas adsorption on acoustic wave propagation in MFI zeolite membrane materials: experiment and molecular simulation.

Science.gov (United States)

Manga, Etoungh D; Blasco, Hugues; Da-Costa, Philippe; Drobek, Martin; Ayral, André; Le Clezio, Emmanuel; Despaux, Gilles; Coasne, Benoit; Julbe, Anne

2014-09-02

The present study reports on the development of a characterization method of porous membrane materials which consists of considering their acoustic properties upon gas adsorption. Using acoustic microscopy experiments and atomistic molecular simulations for helium adsorbed in a silicalite-1 zeolite membrane layer, we showed that acoustic wave propagation could be used, in principle, for controlling the membranes operando. Molecular simulations, which were found to fit experimental data, showed that the compressional modulus of the composite system consisting of silicalite-1 with adsorbed He increases linearly with the He adsorbed amount while its shear modulus remains constant in a large range of applied pressures. These results suggest that the longitudinal and Rayleigh wave velocities (VL and VR) depend on the He adsorbed amount whereas the transverse wave velocity VT remains constant.

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.

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.

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.

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.

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.

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.

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.

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

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

Science.gov (United States)

Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

2016-06-22

The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

2015-12-07

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

International Nuclear Information System (INIS)

Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

2015-01-01

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level

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

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

Science.gov (United States)

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Multiscale Simulation of Thermo-mechancial Processes in Irradiated Fission-reactor Materials.

Energy Technology Data Exchange (ETDEWEB)

Simon R. Phillpot

2012-06-08

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{sub 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{sub 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.

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

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}.

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

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

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

Simulating the Physical World

Science.gov (United States)

Berendsen, Herman J. C.

2004-06-01

The simulation of physical systems requires a simplified, hierarchical approach which models each level from the atomistic to the macroscopic scale. From quantum mechanics to fluid dynamics, this book systematically treats the broad scope of computer modeling and simulations, describing the fundamental theory behind each level of approximation. Berendsen evaluates each stage in relation to its applications giving the reader insight into the possibilities and limitations of the models. Practical guidance for applications and sample programs in Python are provided. With a strong emphasis on molecular models in chemistry and biochemistry, this book will be suitable for advanced undergraduate and graduate courses on molecular modeling and simulation within physics, biophysics, physical chemistry and materials science. It will also be a useful reference to all those working in the field. Additional resources for this title including solutions for instructors and programs are available online at www.cambridge.org/9780521835275. The first book to cover the wide range of modeling and simulations, from atomistic to the macroscopic scale, in a systematic fashion Providing a wealth of background material, it does not assume advanced knowledge and is eminently suitable for course use Contains practical examples and sample programs in Python

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....

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.

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)

Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A Persistent-Embryo Approach

Science.gov (United States)

Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I.; Wang, Cai-Zhuang; Ho, Kai-Ming

2018-02-01

The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B 2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.

Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A Persistent-Embryo Approach.

Science.gov (United States)

Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I; Wang, Cai-Zhuang; Ho, Kai-Ming

2018-02-23

The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.

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...

Molecular dynamics simulation of edge dislocation piled at cuboidal precipitate in Ni-based superalloy

International Nuclear Information System (INIS)

Yashiro, Kisaragi; Naito, Masato; Tomita, Yoshihiro

2003-01-01

In order to clarify the fundamental mechanism of dislocations in the γ/γ' microstructure of Ni-based superalloy, three molecular dynamics simulations are conducted on the behavior of edge dislocations nucleated from a free surface and proceeding in the pure Ni matrix (γ) toward cuboidal Ni 3 Al precipitates (γ') under shear force. One involves dislocations near the apices of two precipitates adjoining each other with the distance of 0.04 μm, as large as the width of the γ channel in real superalloys. Others simulate dislocations piled at the precipitates as well, however, the scale of the microstructure is smaller than that in real superalloys by one order of magnitude, and one of them have precipitates with atomistically sharp edge. Dislocations are pinned at precipitates and bowed-out in the γ channel, then they begin to penetrate into the precipitate at the edge in both the real-scale and smaller microstructures when the precipitates have blunt edges. On the other hand, an edge dislocation splits into a superpartial in the γ' precipitate and a misfit screw dislocation bridging between two adjacent precipitates at the atomistically sharp edge of γ' precipitates. It is also observed that two superpartials glide in the precipitate as a superdislocation with anti-phase boundary (APB), of which the width is evaluated to be about 4 nm. (author)

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.

Probing the limits of metal plasticity with molecular dynamics simulations

Science.gov (United States)

Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.

2017-10-01

Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong

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

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.

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

Molecular Dynamics Studies of Nanofluidic Devices

DEFF Research Database (Denmark)

Zambrano Rodriguez, Harvey Alexander

of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

Molecular modeling and multiscaling issues for electronic material applications

CERN Document Server

Iwamoto, Nancy; Yuen, Matthew; Fan, Haibo

Volume 1 : Molecular Modeling and Multiscaling Issues for Electronic Material Applications provides a snapshot on the progression of molecular modeling in the electronics industry and how molecular modeling is currently being used to understand material performance to solve relevant issues in this field. This book is intended to introduce the reader to the evolving role of molecular modeling, especially seen through the eyes of the IEEE community involved in material modeling for electronic applications.  Part I presents  the role that quantum mechanics can play in performance prediction, such as properties dependent upon electronic structure, but also shows examples how molecular models may be used in performance diagnostics, especially when chemistry is part of the performance issue.  Part II gives examples of large-scale atomistic methods in material failure and shows several examples of transitioning between grain boundary simulations (on the atomistic level)and large-scale models including an example ...

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

International Nuclear Information System (INIS)

Kylasa, S.B.; Aktulga, H.M.; Grama, A.Y.

2014-01-01

We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

Energy Technology Data Exchange (ETDEWEB)

Kylasa, S.B., E-mail: skylasa@purdue.edu [Department of Elec. and Comp. Eng., Purdue University, West Lafayette, IN 47907 (United States); Aktulga, H.M., E-mail: hmaktulga@lbl.gov [Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS 50F-1650, Berkeley, CA 94720 (United States); Grama, A.Y., E-mail: ayg@cs.purdue.edu [Department of Computer Science, Purdue University, West Lafayette, IN 47907 (United States)

2014-09-01

We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.

Structure of Cu64.5Zr35.5 metallic glass by reverse Monte Carlo simulations

International Nuclear Information System (INIS)

Fang, X. W.; Huang, Li; Wang, C. Z.; Ho, K. M.; Ding, Z. J.

2014-01-01

Reverse Monte Carlo simulations (RMC) have been widely used to generate three dimensional (3D) atomistic models for glass systems. To examine the reliability of the method for metallic glass, we use RMC to predict the atomic configurations of a “known” structure from molecular dynamics (MD) simulations, and then compare the structure obtained from the RMC with the target structure from MD. We show that when the structure factors and partial pair correlation functions from the MD simulations are used as inputs for RMC simulations, the 3D atomistic structure of the glass obtained from the RMC gives the short- and medium-range order in good agreement with those from the target structure by the MD simulation. These results suggest that 3D atomistic structure model of the metallic glass alloys can be reasonably well reproduced by RMC method with a proper choice of input constraints

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)

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

In situ diffraction profile analysis during tensile deformation motivated by molecular dynamics

International Nuclear Information System (INIS)

Van Swygenhoven, H.; Budrovic, Z.; Derlet, P.M.; Froseth, A.G.; Van Petegem, S.

2005-01-01

Molecular dynamics simulations can provide insight into the slip mechanism at the atomic scale and suggest that in nanocrystalline metals dislocations are nucleated and absorbed by the grain boundaries. However, this technique is limited by very short simulation times. Using suggestions from molecular dynamics, we have developed a new in situ X-ray diffraction technique wherein the profile analysis of several Bragg diffraction peaks during tensile deformation is possible. Combining experiment and careful structural analysis the results confirm the suggestions from atomistic simulations

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...

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.

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.

The extent of the glass transition from molecular simulation revealing an overcrank effect.

Science.gov (United States)

Godey, François; Fleury, Alexandre; Ghoufi, Aziz; Soldera, Armand

2018-02-15

A deep understanding of the transition between rubber and amorphous state characterized by a glass transition temperature, T g , is still a source of discussions. In this work, we highlight the role of molecular simulation in revealing explicitly this temperature dependent behavior. By reporting the specific volume, the thermal expansion coefficient and the heat capacity versus the temperature, we actually show that the glass transition domain extends to a greater range of temperature, compared with experiments. This significant enlargement width is due to the fast cooling rate, and actually explains the difficulty to locate T g . This result is the manifestation of an overcranking effect used by high-speed cameras to reveal slow-motion. Accordingly, atomistic simulation offers the significant opportunity to show that the transition from the rubber state to the glass phase should be detailed in terms of the degrees of freedom freeze. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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)

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.

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)

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 ...

Self-motion and the α-relaxation in glass-forming polymers. Molecular dynamic simulation and quasielastic neutron scattering results in polyisoprene

International Nuclear Information System (INIS)

Colmenero, Juan; Arbe, Arantxa; Alvarez, Fernando; Monkenbusch, Michael; Richter, Dieter; Farago, Bela; Frick, Bernhard

2003-01-01

The momentum transfer dependence of the self-motion of main chain hydrogens in the α-relaxation regime of a glass forming polymer, polyisoprene, has been thoroughly investigated by a combined effort involving fully atomistic molecular dynamic simulations and quasielastic neutron scattering measurements. In this way, we have established the existence of a crossover from a Gaussian regime of sublinear diffusion to a strongly non-Gaussian regime at short distances. We show that an anomalous jump diffusion model with a distribution of jump lengths gives rise to such a crossover. This model leads to a time-dependent non-Gaussian parameter exhibiting all features revealed so far from various simulations of different glass forming systems

Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins

Science.gov (United States)

Chun, Chan; Haohua, Wen; Lanyuan, Lu; Jun, Fan

2016-01-01

Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an active, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs (BAR) superfamily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics (MD) simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for developing novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling controlled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling processes. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins. Project supported by the National Natural Science Foundation of China (Grant No. 21403182) and the Research Grants Council of Hong Kong, China (Grant No. CityU 21300014).

Multiscale equation-free algorithms for molecular dynamics

Science.gov (United States)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

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.

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.

Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

Science.gov (United States)

Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F.; Perez, Danny

2017-10-01

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

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.

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

Development of a quantum chemical molecular dynamics tribochemical simulator and its application to tribochemical reaction dynamics of lubricant additives

International Nuclear Information System (INIS)

Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M

2010-01-01

Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives

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

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)

SELF-HEALING NANOMATERIALS: MULTIMILLION-ATOM REACTIVE MOLECULAR DYNAMICS SIMULATIONS

Energy Technology Data Exchange (ETDEWEB)

Hakamata, Tomoya [Kumamoto Univ., Kumamoto (Japan); Shimamura, Kohei [Kumamoto Univ., Kumamoto (Japan); Univ. of Southern California, Los Angeles, CA (United States); Kobe Univ., Kobe (Japan); Shimojo, Fuyuki [Kumamoto Univ., Kumamoto (Japan); Kalia, Rajiv K. [Univ. of Southern California, Los Angeles, CA (United States); Nakano, Aiichiro [Univ. of Southern California, Los Angeles, CA (United States); Vashishta, Priya [Univ. of Southern California, Los Angeles, CA (United States)

2017-10-20

Organometal halide perovskites are attracting great attention as promising material for solar cells because of their high power conversion efficiency. The high performance has been attributed to the existence of free charge carriers and their large diffusion lengths, but the nature of carrier transport at the atomistic level remains elusive. Here, nonadiabatic quantum molecular dynamics simulations elucidate the mechanisms underlying the excellent free-carrier transport in CH₃NH₃PbI₃. Pb and I sublattices act as disjunct pathways for rapid and balanced transport of photoexcited electrons and holes, respectively, while minimizing efficiency-degrading charge recombination. On the other hand, CH₃NH₃ sublattice quickly screens out electrostatic electron-hole attraction to generate free carriers within 1 ps. Together this nano-architecture lets photoexcited electrons and holes dissociate instantaneously and travel far away to be harvested before dissipated as heat. As a result, this work provides much needed structure-property relationships and time-resolved information that potentially lead to rational design of efficient solar cells.

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.

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.

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses.

Science.gov (United States)

Huber, Roland G; Marzinek, Jan K; Holdbrook, Daniel A; Bond, Peter J

2017-09-01

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Liquid-Phase Exfoliation of Phosphorene: Design Rules from Molecular Dynamics Simulations.

Science.gov (United States)

Sresht, Vishnu; Pádua, Agílio A H; Blankschtein, Daniel

2015-08-25

The liquid-phase exfoliation of phosphorene, the two-dimensional derivative of black phosphorus, in the solvents dimethyl sulfoxide (DMSO), dimethylformamide (DMF), isopropyl alcohol, N-methyl-2-pyrrolidone, and N-cyclohexyl-2-pyrrolidone is investigated using three molecular-scale "computer experiments". We modeled solvent-phosphorene interactions using an atomistic force field, based on ab initio calculations and lattice dynamics, that accurately reproduces experimental mechanical properties. We probed solvent molecule ordering at phosphorene/solvent interfaces and discovered that planar molecules such as N-methyl-2-pyrrolidone preferentially orient parallel to the interface. We subsequently measured the energy required to peel a single phosphorene monolayer from a stack of black phosphorus and analyzed the role of "wedges" of solvent molecules intercalating between phosphorene sheets in initiating exfoliation. The exfoliation efficacy of a solvent is enhanced when either molecular planarity "sharpens" this molecular wedge or strong phosphorene-solvent adhesion stabilizes the newly exposed phosphorene surfaces. Finally, we examined the colloidal stability of exfoliated flakes by simulating their aggregation and showed that dispersion is favored when the cohesive energy between the molecules in the solvent monolayer confined between the phosphorene sheets is high (as with DMSO) and is hindered when the adhesion between these molecules and phosphorene is strong; the molecular planarity in solvents like DMF enhances the cohesive energy. Our results are consistent with, and provide a molecular context for, experimental exfoliation studies of phosphorene and other layered solids, and our molecular insights into the significant role of solvent molecular geometry and ordering should complement prevalent solubility-parameter-based approaches in establishing design rules for effective nanomaterial exfoliation media.

From molecular dynamics and particle simulations towards constitutive relations for continuum theory

NARCIS (Netherlands)

Luding, Stefan; Koren, B.; Vuik, K.

2009-01-01

A challenge of today‖s research is the realistic simulation of disordered atomistic systems or particulate and granular materials like sand, powders, ceramics or composites, which consist of many millions of atoms/particles. The inhomogeneous fine-structure of such materials makes it very difficult

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

Science.gov (United States)

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach.

Science.gov (United States)

Skarmoutsos, Ioannis; Samios, Jannis

2006-11-02

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.

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.

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.

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.

Tacticity-Dependent Interchain Interactions of Poly(N-Isopropylacrylamide in Water: Toward the Molecular Dynamics Simulation of a Thermoresponsive Microgel

Directory of Open Access Journals (Sweden)

Gaio Paradossi

2017-04-01

Full Text Available The discovery that the lower critical solution temperature (LCST of poly(N-Isopropylacrylamide (PNIPAM in water is affected by the tacticity opens the perspective to tune the volume phase transition temperature of PNIPAM microgels by changing the content of meso dyads in the polymer network. The increased hydrophobicity of isotactic-rich PNIPAM originates from self-assembly processes in aqueous solutions also below the LCST. The present work aims to detect the characteristics of the pair interaction between polymer chains, occurring in a concentration regime close to the chain overlap concentration, by comparing atactic and isotactic-rich PNIPAM solutions. Using atomistic molecular dynamics simulations, we successfully modelled the increased association ability of the meso-dyad-rich polymer in water below the LCST, and gain information on the features of the interchain junctions as a function of tacticity. Simulations carried out above the LCST display the PNIPAM transition to the insoluble state and do not detect a relevant influence of stereochemistry on the structure of the polymer ensemble. The results obtained at 323 K provide an estimate of the swelling ratio of non-stereocontrolled PNIPAM microgels which is in agreement with experimental findings for microgels prepared with low cross-linker/monomer feed ratios. This study represents the first step toward the atomistic modelling of PNIPAM microgels with a controlled tacticity.

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.

An atomistic model for cross-linked HNBR elastomers used in seals

Science.gov (United States)

Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

2015-03-01

Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

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.

The mechanism of selective molecular capture in carbon nanotube networks.

Science.gov (United States)

Wan, Yu; Guan, Jun; Yang, Xudong; Zheng, Quanshui; Xu, Zhiping

2014-07-28

Recently, air pollution issues have drawn significant attention to the development of efficient air filters, and one of the most promising materials for this purpose is nanofibers. We explore here the mechanism of selective molecular capture of volatile organic compounds in carbon nanotube networks by performing atomistic simulations. The results are discussed with respect to the two key parameters that define the performance of nanofiltration, i.e. the capture efficiency and flow resistance, which demonstrate the advantages of carbon nanotube networks with high surface-to-volume ratio and atomistically smooth surfaces. We also reveal the important roles of interfacial adhesion and diffusion that govern selective gas transport through the network.

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

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

Exploring Biomolecular Interactions Through Single-Molecule Force Spectroscopy and Computational Simulation

OpenAIRE

Yang, Darren

2016-01-01

Molecular interactions between cellular components such as proteins and nucleic acids govern the fundamental processes of living systems. Technological advancements in the past decade have allowed the characterization of these molecular interactions at the single-molecule level with high temporal and spatial resolution. Simultaneously, progress in computer simulation has enabled theoretical research at the atomistic level, assisting in the interpretation of experimental results. This thesi...

Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique

Science.gov (United States)

Shadrack Jabes, B.; Krekeler, C.; Klein, R.; Delle Site, L.

2018-05-01

We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.

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.

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.

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.

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)

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

Examining the mechanical equilibrium of microscopic stresses in molecular simulations

OpenAIRE

Torres Sánchez, Alejandro; Vanegas, Juan Manuel; Arroyo Balaguer, Marino

2015-01-01

The microscopic stress field provides a unique connection between atomistic simulations and mechanics at the nanoscale. However, its definition remains ambiguous. Rather than a mere theoretical preoccupation, we show that this fact acutely manifests itself in local stress calculations of defective graphene, lipid bilayers, and fibrous proteins. We find that popular definitions of the microscopic stress violate the continuum statements of mechanical equilibrium, and we propose an unambiguous a...

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

Science.gov (United States)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high

Microscopic Rate Constants of Crystal Growth from Molecular Dynamic Simulations Combined with Metadynamics

Directory of Open Access Journals (Sweden)

Dániel Kozma

2012-01-01

Full Text Available Atomistic simulation of crystal growth can be decomposed into two steps: the determination of the microscopic rate constants and a mesoscopic kinetic Monte Carlo simulation. We proposed a method to determine kinetic rate constants of crystal growth. We performed classical molecular dynamics on the equilibrium liquid/crystal interface of argon. Metadynamics was used to explore the free energy surface of crystal growth. A crystalline atom was selected at the interface, and it was displaced to the liquid phase by adding repulsive Gaussian potentials. The activation free energy of this process was calculated as the maximal potential energy density of the Gaussian potentials. We calculated the rate constants at different interfacial structures using the transition state theory. In order to mimic real crystallization, we applied a temperature difference in the calculations of the two opposite rate constants, and they were applied in kinetic Monte Carlo simulation. The novelty of our technique is that it can be used for slow crystallization processes, while the simple following of trajectories can be applied only for fast reactions. Our method is a possibility for determination of elementary rate constants of crystal growth that seems to be necessary for the long-time goal of computer-aided crystal design.

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

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.

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...

Systematic examination of polymorphism in amyloid fibrils by molecular-dynamics simulation.

Science.gov (United States)

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

2011-05-04

Amyloid fibrils often exhibit polymorphism. Polymorphs are formed when proteins or peptides with identical sequences self-assemble into fibrils containing substantially different arrangements of the β-strands. We used atomistic molecular-dynamics simulation to examine the thermodynamic stability of a amyloid fibrils in different polymorphic forms by performing a systematic investigation of sequence and symmetry space for a series of peptides with a range of physicochemical properties. We show that the stability of fibrils depends on both sequence and the symmetry because these factors determine the availability of favorable interactions between the peptide strands within a sheet and in intersheet packing. By performing a detailed analysis of these interactions as a function of symmetry, we obtained a series of simple design rules that can be used to determine which polymorphs of a given sequence are most likely to form thermodynamically stable fibrils. These rules can potentially be employed to design peptide sequences that aggregate into a preferred polymorphic form for nanotechnological purposes. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals.

Science.gov (United States)

Kazachenko, Sergey; Giovinazzo, Mark; Hall, Kyle Wm; Cann, Natalie M

2015-09-15

A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n-hexane/2-propanol mixture; and a liquid crystal mesogen, 2-(4-butyloxyphenyl)-5-octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33-119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69-287 fold improvement and three GPUs yield a 101-377 fold speedup. © 2015 Wiley Periodicals, Inc.

Computer simulation of liquid crystals

International Nuclear Information System (INIS)

McBride, C.

1999-01-01

Molecular dynamics simulation performed on modern computer workstations provides a powerful tool for the investigation of the static and dynamic characteristics of liquid crystal phases. In this thesis molecular dynamics computer simulations have been performed for two model systems. Simulations of 4,4'-di-n-pentyl-bibicyclo[2.2.2]octane demonstrate the growth of a structurally ordered phase directly from an isotropic fluid. This is the first time that this has been achieved for an atomistic model. The results demonstrate a strong coupling between orientational ordering and molecular shape, but indicate that the coupling between molecular conformational changes and molecular reorientation is relatively weak. Simulations have also been performed for a hybrid Gay-Berne/Lennard-Jones model resulting in thermodynamically stable nematic and smectic phases. Frank elastic constants have been calculated for the nematic phase formed by the hybrid model through analysis of the fluctuations of the nematic director, giving results comparable with those found experimentally. Work presented in this thesis also describes the parameterization of the torsional potential of a fragment of a dimethyl siloxane polymer chain, disiloxane diol (HOMe 2 Si) 2 O, using ab initio quantum mechanical calculations. (author)

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

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.

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....

Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

International Nuclear Information System (INIS)

More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

2012-01-01

Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)

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).

Adaptive resolution simulation of supramolecular water : The concurrent making, breaking, and remaking of water bundles

NARCIS (Netherlands)

Zavadlav, Julija; Marrink, Siewert J; Praprotnik, Matej

The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to

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.

Molecular dynamics simulations of conformation changes of HIV-1 regulatory protein on graphene

Energy Technology Data Exchange (ETDEWEB)

Zhao, Daohui; Li, Libo; He, Daohang; Zhou, Jian, E-mail: jianzhou@scut.edu.cn

2016-07-30

Graphical abstract: Preferential adsorption of Vpr13-33 on graphene accompanied by early conformational change from α-helix to β-sheet structures was observed by molecular simulations. This work presents the molecular mechanism of graphene-induced peptide conformational alteration and sheds light on developing graphene-based materials to inhibit HIV. - Highlights: • Graphene induced early structural transition of Vpr13-33 is studied by MD simulations. • Both π-π stacking and hydrophobic interactions orchestrate the peptide adsorption. • Vpr has an increased propensity of β-sheet content on graphene surface. • To develop graphene-based materials to inhibit HIV is possible. - Abstract: The fragment of viral protein R (Vpr), Vpr13-33, plays an important role in regulating nuclear importing of HIV genes through channel formation in which it adopts a leucine-zipper-like alpha-helical conformation. A recent experimental study reported that helical Vpr13-33 would transform to β-sheet or random coil structures and aggregate on the surface of graphene or graphene oxide through hydrophobic interactions. Due to experimental limitations, however, there is still a considerable lack of understanding on the adsorption dynamics at the early stage of the conformational transition at water-graphene interface and the underlying driving force at molecular level. In this study, atomistic molecular dynamics simulations were used to explore the conformation transition phenomena. Vpr13-33 kept α-helical structure in solution, but changed to β-sheet structure when strongly adsorbed onto graphene. Preferential adsorption of Vpr13-33 on graphene is dominated by hydrophobic interactions. The cluster analysis identified the most significant populated conformation and the early stage of structure conversion from α-helical to β-sheet was found, but the full β-sheet propagation was not observed. Free energy landscape analysis further complemented the transformation analysis of

Molecular dynamics simulations of conformation changes of HIV-1 regulatory protein on graphene

International Nuclear Information System (INIS)

Zhao, Daohui; Li, Libo; He, Daohang; Zhou, Jian

2016-01-01

Graphical abstract: Preferential adsorption of Vpr13-33 on graphene accompanied by early conformational change from α-helix to β-sheet structures was observed by molecular simulations. This work presents the molecular mechanism of graphene-induced peptide conformational alteration and sheds light on developing graphene-based materials to inhibit HIV. - Highlights: • Graphene induced early structural transition of Vpr13-33 is studied by MD simulations. • Both π-π stacking and hydrophobic interactions orchestrate the peptide adsorption. • Vpr has an increased propensity of β-sheet content on graphene surface. • To develop graphene-based materials to inhibit HIV is possible. - Abstract: The fragment of viral protein R (Vpr), Vpr13-33, plays an important role in regulating nuclear importing of HIV genes through channel formation in which it adopts a leucine-zipper-like alpha-helical conformation. A recent experimental study reported that helical Vpr13-33 would transform to β-sheet or random coil structures and aggregate on the surface of graphene or graphene oxide through hydrophobic interactions. Due to experimental limitations, however, there is still a considerable lack of understanding on the adsorption dynamics at the early stage of the conformational transition at water-graphene interface and the underlying driving force at molecular level. In this study, atomistic molecular dynamics simulations were used to explore the conformation transition phenomena. Vpr13-33 kept α-helical structure in solution, but changed to β-sheet structure when strongly adsorbed onto graphene. Preferential adsorption of Vpr13-33 on graphene is dominated by hydrophobic interactions. The cluster analysis identified the most significant populated conformation and the early stage of structure conversion from α-helical to β-sheet was found, but the full β-sheet propagation was not observed. Free energy landscape analysis further complemented the transformation analysis of

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

Science.gov (United States)

Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

2016-01-21

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

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.

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...

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

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.

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.

Cohesion between two clay lamellae: From Primitive Model to Full Molecular Simulation

International Nuclear Information System (INIS)

Carrier, Benoit; Vandamme, Matthieu; Pellenq, Roland; Van Damme, Henri

2012-01-01

reference. Then, starting from DLVO model we increase the complexity in a step-wise fashion: Molecularity of the counter-ions, molecularity of the solvent and finally full atomistic description of water and of the clay lamellae. For each system, we generate a family of slit pores of various widths and we run Monte-Carlo and Molecular Dynamics simulations. We present the ionic profiles and the pressure between the charged lamellae for each model. In particular, we investigate the influence of the amplitude of the electrostatic coupling. We also compute the dielectric constant of water for the Explicit Solvent Primitive Model and for the full molecular model and show for which systems assuming inter-layer water to behave like bulk water is a relevant hypothesis. (authors)

Intermolecular Interactions and Cooperative Effects from Electronic Structure Calculations: An Effective Means for Developing Interaction Potentials for Condensed Phase Simulations

Energy Technology Data Exchange (ETDEWEB)

Xantheas, Sotiris S.

2004-05-01

The modeling of the macroscopic properties of homogeneous and inhomogeneous systems via atomistic simulations such as molecular dynamics (MD) or Monte Carlo (MC) techniques is based on the accurate description of the relevant solvent-solute and solvent-solvent intermolecular interactions. The total energy (U) of an n-body molecular system can be formally written as [1,2,3

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.

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.

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.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

Science.gov (United States)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

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.

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.

Simulation and visualization of ion-implantation in diamond

International Nuclear Information System (INIS)

Adler, Joan; Silverman, Amihai; Ierushalmi, Niv; Sorkin, Anastassia; Kalish, Rafi

2014-01-01

We have explored aspects of ion implantation in diamonds with molecular dynamics and tightbinding atomistic simulations. Relevant experiments and their potential applications as well as our computer models and computational approaches are described. Our simulations have been designed to answer questions proposed by experimental researchers concerning optimal laboratory schedules for the preparation of samples with potential applications to diamond membranes and NV centers for quantum computers. Simulation and visualization of results enable us to peek inside samples where experimental techniques cannot tread. In order to provide the requisite Brazilian component a new connection between these models and bootstrap percolation is made

Multiresolution molecular mechanics: Surface effects in nanoscale materials

Energy Technology Data Exchange (ETDEWEB)

Yang, Qingcheng, E-mail: qiy9@pitt.edu; To, Albert C., E-mail: albertto@pitt.edu

2017-05-01

Surface effects have been observed to contribute significantly to the mechanical response of nanoscale structures. The newly proposed energy-based coarse-grained atomistic method Multiresolution Molecular Mechanics (MMM) (Yang, To (2015), ) is applied to capture surface effect for nanosized structures by designing a surface summation rule SR{sup S} within the framework of MMM. Combined with previously proposed bulk summation rule SR{sup B}, the MMM summation rule SR{sup MMM} is completed. SR{sup S} and SR{sup B} are consistently formed within SR{sup MMM} for general finite element shape functions. Analogous to quadrature rules in finite element method (FEM), the key idea to the good performance of SR{sup MMM} lies in that the order or distribution of energy for coarse-grained atomistic model is mathematically derived such that the number, position and weight of quadrature-type (sampling) atoms can be determined. Mathematically, the derived energy distribution of surface area is different from that of bulk region. Physically, the difference is due to the fact that surface atoms lack neighboring bonding. As such, SR{sup S} and SR{sup B} are employed for surface and bulk domains, respectively. Two- and three-dimensional numerical examples using the respective 4-node bilinear quadrilateral, 8-node quadratic quadrilateral and 8-node hexahedral meshes are employed to verify and validate the proposed approach. It is shown that MMM with SR{sup MMM} accurately captures corner, edge and surface effects with less 0.3% degrees of freedom of the original atomistic system, compared against full atomistic simulation. The effectiveness of SR{sup MMM} with respect to high order element is also demonstrated by employing the 8-node quadratic quadrilateral to solve a beam bending problem considering surface effect. In addition, the introduced sampling error with SR{sup MMM} that is analogous to numerical integration error with quadrature rule in FEM is very small. - Highlights: �

Modeling complex and multi-component food systems in molecular dynamics simulations on the example of chocolate conching.

Science.gov (United States)

Greiner, Maximilian; Sonnleitner, Bettina; Mailänder, Markus; Briesen, Heiko

2014-02-01

Additional benefits of foods are an increasing factor in the consumer's purchase. To produce foods with the properties the consumer demands, understanding the micro- and nanostructure is becoming more important in food research today. We present molecular dynamics (MD) simulations as a tool to study complex and multi-component food systems on the example of chocolate conching. The process of conching is chosen because of the interesting challenges it provides: the components (fats, emulsifiers and carbohydrates) contain diverse functional groups, are naturally fluctuating in their chemical composition, and have a high number of internal degrees of freedom. Further, slow diffusion in the non-aqueous medium is expected. All of these challenges are typical to food systems in general. Simulation results show the suitability of present force fields to correctly model the liquid and crystal density of cocoa butter and sucrose, respectively. Amphiphilic properties of emulsifiers are observed by micelle formation in water. For non-aqueous media, pulling simulations reveal high energy barriers for motion in the viscous cocoa butter. The work for detachment of an emulsifier from the sucrose crystal is calculated and matched with detachment of the head and tail groups separately. Hydrogen bonding is shown to be the dominant interaction between the emulsifier and the crystal surface. Thus, MD simulations are suited to model the interaction between the emulsifier and sugar crystal interface in non-aqueous media, revealing detailed information about the structuring and interactions on a molecular level. With interaction parameters being available for a wide variety of chemical groups, MD simulations are a valuable tool to understand complex and multi-component food systems in general. MD simulations provide a substantial benefit to researchers to verify their hypothesis in dynamic simulations with an atomistic resolution. Rapid rise of computational resources successively

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...

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)

A n-vector model for charge transport in molecular semiconductors.

Science.gov (United States)

Jackson, Nicholas E; Kohlstedt, Kevin L; Chen, Lin X; Ratner, Mark A

2016-11-28

We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topology-dependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors.

A generalized Poisson solver for first-principles device simulations

Energy Technology Data Exchange (ETDEWEB)

Bani-Hashemian, Mohammad Hossein; VandeVondele, Joost, E-mail: joost.vandevondele@mat.ethz.ch [Nanoscale Simulations, ETH Zürich, 8093 Zürich (Switzerland); Brück, Sascha; Luisier, Mathieu [Integrated Systems Laboratory, ETH Zürich, 8092 Zürich (Switzerland)

2016-01-28

Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative method in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated.

Characteristics of Sucrose Transport through the Sucrose-Specific Porin ScrY Studied by Molecular Dynamics Simulations

Directory of Open Access Journals (Sweden)

Liping eSun

2016-02-01

Full Text Available Sucrose-specific porin (ScrY is a transmembrane protein that allows for the uptake of sucrose under growth-limiting conditions. The crystal structure of ScrY was resolved before by X-ray crystallography, both in its uncomplexed form and with bound sucrose. However, little is known about the molecular characteristics of the transport mechanism of ScrY. To date, there has not yet been any clear demonstration for sucrose transport through the ScrY.Here, the dynamics of the ScrY trimer embedded in a phospholipid bilayer as well as the characteristics of sucrose translocation were investigated by means of atomistic molecular dynamics (MD simulations. The potential of mean force (PMF for sucrose translocation through the pore showed two main energy barriers within the constriction region of ScrY. Energy decomposition allowed to pinpoint three aspartic acids as key residues opposing the passage of sucrose, all located within the L3 loop. Mutation of two aspartic acids to uncharged residues resulted in an accordingly modified electrostatics and decreased PMF barrier. The chosen methodology and results will aid in the design of porins with modified transport specificities.

Molecular dynamic simulation of the self-assembly of DAP12-NKG2C activating immunoreceptor complex.

Directory of Open Access Journals (Sweden)

Peng Wei

Full Text Available The DAP12-NKG2C activating immunoreceptor complex is one of the multisubunit transmembrane protein complexes in which ligand-binding receptor chains assemble with dimeric signal-transducing modules through non-covalent associations in their transmembrane (TM domains. In this work, both coarse grained and atomistic molecular dynamic simulation methods were applied to investigate the self-assembly dynamics of the transmembrane domains of the DAP12-NKG2C activating immunoreceptor complex. Through simulating the dynamics of DAP12-NKG2C TM heterotrimer and point mutations, we demonstrated that a five-polar-residue motif including: 2 Asps and 2 Thrs in DAP12 dimer, as well as 1 Lys in NKG2C TM plays an important role in the assembly structure of the DAP12-NKG2C TM heterotrimer. Furthermore, we provided clear evidences to exclude the possibility that another NKG2C could stably associate with the DAP12-NKG2C heterotrimer. Based on the simulation results, we proposed a revised model for the self-assembly of DAP12-NKG2C activating immunoreceptor complex, along with a plausible explanation for the association of only one NKG2C with a DAP12 dimer.

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...

Interaction of amyloid inhibitor proteins with amyloid beta peptides: insight from molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Payel Das

Full Text Available Knowledge of the detailed mechanism by which proteins such as human αB- crystallin and human lysozyme inhibit amyloid beta (Aβ peptide aggregation is crucial for designing treatment for Alzheimer's disease. Thus, unconstrained, atomistic molecular dynamics simulations in explicit solvent have been performed to characterize the Aβ17-42 assembly in presence of the αB-crystallin core domain and of lysozyme. Simulations reveal that both inhibitor proteins compete with inter-peptide interaction by binding to the peptides during the early stage of aggregation, which is consistent with their inhibitory action reported in experiments. However, the Aβ binding dynamics appear different for each inhibitor. The binding between crystallin and the peptide monomer, dominated by electrostatics, is relatively weak and transient due to the heterogeneous amino acid distribution of the inhibitor surface. The crystallin-bound Aβ oligomers are relatively long-lived, as they form more extensive contact surface with the inhibitor protein. In contrast, a high local density of arginines from lysozyme allows strong binding with Aβ peptide monomers, resulting in stable complexes. Our findings not only illustrate, in atomic detail, how the amyloid inhibitory mechanism of human αB-crystallin, a natural chaperone, is different from that of human lysozyme, but also may aid de novo design of amyloid inhibitors.

A W−Ne interatomic potential for simulation of neon implantation in tungsten

Energy Technology Data Exchange (ETDEWEB)

Backman, Marie; Juslin, Niklas; Huang, Guiyang [Department of Nuclear Engineering, University of Tennessee, Knoxville, TN 37996-2300 (United States); Wirth, Brian D., E-mail: bdwirth@utk.edu [Department of Nuclear Engineering, University of Tennessee, Knoxville, TN 37996-2300 (United States); P.O. Box 2008, MS-6003, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)

2016-08-15

An interatomic pair potential for W−Ne is developed for atomistic molecular dynamics simulations of neon implantation in tungsten. The new potential predicts point defect energies and binding energies of small clusters that are in good agreement with electronic structure calculations. Molecular dynamics simulations of small neon clusters in tungsten show that trap mutation, in which an interstitial neon cluster displaces a tungsten atom from its lattice site, occurs for clusters of three or more neon atoms. However, near a free surface, trap mutation can occur at smaller sizes, including even a single neon interstitial in close proximity to a (100) or (110) surface.

Mechanisms of recognition and binding of α-TTP to the plasma membrane by multi-scale molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Christos eLamprakis

2015-07-01

Full Text Available We used multiple sets of simulations both at the atomistic and coarse-grained level of resolution, to investigate interaction and binding of α-tochoperol transfer protein (α-TTP to phosphatidylinositol phosphate lipids (PIPs. Our calculations indicate that enrichment of membranes with such lipids facilitate membrane anchoring. Atomistic models suggest that PIP can be incorporated into the binding cavity of α-TTP and therefore confirm that such protein can work as lipid exchanger between the endosome and the plasma membrane. Comparison of the atomistic models of the α-TTP / PIPs complex with membrane-bound α-TTP revealed different roles for the various basic residues composing the basic patch that is key for the protein / ligand interaction. Such residues are of critical importance as several point mutations at their position lead to severe forms of ataxia with vitamin E deficiency (AVED phenotypes. Specifically, R221 is main residue responsible for the stabilisation of the complex. R68 and R192 exchange strong interactions in the protein or in the membrane complex only, suggesting that the two residues alternate contact formation, thus facilitating lipid flipping from the membrane into the protein cavity during the lipid exchange process. Finally, R59 shows weaker interactions with PIPs anyway with a clear preference for specific phosphorylation positions, hinting a role in early membrane selectivity for the protein. Altogether, our simulations reveal significant aspects at the atomistic scale of interactions of α-TTP with the plasma membrane and with PIP, providing clarifications on the mechanism of intracellular vitamin E trafficking and helping establishing the role of key residue for the functionality of α-TTP.

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

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

Science.gov (United States)

Prior, Christopher; Oganesyan, Vasily S

2017-09-21

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

International Nuclear Information System (INIS)

Sanz-Navarro, Carlos F.

2002-01-01

The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

Molecular dynamics simulation of cyclodextrin aggregation and extraction of Anthracene from non-aqueous liquid phase

Energy Technology Data Exchange (ETDEWEB)

Zhu, Xinzhe [Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment, Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055 (China); School of Environment, Tsinghua University, Beijing 100084 (China); Wu, Guozhong [Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment, Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055 (China); Chen, Daoyi, E-mail: chen.daoyi@sz.tsinghua.edu.cn [Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment, Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055 (China)

2016-12-15

Cyclodextrin (CD) extraction is widely used for the remediation of polycyclic aromatic hydrocarbons (PAH) pollution, but it remains unclear about the influence of CD aggregation on the PAH transport from non-aqueous liquid phase to water. The atomistic adsorption and complexation of PAHs (32 anthracenes) by CD aggregates (48 β-cyclodextrins) were studied by molecular dynamics simulations at hundreds of nanoseconds time scale. Results indicated that high temperature promoted the βCD aggregation in bulk oil, which was not found in bulk water. Nevertheless, the fractions of anthracenes entrapped inside the βCDs cavity in both scenarios were significantly increased when temperature increased from 298 to 328 K. Free energy calculation for the sub-steps of CD extraction demonstrated that the anthracenes could be extracted when the βCDs arrived at the water-oil interface or after the βCDs entered the bulk oil. The former was kinetic-controlled while the latter was thermodynamic-limited process. Results also highlighted the formation of porous structures by CD aggregates in water, which was able to sequestrate PAH clusters with the size obviously larger than the cavity diameter of individual CD. This provided an opportunity for the extraction of recalcitrant PAHs with molecular size larger than anthracenes by cyclodextrins.

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

Science.gov (United States)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

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.

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.

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

Molecular Dynamics Study of Thermally Augmented Nanodroplet Motion on Chemical Energy Induced Wettability Gradient Surfaces.

Science.gov (United States)

Chakraborty, Monojit; Chowdhury, Anamika; Bhusan, Richa; DasGupta, Sunando

2015-10-20

Droplet motion on a surface with chemical energy induced wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics of molecular movement near the solid-liquid interface including the contact line friction. The simulations mimic experiments in a comprehensive manner wherein microsized droplets are propelled by the surface wettability gradient against forces opposed to motion. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature are varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction is observed to be a strong function of temperature at atomistic scales, confirming their experimentally observed inverse functionality. Additionally, the MD simulation results are successfully compared with those from an analytical model for self-propelled droplet motion on gradient surfaces.

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

Understanding molecular simulation: from algorithms to applications

NARCIS (Netherlands)

Frenkel, D.; Smit, B.

2002-01-01

Second and revised edition Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique

Predicting Flory-Huggins χ from Simulations

Science.gov (United States)

Zhang, Wenlin; Gomez, Enrique D.; Milner, Scott T.

2017-07-01

We introduce a method, based on a novel thermodynamic integration scheme, to extract the Flory-Huggins χ parameter as small as 10-3k T for polymer blends from molecular dynamics (MD) simulations. We obtain χ for the archetypical coarse-grained model of nonpolar polymer blends: flexible bead-spring chains with different Lennard-Jones interactions between A and B monomers. Using these χ values and a lattice version of self-consistent field theory (SCFT), we predict the shape of planar interfaces for phase-separated binary blends. Our SCFT results agree with MD simulations, validating both the predicted χ values and our thermodynamic integration method. Combined with atomistic simulations, our method can be applied to predict χ for new polymers from their chemical structures.

Multiscale modeling of polyisoprene on graphite

International Nuclear Information System (INIS)

Pandey, Yogendra Narayan; Brayton, Alexander; Doxastakis, Manolis; Burkhart, Craig; Papakonstantopoulos, George J.

2014-01-01

The local dynamics and the conformational properties of polyisoprene next to a smooth graphite surface constructed by graphene layers are studied by a multiscale methodology. First, fully atomistic molecular dynamics simulations of oligomers next to the surface are performed. Subsequently, Monte Carlo simulations of a systematically derived coarse-grained model generate numerous uncorrelated structures for polymer systems. A new reverse backmapping strategy is presented that reintroduces atomistic detail. Finally, multiple extensive fully atomistic simulations with large systems of long macromolecules are employed to examine local dynamics in proximity to graphite. Polyisoprene repeat units arrange close to a parallel configuration with chains exhibiting a distribution of contact lengths. Efficient Monte Carlo algorithms with the coarse-grain model are capable of sampling these distributions for any molecular weight in quantitative agreement with predictions from atomistic models. Furthermore, molecular dynamics simulations with well-equilibrated systems at all length-scales support an increased dynamic heterogeneity that is emerging from both intermolecular interactions with the flat surface and intramolecular cooperativity. This study provides a detailed comprehensive picture of polyisoprene on a flat surface and consists of an effort to characterize such systems in atomistic detail

Parallel multiscale simulations of a brain aneurysm

Energy Technology Data Exchange (ETDEWEB)

Grinberg, Leopold [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States); Fedosov, Dmitry A. [Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich 52425 (Germany); Karniadakis, George Em, E-mail: george_karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States)

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in

Parallel multiscale simulations of a brain aneurysm

International Nuclear Information System (INIS)

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2013-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in

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.

Predict the glass transition temperature and plasticization of β-cyclodextrin/water binary system by molecular dynamics simulation.

Science.gov (United States)

Zhou, Guohui; Zhao, Tianhai; Wan, Jie; Liu, Chengmei; Liu, Wei; Wang, Risi

2015-01-12

The glass transition temperature, diffusion behavior and plasticization of β-cyclodextrin (β-CD), and three amorphous β-CD/water mixtures (3%, 5% and 10% [w/w] water, respectively) were investigated by molecular dynamics simulation, which were performed using Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field and isothermal-isobaric ensembles. The specific volumes of four amorphous cells were obtained as a function of temperature. The glass transition temperatures (T(g)) were estimated to be 334.25 K, 325.12 K, 317.32 K, and 305.41 K for amorphous β-CD containing 0%, 3%, 5% and 10% w/w water, respectively, which compares well with the values observed in published literature. The radial distribution function was computed to elucidate the intermolecular interactions between amorphous β-CD and water, which acts as a plasticizer. These results indicate that the hydrogen bond interactions of oxygen in hydroxyl ions was higher than oxygen in acetal groups in β-CD amorphous mixtures with that in water, due to less accessibility of ring oxygens to the surrounding water molecules. The mobility of water molecules was investigated over various temperature ranges, including the rubbery and glassy phases of the β-CD/water mixtures, by calculating the diffusion coefficients and the fractional free volume. In β-CD amorphous models, the higher mobility of water molecules was observed at temperatures above Tg, and almost no change was observed at temperatures below T(g). Copyright © 2014 Elsevier Ltd. All rights reserved.

Insight or illusion? seeing inside the cell with mesoscopic simulations

DEFF Research Database (Denmark)

Shillcock, Julian C.

2008-01-01

 the dynamics of spatially heterogeneous membranes and the crowded cytoplasmic environment to be followed at a modest computational cost. The price for such power is that the atomic detail of the constituents is much lower than in atomistic Molecular Dynamics simulations. We argue that this price is worth...... by spatial resolution and the speed of molecular rearrangements. The increase in computing power of the last few decades enables the construction of computational tools for observing cellular processes in silico. As experiments yield increasing amounts of data on the protein and lipid constituents...... of the cell, computer simulations parametrized using this data are beginning to allow models of cellular processes to be interrogated in ways unavailable in the laboratory. Mesoscopic simulations retain only those molecular features that are believed to be relevant to the processes of interest. This allows...

Nonequilibrium molecular dynamics: The first 25 years

International Nuclear Information System (INIS)

Hoover, W.G.

1992-08-01

Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments

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.

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales.

Science.gov (United States)

Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

2017-09-21

Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales

Science.gov (United States)

Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

2017-09-01

Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

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.)

A concurrent multiscale micromorphic molecular dynamics

International Nuclear Information System (INIS)

Li, Shaofan; Tong, Qi

2015-01-01

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

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

Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation

Science.gov (United States)

Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

2016-12-01

NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.

Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

Energy Technology Data Exchange (ETDEWEB)

Kim, Seonghan; Chang, Rakwoo [Kwangwoon University, Seoul (Korea, Republic of)

2016-07-15

Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel-like (L{sub β}' or P{sub β}') phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel-like phase into the completely liquid-crystalline phase (L{sub α}). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half-maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness)can be used as order parameters for the membrane phase transition.

Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

International Nuclear Information System (INIS)

Kim, Seonghan; Chang, Rakwoo

2016-01-01

Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel-like (L_β' or P_β') phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel-like phase into the completely liquid-crystalline phase (L_α). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half-maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness)can be used as order parameters for the membrane phase transition.

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

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.

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

Translational and rotational diffusion of dilute solid amorphous spherical nanocolloids by molecular dynamics simulation

Science.gov (United States)

Heyes, D. M.; Nuevo, M. J.; Morales, J. J.

Following on from our previous study (Heyes, D. M., Nuevo, M. J, and Morales, J. J., 1996, Molec. Phys., 88, 1503), molecular dynamics simulations have been carried out of translational and rotational diffusion of atomistically rough near-spherical solid Lennard-Jones (LJ) clusters immersed in a Weeks-Chandler-Andersen liquid solvent. A single cluster consisting of up to about 100LJ particles as part of an 8000 atom fluid system was considered in each case. The translational and rotational diffusion coefficients decrease with increasing cluster size and solvent density (roughly in proportion to the molar volume of the solvent). The simulations reveal that for clusters in excess of about 30LJ atoms there is a clear separation of timescales between angular velocity and orientation relaxation which adhere well to the small-step diffusion model encapsulated in Hubbard's relationship. For 100 atom clusters both the StokesEinstein (translation) and Stokes-Einstein-Debye (rotation) equations apply approximately. The small departures from these reference solutions indicate that the translational relaxation experiences a local viscosity in excess of the bulk value (typically by ~ 30%), whereas rotational relaxation experiences a smaller viscosity than the bulk (typically by ~ 30%) reasonably in accord with the Gierer-Wirtz model. Both of these observations are consistent with an observed layering of the liquid molecules next to the cluster observed in our previous study.

Effect of strain field on displacement cascade in tungsten studied by molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Wang, D. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Gao, N., E-mail: ning.gao@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Wang, Z.G., E-mail: zhgwang@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gao, X. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); He, W.H. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Cui, M.H.; Pang, L.L.; Zhu, Y.B. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

2016-10-01

Using atomistic methods, the coupling effect of strain field and displacement cascade in body-centered cubic (BCC) tungsten is directly simulated by molecular dynamics (MD) simulations at different temperatures. The values of the hydrostatic and uniaxial (parallel or perpendicular to primary knock-on atom (PKA) direction) strains are from −2% to 2% and the temperature is from 100 to 1000 K. Because of the annealing effect, the influence of strain on radiation damage at low temperature has been proved to be more significant than that at high temperature. When the cascade proceeds under the hydrostatic strain, the Frenkel Pair (FP) production, the fraction of defect in cluster and the average size of the defect cluster, all increase at tensile state and decrease at compressive state. When the cascade is under uniaxial strain, the effect of strain parallel to PKA direction is less than the effect of hydrostatic strain, while the effect of strain perpendicular to PKA direction can be negligible. Under the uniaxial strain along 〈1 1 1〉 direction, the SIA and SIA cluster is observed to orientate along the strain direction at tensile state and the uniaxial compressive strain with direction perpendicular to 〈1 1 1〉 has led to the similar preferred nucleation. All these results indicate that under irradiation, the tensile state should be avoided for materials used in nuclear power plants.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

Science.gov (United States)

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and

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.

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

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 ...

Radiation-induced amorphization of intermetallic compounds: A molecular-dynamics study of CuTi and Cu4Ti3

International Nuclear Information System (INIS)

Lam, N.Q.; Okamoto, P.R.; Sabochick, M.J.

1991-06-01

In the present paper, important results of our recent computer simulation of radiation-induced amorphization in the ordered compounds CuTi and Cu 4 Ti 3 are summarized. The energetic, structural, thermodynamic and mechanical responses of these intermetallics during chemical disordering, point-defect production and heating were simulated, using molecular dynamics and embedded-atom potentials. From the atomistic details obtained, the critical role of radiation-induced structural disorder in driving the crystalline-to-amorphous phase transformation is discussed. 25 refs., 4 figs

Carbon cluster formation during thermal decomposition of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine and 1,3,5-triamino-2,4,6-trinitrobenzene high explosives from ReaxFF reactive molecular dynamics simulations.

Science.gov (United States)

Zhang, Luzheng; Zybin, Sergey V; van Duin, Adri C T; Dasgupta, Siddharth; Goddard, William A; Kober, Edward M

2009-10-08

We report molecular dynamics (MD) simulations using the first-principles-based ReaxFF reactive force field to study the thermal decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at various densities and temperatures. TATB is known to produce a large amount (15-30%) of high-molecular-weight carbon clusters, whereas detonation of nitramines such as HMX and RDX (1,3,5-trinitroperhydro-1,3,5-triazine) generate predominantly low-molecular-weight products. In agreement with experimental observation, these simulations predict that TATB decomposition quickly (by 30 ps) initiates the formation of large carbonaceous clusters (more than 4000 amu, or approximately 15-30% of the total system mass), and HMX decomposition leads almost exclusively to small-molecule products. We find that HMX decomposes readily on this time scale at lower temperatures, for which the decomposition rate of TATB is about an order of magnitude slower. Analyzing the ReaxFF MD results leads to the detailed atomistic structure of this carbon-rich phase of TATB and allows characterization of the kinetics and chemistry related to this phase and their dependence on system density and temperature. The carbon-rich phase formed from TATB contains mainly polyaromatic rings with large oxygen content, leading to graphitic regions. We use these results to describe the initial reaction steps of thermal decomposition of HMX and TATB in terms of the rates for forming primary and secondary products, allowing comparison to experimentally derived models. These studies show that MD using the ReaxFF reactive force field provides detailed atomistic information that explains such macroscopic observations as the dramatic difference in carbon cluster formation between TATB and HMX. This shows that ReaxFF MD captures the fundamental differences in the mechanisms of such systems and illustrates how the ReaxFF may be applied to model complex chemical phenomena

raaSAFT: A framework enabling coarse-grained molecular dynamics simulations based on the SAFT- γ Mie force field

Science.gov (United States)

Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.

2017-03-01

We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.

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.

Human serum albumin interactions with C{sub 60} fullerene studied by spectroscopy, small-angle neutron scattering, and molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Li, Song [Vanderbilt University, Department of Chemical and Biomolecular Engineering (United States); Zhao, Xiongce [NIDDK, National Institutes of Health (United States); Mo, Yiming [Institute of Agriculture, University of Tennessee (United States); Cummings, Peter T., E-mail: cummingspt@ornl.gov [Vanderbilt University, Department of Chemical and Biomolecular Engineering (United States); Heller, William T., E-mail: hellerwt@ornl.gov [Oak Ridge National Laboratory, Center for Structural Molecular Biology (United States)

2013-07-15

Concern about the toxicity of engineered nanoparticles, such as the prototypical nanomaterial C{sub 60} fullerene, continues to grow. While, evidence continues to mount that C{sub 60} and its derivatives may pose health hazards, the specific molecular interactions of these particles with biological macromolecules require further investigation. In this article, we report combined experimental and theoretical studies on the interaction of one of the most prevalent proteins in the human body, human serum albumin (HSA), with C{sub 60} in an aqueous environment. The C{sub 60}-HSA interaction was probed by circular dichroism (CD) spectroscopy, small-angle neutron scattering (SANS), and atomistic molecular dynamics (MD) simulations to understand C{sub 60}-driven changes in the structure of HSA in solution. The CD spectroscopy demonstrates that the secondary structure of the protein decreases in {alpha}-helical content in response to the presence of C{sub 60} (0.68 nm in diameter). Similarly, C{sub 60} produces subtle changes in the solution conformation of HSA (an 8.0 nm Multiplication-Sign 3.8 nm protein), as evidenced by the SANS data and MD simulations, but the data do not indicate that C{sub 60} changes the oligomerization state of the protein, such as by inducing aggregation. The results demonstrate that the interaction is not highly disruptive to the protein in a manner that would prevent it from performing its physiological function.

Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations.

Science.gov (United States)

Boggio-Pasqua, Martial; Burmeister, Carl F; Robb, Michael A; Groenhof, Gerrit

2012-06-14

Organisms have evolved a wide variety of mechanisms to utilize and respond to light. In many cases, the biological response is mediated by structural changes that follow photon absorption in a protein complex. The initial step in such cases is normally the photoisomerization of a highly conjugated prosthetic group. To understand better the factors controlling the isomerization, we perform atomistic molecular dynamics simulations. In this perspective article we briefly review the key theoretical concepts of photochemical reactions and present a practical simulation scheme for simulating photochemical reactions in biomolecular systems. In our scheme, a multi-configurational quantum mechanical description is used to model the electronic rearrangement for those parts of the system that are involved in the photon absorption. For the remainder, typically consisting of the apo-protein and the solvent, a simple force field model is used. The interactions in the systems are thus computed within a hybrid quantum/classical framework. Forces are calculated on-the-fly, and a diabatic surface hopping procedure is used to model the excited-state decay. To demonstrate how this method is used we review our studies on photoactivation of the photoactive yellow protein, a bacterial photoreceptor. We will show what information can be obtained from the simulations, and, by comparing to recent experimental findings, what the limitations of our simulations are.

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

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.

Understanding molecular simulation from algorithms to applications

CERN Document Server

Frenkel, Daan

2001-01-01

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the ""recipes"" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practic

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

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.

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.

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal.

Science.gov (United States)

Neale, Chris; Madill, Chris; Rauscher, Sarah; Pomès, Régis

2013-08-13

All molecular dynamics simulations are susceptible to sampling errors, which degrade the accuracy and precision of observed values. The statistical convergence of simulations containing atomistic lipid bilayers is limited by the slow relaxation of the lipid phase, which can exceed hundreds of nanoseconds. These long conformational autocorrelation times are exacerbated in the presence of charged solutes, which can induce significant distortions of the bilayer structure. Such long relaxation times represent hidden barriers that induce systematic sampling errors in simulations of solute insertion. To identify optimal methods for enhancing sampling efficiency, we quantitatively evaluate convergence rates using generalized ensemble sampling algorithms in calculations of the potential of mean force for the insertion of the ionic side chain analog of arginine in a lipid bilayer. Umbrella sampling (US) is used to restrain solute insertion depth along the bilayer normal, the order parameter commonly used in simulations of molecular solutes in lipid bilayers. When US simulations are modified to conduct random walks along the bilayer normal using a Hamiltonian exchange algorithm, systematic sampling errors are eliminated more rapidly and the rate of statistical convergence of the standard free energy of binding of the solute to the lipid bilayer is increased 3-fold. We compute the ratio of the replica flux transmitted across a defined region of the order parameter to the replica flux that entered that region in Hamiltonian exchange simulations. We show that this quantity, the transmission factor, identifies sampling barriers in degrees of freedom orthogonal to the order parameter. The transmission factor is used to estimate the depth-dependent conformational autocorrelation times of the simulation system, some of which exceed the simulation time, and thereby identify solute insertion depths that are prone to systematic sampling errors and estimate the lower bound of the

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

Energy Technology Data Exchange (ETDEWEB)

Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

2015-11-14

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

Molecular Dynamics Simulations of Grain Boundary and Bulk Diffusion in Metals.

Science.gov (United States)

Plimpton, Steven James

Diffusion is a microscopic mass transport mechanism that underlies many important macroscopic phenomena affecting the structural, electrical, and mechanical properties of metals. This thesis presents results from atomistic simulation studies of diffusion both in bulk and in the fast diffusion paths known as grain boundaries. Using the principles of molecular dynamics single boundaries are studied and their structure and dynamic properties characterized. In particular, tilt boundary bicrystal and bulk models of fcc Al and bcc alpha-Fe are simulated. Diffusion coefficients and activation energies for atomic motion are calculated for both models and compared to experimental data. The influence of the interatomic pair potential on the diffusion is studied in detail. A universal relation between the melting temperature that a pair potential induces in a simulated bulk model and the potential energy barrier height for atomic hopping is derived and used to correlate results for a wide variety of pair potentials. Using these techniques grain boundary and bulk diffusion coefficients for any fcc material can be estimated from simple static calculations without the need to perform more time-consuming dynamic simulations. The influences of two other factors on grain boundary diffusion are also studied because of the interest of the microelectronics industry in the diffusion related reliability problem known as electromigration. The first factor, known to affect the self diffusion rate of Al, is the presence of Cu impurity atoms in Al tilt boundaries. The bicrystal model for Al is seeded randomly with Cu atoms and a simple hybrid Morse potential used to model the Al-Cu interaction. While some effect due to the Cu is noted, it is concluded that pair potentials are likely an inadequate approximation for the alloy system. The second factor studied is the effect of the boundary orientation angle on the diffusion rate. Symmetric bcc Fe boundaries are relaxed to find optimal

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...

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

Science.gov (United States)

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

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.

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

Coarse-grained simulation of molecular mechanisms of recovery in thermally activated shape-memory polymers

Science.gov (United States)

Abberton, Brendan C.; Liu, Wing Kam; Keten, Sinan

2013-12-01

Thermally actuated shape-memory polymers (SMPs) are capable of being programmed into a temporary shape and then recovering their permanent reference shape upon exposure to heat, which facilitates a phase transition that allows dramatic increase in molecular mobility. Experimental, analytical, and computational studies have established empirical relations of the thermomechanical behavior of SMPs that have been instrumental in device design. However, the underlying mechanisms of the recovery behavior and dependence on polymer microstructure remain to be fully understood for copolymer systems. This presents an opportunity for bottom-up studies through molecular modeling; however, the limited time-scales of atomistic simulations prohibit the study of key performance metrics pertaining to recovery. In order to elucidate the effects of phase fraction, recovery temperature, and deformation temperature on shape recovery, here we investigate the shape-memory behavior in a copolymer model with coarse-grained potentials using a two-phase molecular model that reproduces physical crosslinking. Our simulation protocol allows observation of upwards of 90% strain recovery in some cases, at time-scales that are on the order of the timescale of the relevant relaxation mechanism (stress relaxation in the unentangled soft-phase). Partial disintegration of the glassy phase during mechanical deformation is found to contribute to irrecoverable strain. Temperature dependence of the recovery indicates nearly full elastic recovery above the trigger temperature, which is near the glass-transition temperature of the rubbery switching matrix. We find that the trigger temperature is also directly correlated with the deformation temperature, indicating that deformation temperature influences the recovery temperatures required to obtain a given amount of shape recovery, until the plateau regions overlap above the transition region. Increasing the fraction of glassy phase results in higher strain

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.

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.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

Science.gov (United States)

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-01

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-06

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

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

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)

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)

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

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

Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

Science.gov (United States)

Lee, M.W.; Meuwly, M.

2013-01-01

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

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...

Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the μm-Scale.

Directory of Open Access Journals (Sweden)

Dirk Zahn

Full Text Available Fracture mechanisms of an enamel-like hydroxyapatite-collagen composite model are elaborated by means of molecular and coarse-grained dynamics simulation. Using fully atomistic models, we uncover molecular-scale plastic deformation and fracture processes initiated at the organic-inorganic interface. Furthermore, coarse-grained models are developed to investigate fracture patterns at the μm-scale. At the meso-scale, micro-fractures are shown to reduce local stress and thus prevent material failure after loading beyond the elastic limit. On the basis of our multi-scale simulation approach, we provide a molecular scale rationalization of this phenomenon, which seems key to the resilience of hierarchical biominerals, including teeth and bone.

MOLECULAR DYNAMICS SIMULATION AND EXPERIMENTAL STUDIES OF GOLD NANOPARTICLE TEMPLATED HDL-LIKE NANOPARTICLES FOR CHOLESTEROL (POSTPRINT)

Science.gov (United States)

2016-12-21

Another possibility is that the DPPC lipids are in a gel phase at 300 K that makes it less dynamic to diffuse to the AuNP surface. This can also be...Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. J. Chem. Theory Comput. 2014, 10, 676−690. (31) Meurs, I.; Van...Integration of the Cartesian Equations of Motion of a System with Constraints : Molecular Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23, 327−341

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

Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

Science.gov (United States)

Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

2018-02-12

The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

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.

Free-energy Calculations Using Classical Molecular Simulation: Application to the Determination of the Melting Point and Chemical Potential of a Flexible RDX Model.

Czech Academy of Sciences Publication Activity Database

Sellers, M.S.; Lísal, Martin; Brennan, J.K.

2016-01-01

Roč. 18, č. 11 (2016), s. 7841-7850 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA13-02938S Grant - others:ARL(US) W911NF-10-2-0039 Institutional support: RVO:67985858 Keywords : solid-liquid coexistence * atomistic simulation * dynamics simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.123, year: 2016

Bulk viscosity of molecular fluids

Science.gov (United States)

Jaeger, Frederike; Matar, Omar K.; Müller, Erich A.

2018-05-01

The bulk viscosity of molecular models of gases and liquids is determined by molecular simulations as a combination of a dilute gas contribution, arising due to the relaxation of internal degrees of freedom, and a configurational contribution, due to the presence of intermolecular interactions. The dilute gas contribution is evaluated using experimental data for the relaxation times of vibrational and rotational degrees of freedom. The configurational part is calculated using Green-Kubo relations for the fluctuations of the pressure tensor obtained from equilibrium microcanonical molecular dynamics simulations. As a benchmark, the Lennard-Jones fluid is studied. Both atomistic and coarse-grained force fields for water, CO2, and n-decane are considered and tested for their accuracy, and where possible, compared to experimental data. The dilute gas contribution to the bulk viscosity is seen to be significant only in the cases when intramolecular relaxation times are in the μs range, and for low vibrational wave numbers (<1000 cm-1); This explains the abnormally high values of bulk viscosity reported for CO2. In all other cases studied, the dilute gas contribution is negligible and the configurational contribution dominates the overall behavior. In particular, the configurational term is responsible for the enhancement of the bulk viscosity near the critical point.

Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

Science.gov (United States)

Chung, Pil Seung; Song, Wonyup; Biegler, Lorenz T.; Jhon, Myung S.

2017-05-01

During the operation of hard disk drive (HDD), the perfluoropolyether (PFPE) lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic) and loss (viscous) moduli (G' and G″) by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

Directory of Open Access Journals (Sweden)

Pil Seung Chung

2017-05-01

Full Text Available During the operation of hard disk drive (HDD, the perfluoropolyether (PFPE lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic and loss (viscous moduli (G′ and G″ by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

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.

The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

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...

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

Predicting the solubility of gases in Nitrile Butadiene Rubber in extreme conditions using molecular simulation

Science.gov (United States)

Khawaja, Musab; Molinari, Nicola; Sutton, Adrian; Mostofi, Arash

In the oil and gas industry, elastomer seals play an important role in protecting sensitive monitoring equipment from contamination by gases - a problem that is exacerbated by the high pressures and temperatures found down-hole. The ability to predict and prevent such permeative failure has proved elusive to-date. Nitrile butadiene rubber (NBR) is a common choice of elastomer for seals due to its resistance to heat and fuels. In the conditions found in the well it readily absorbs small molecular weight gases. How this behaviour changes quantitatively for different gases as a function of temperature and pressure is not well-understood. In this work a series of fully atomistic simulations are performed to understand the effect of extreme conditions on gas solubility in NBR. Widom particle insertion is used to compute solubilities. The importance of sampling and allowing structural relaxation upon compression are highlighted, and qualitatively reasonable trends reproduced. Finally, while at STP it has previously been shown that the solubility of CO2 is higher than that of He in NBR, we observe that under the right circumstances it is possible to reverse this trend.

Molecular simulations and visualization: introduction and overview.

Science.gov (United States)

Hirst, Jonathan D; Glowacki, David R; Baaden, Marc

2014-01-01

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

Departure of microscopic friction from macroscopic drag in molecular fluid dynamics

Energy Technology Data Exchange (ETDEWEB)

Hanasaki, Itsuo [Institute of Engineering, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588 (Japan); Fujiwara, Daiki; Kawano, Satoyuki, E-mail: kawano@me.es.osaka-u.ac.jp [Graduate School of Engineering Science, Osaka University, Machikaneyama-cho 1-3, Toyonaka, Osaka 560-8531 (Japan)

2016-03-07

Friction coefficient of the Langevin equation and drag of spherical macroscopic objects in steady flow at low Reynolds numbers are usually regarded as equivalent. We show that the microscopic friction can be different from the macroscopic drag when the mass is taken into account for particles with comparable scale to the surrounding fluid molecules. We illustrate it numerically by molecular dynamics simulation of chloride ion in water. Friction variation by the atomistic mass effect beyond the Langevin regime can be of use in the drag reduction technology as well as the electro or thermophoresis.

Multiscale development of a fission gas thermal conductivity model: Coupling atomic, meso and continuum level simulations

International Nuclear Information System (INIS)

Tonks, Michael R.; Millett, Paul C.; Nerikar, Pankaj; Du, Shiyu; Andersson, David; Stanek, Christopher R.; Gaston, Derek; Andrs, David; Williamson, Richard

2013-01-01

Fission gas production and evolution significantly impact the fuel performance, causing swelling, a reduction in the thermal conductivity and fission gas release. However, typical empirical models of fuel properties treat each of these effects separately and uncoupled. Here, we couple a fission gas release model to a model of the impact of fission gas on the fuel thermal conductivity. To quantify the specific impact of grain boundary (GB) bubbles on the thermal conductivity, we use atomistic and mesoscale simulations. Atomistic molecular dynamic simulations were employed to determine the GB thermal resistance. These values were then used in mesoscale heat conduction simulations to develop a mechanistic expression for the effective GB thermal resistance of a GB containing gas bubbles, as a function of the percentage of the GB covered by fission gas. The coupled fission gas release and thermal conductivity model was implemented in Idaho National Laboratory’s BISON fuel performance code to model the behavior of a 10-pellet LWR fuel rodlet, showing how the fission gas impacts the UO 2 thermal conductivity. Furthermore, additional BISON simulations were conducted to demonstrate the impact of average grain size on both the fuel thermal conductivity and the fission gas release

Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

KAUST Repository

Kadoura, Ahmad Salim

2016-01-01

This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method

ATK-ForceField: a new generation molecular dynamics software package

Science.gov (United States)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

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.

A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties

Science.gov (United States)

Fu, Chia-Chun; Kulkarni, Pandurang M.; Scott Shell, M.; Gary Leal, L.

2012-10-01

Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-ϕ)N mesoscale particle system, where ϕ is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of �

Effect of surface hydrophobicity on the dynamics of water at the nanoscale confinement: A molecular dynamics simulation study

International Nuclear Information System (INIS)

Choudhury, Niharendu

2013-01-01

Highlights: • We present atomistic MD simulation of water confined between two paraffin-like plates. • Effect of plate hydrophobicity on the confined water dynamics is investigated. • Diffusivity of confined water is calculated from mean squared displacements. • Rotational dynamics of the confined water has bimodal nature of relaxation. • Monotonic dependence of translational and rotational dynamics on hydrophobicity. - Abstract: We present detailed molecular dynamics simulations of water in and around a pair of plates immersed in water to investigate the effect of degree of hydrophobicity or hydrophilicity of the plates on dynamics of water confined between the two plates. The nature of the plate has been tuned from hydrophobic to hydrophilic and vice versa by varying plate-water dispersion interaction. Analyses of the translational dynamics as performed by calculating mean squared displacements of the confined water reveal a monotonically decreasing trend of the diffusivity with increasing hydrophilicity of the plates. Orientational dynamics of the confined water also follows the same monotonic trend. Although orientational time constant almost does not change with the increase of plate-water dispersion interaction in the hydrophobic regime corresponding to the smaller plate-water attraction, it changes considerably in the hydrophilic regime corresponding to larger plate-water dispersion interactions

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

On simulation of local fluxes in molecular junctions

Science.gov (United States)

Cabra, Gabriel; Jensen, Anders; Galperin, Michael

2018-05-01

We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

Molecular Origin of Gerstmann-Str ussler-Scheinker Syndrome: Insight from Computer Simulation of an Amyloidogenic Prion Peptide

Energy Technology Data Exchange (ETDEWEB)

Diadone, Isabella [University of L' Aquila, L' Aquila, Italy; DiNola, Alfredo [University of Rome; Smith, Jeremy C [ORNL

2011-01-01

Prion proteins become pathogenic through misfolding. Here, we characterize the folding of a peptide consisting of residues 109 122 of the Syrian hamster prion protein (the H1 peptide) and of a more amyloidogenic A117V point mutant that leads in humans to an inheritable form of the Gerstmann-Straeussler-Scheinker syndrome. Atomistic molecular dynamics simulations are performed for 2.5 s. Both peptides lose their -helical starting conformations and assume a -hairpin that is structurally similar in both systems. In each simulation several unfolding/refolding events occur, leading to convergence of the thermodynamics of the conformational states to within 1 kJ/mol. The similar stability of the -hairpin relative to the unfolded state is observed in the two peptides. However, substantial differences are found between the two unfolded states. A local minimum is found within the free energy unfolded basin of the A117V mutant populated by misfolded collapsed conformations of comparable stability to the -hairpin state, consistent with increased amyloidogenicity. This population, in which V117 stabilizes a hydrophobic core, is absent in the wild-type peptide. These results are supported by simulations of oligomers showing a slightly higher stability of the associated structures and a lower barrier to association for the mutated peptide. Hence, a single point mutation carrying only two additional methyl groups is here shown to be responsible for rather dramatic differences of structuring within the unfolded (misfolded) state.

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.

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)

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.

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

Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation.

Science.gov (United States)

Hu, Xiao Liang; Piccinin, Simone; Laio, Alessandro; Fabris, Stefano

2012-12-21

Solar-driven water splitting is a key photochemical reaction that underpins the feasible and sustainable production of solar fuels. An amorphous cobalt-phosphate catalyst (Co-Pi) based on earth-abundant elements has been recently reported to efficiently promote water oxidation to protons and dioxygen, a main bottleneck for the overall process. The structure of this material remains largely unknown. We here exploit ab initio and classical atomistic simulations combined with metadynamics to build a realistic and statistically meaningful model of Co-Pi nanoparticles. We demonstrate the emergence and stability of molecular-size ordered crystallites in nanoparticles initially formed by a disordered Co-O network and phosphate groups. The stable crystallites consist of bis-oxo-bridged Co centers that assemble into layered structures (edge-sharing CoO(6) octahedra) as well as in corner- and face-sharing cubane units. These layered and cubane motifs coexist in the crystallites, which always incorporate disordered phosphate groups at the edges. Our computational nanoparticles, although limited in size to ~1 nm, can contain more than one crystallite and incorporate up to 18 Co centers in the cubane/layered structures. The crystallites are structurally stable up to high temperatures. We simulate the extended X-ray absorption fine structure (EXAFS) of our nanoparticles. Those containing several complete and incomplete cubane motifs-which are believed to be essential for the catalytic activity-display a very good agreement with the experimental EXAFS spectra of Co-Pi grains. We propose that the crystallites in our nanoparticles are reliable structural models of the Co-Pi catalyst surface. They will be useful to reveal the origin of the catalytic efficiency of these novel water-oxidation catalysts.

Simulation of Initiation in Hexanitrostilbene

Science.gov (United States)

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

We report on the effect of isolated voids and pairs of nearby voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock loading. 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. Micron-scale molecular dynamics simulations of a supported shockwave propagating in HNS crystal along the [010] orientation are performed (up = 1.25 km/s, Us =4.0 km/s, P = 11GPa.) We compare the effect on hot spot formation and growth rate of isolated cylindrical voids up to 0.1 µm in size with that of two 50nm voids set 100nm apart. 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 Lock- heed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics

Energy Technology Data Exchange (ETDEWEB)

Alekseeva, Uliana, E-mail: Alekseeva@itc.rwth-aachen.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); German Research School for Simulation Sciences (GRS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Winkler, Roland G., E-mail: r.winkler@fz-juelich.de [Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Sutmann, Godehard, E-mail: g.sutmann@fz-juelich.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); ICAMS, Ruhr-University Bochum, D-44801 Bochum (Germany)

2016-06-01

A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations.

Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response.

Directory of Open Access Journals (Sweden)

Elio A Cino

Full Text Available Intrinsically disordered proteins (IDPs are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTα and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2, with a common binding partner, Kelch-like ECH-associated protein 1(Keap1, are essential for regulating cellular response to oxidative stress. Misregulation of this pathway can lead to neurodegenerative diseases, premature aging and cancer. In order to understand the mechanisms these two disordered proteins employ to bind to Keap1, we performed extensive 0.5-1.0 microsecond atomistic molecular dynamics (MD simulations and isothermal titration calorimetry experiments to investigate the structure/dynamics of free-state ProTα and Neh2 and their thermodynamics of bindings. The results show that in their free states, both ProTα and Neh2 have propensities to form bound-state-like β-turn structures but to different extents. We also found that, for both proteins, residues outside the Keap1-binding motifs may play important roles in stabilizing the bound-state-like structures. Based on our findings, we propose that the binding of disordered ProTα and Neh2 to Keap1 occurs synergistically via preformed structural elements (PSEs and coupled folding and binding, with a heavy bias towards PSEs, particularly for Neh2. Our results provide insights into the molecular mechanisms Neh2 and ProTα bind to Keap1, information that is useful for developing therapeutics to enhance the oxidative stress response.

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.

Vision-Augmented Molecular Dynamics Simulation of Nanoindentation

Directory of Open Access Journals (Sweden)

Rajab Al-Sayegh

2015-01-01

Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.

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.

Molecular simulation studies on thermophysical properties with application to working fluids

CERN Document Server

Raabe, Gabriele

2017-01-01

This book discusses the fundamentals of molecular simulation, starting with the basics of statistical mechanics and providing introductions to Monte Carlo and molecular dynamics simulation techniques. It also offers an overview of force-field models for molecular simulations and their parameterization, with a discussion of specific aspects. The book then summarizes the available know-how for analyzing molecular simulation outputs to derive information on thermophysical and structural properties. Both the force-field modeling and the analysis of simulation outputs are illustrated by various examples. Simulation studies on recently introduced HFO compounds as working fluids for different technical applications demonstrate the value of molecular simulations in providing predictions for poorly understood compounds and gaining a molecular-level understanding of their properties. This book will prove a valuable resource to researchers and students alike.

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

Science.gov (United States)

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

Development of tight-binding, chemical-reaction-dynamics simulator for combinatorial computational chemistry

International Nuclear Information System (INIS)

Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira

2004-01-01

Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated

The atomic simulation environment-a Python library for working with atoms.

Science.gov (United States)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Assessment of Molecular Modeling & Simulation

Energy Technology Data Exchange (ETDEWEB)

None

2002-01-03

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

Molecular automata assembly: principles and simulation of bacterial membrane construction.

Science.gov (United States)

Lahoz-Beltra, R

1997-01-01

The motivation to understand the basic rules and principles governing molecular self-assembly may be relevant to explain in the context of molecular biology the self-organization and biological functions exhibited within cells. This paper presents a molecular automata model to simulate molecular self-assembly introducing the concept of molecular programming to simulate the biological function or operation performed by an assembled molecular state machine. The method is illustrated modelling Escherichia coli membrane construction including the assembly and operation of ATP synthase as well as the assembly of the bacterial flagellar motor. Flagellar motor operation was simulated using a different approach based on state machine definition used in virtual reality systems. The proposed methodology provides a modelling framework for simulation of biological functions performed by cellular components and other biological systems suitable to be modelled as molecular state machines.

Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

Science.gov (United States)

Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

2018-04-01

Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

Molecular-Level Simulations of the Turbulent Taylor-Green Flow

Science.gov (United States)

Gallis, M. A.; Bitter, N. P.; Koehler, T. P.; Plimpton, S. J.; Torczynski, J. R.; Papadakis, G.

2017-11-01

The Direct Simulation Monte Carlo (DSMC) method, a statistical, molecular-level technique that provides accurate solutions to the Boltzmann equation, is applied to the turbulent Taylor-Green vortex flow. The goal of this work is to investigate whether DSMC can accurately simulate energy decay in a turbulent flow. If so, then simulating turbulent flows at the molecular level can provide new insights because the energy decay can be examined in detail from molecular to macroscopic length scales, thereby directly linking molecular relaxation processes to macroscopic transport processes. The DSMC simulations are performed on half a million cores of Sequoia, the 17 Pflop platform at Lawrence Livermore National Laboratory, and the kinetic-energy dissipation rate and the energy spectrum are computed directly from the molecular velocities. The DSMC simulations are found to reproduce the Kolmogorov -5/3 law and to agree with corresponding Navier-Stokes simulations obtained using a spectral method. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

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

Mobility of hydrogen-helium clusters in tungsten studied by molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Grigorev, Petr, E-mail: grigorievpit@gmail.com [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol, 2400 (Belgium); Ghent University, Applied Physics EA17 FUSION-DC, St.Pietersnieuwstraat, 41 B4, B-9000, Gent (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnologies, and Telecommunications, Peter the Great St.Petersburg Polytechnic University, St. Petersburg (Russian Federation); Terentyev, Dmitry; Bonny, Giovanni [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol, 2400 (Belgium); Zhurkin, Evgeny E. [Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnologies, and Telecommunications, Peter the Great St.Petersburg Polytechnic University, St. Petersburg (Russian Federation); Oost, Guido van [Ghent University, Applied Physics EA17 FUSION-DC, St.Pietersnieuwstraat, 41 B4, B-9000, Gent (Belgium); Noterdaeme, Jean-Marie [Ghent University, Applied Physics EA17 FUSION-DC, St.Pietersnieuwstraat, 41 B4, B-9000, Gent (Belgium); Max-Planck-Institut für Plasmaphysik, Garching (Germany)

2016-06-15

Tungsten is a primary candidate material for plasma facing components in fusion reactors. Interaction of plasma components with the material is unavoidable and will lead to degradation of the performance and the lifetime of the in-vessel components. In order to gain better understanding the mechanisms driving the material degradation at atomic level, atomistic simulations are employed. In this work we study migration, stability and self-trapping properties of pure helium and mixed helium-hydrogen clusters in tungsten by means of molecular dynamics simulations. We test two versions of an embedded atom model interatomic potential by comparing it with ab initio data regarding the binding properties of He clusters. By analysing the trajectories of the clusters during molecular dynamics simulations at finite temperatures we obtain the diffusion parameters. The results show that the diffusivity of mixed clusters is significantly lower, than that of pure helium clusters. The latter suggest that the formation of mixed clusters during mixed hydrogen helium plasma exposure will affect the helium diffusivity in the material.

Temperature control in molecular dynamic simulations of non-equilibrium processes

International Nuclear Information System (INIS)

Toton, Dawid; Lorenz, Christian D; Rompotis, Nikolaos; Martsinovich, Natalia; Kantorovich, Lev

2010-01-01

Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NVT ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NVT thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF 2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO 2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic

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.

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)

Effects of molecular structure on microscopic heat transport in chain polymer liquids

International Nuclear Information System (INIS)

Matsubara, Hiroki; Kikugawa, Gota; Ohara, Taku; Bessho, Takeshi; Yamashita, Seiji

2015-01-01

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T c ) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs

Effects of molecular structure on microscopic heat transport in chain polymer liquids

Energy Technology Data Exchange (ETDEWEB)

Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

2015-04-28

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

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.

PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

Directory of Open Access Journals (Sweden)

Radhakrishna Bettadapura

2015-10-01

Full Text Available There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data, and 3D reconstructed cryo-electron microscopy (3D EM maps (albeit at coarser resolution of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2 fit (Polar Fast Fourier Fitting for the best possible structural alignment of atomistic structures with 3D EM. While PF(2 fit enables only a rigid, six dimensional (6D alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

Molecular dynamics simulation of carbon molecular sieve preparation for air separation

International Nuclear Information System (INIS)

Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh; Shariaty-Niassar, Mojtaba

2015-01-01

Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments

Molecular dynamics simulation of carbon molecular sieve preparation for air separation

Energy Technology Data Exchange (ETDEWEB)

Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh [Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Shariaty-Niassar, Mojtaba [University of Tehran, Tehran(Iran, Islamic Republic of)

2015-03-15

Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments.

Simulating the production of free defects in irradiated metals

International Nuclear Information System (INIS)

Heinisch, H.L.

1995-01-01

Under cascade-producing irradiation by high energy neutrons or charged particles, only a small fraction of the initially displaced atoms contribute to the population of free defects that are available to migrate throughout the metal and cause microstructural changes. Although, in principle, computer simulations of free defect production could best be done using molecular dynamics, in practice, the wide ranges of time and distance scales involved can be done only by a combination of atomistic models that employ various levels of approximation. An atomic-scale, multi-model approach has been developed that combines molecular dynamics, binary collision models and stochastic annealing simulation. The annealing simulation is utilized in calibrating binary collision simulations to the results of molecular dynamics calculations, as well as to model the subsequent migration of the defects on more macroscopic time and size scales. The annealing simulation and the method of calibrating the multi-model approach are discussed, and the results of simulations of cascades in copper are presented. The temperature dependence of free defect production following simulated annealing of isolated cascades in copper shows a differential in the fractions of free vacancies and interstitial defects escaping from the cascade above stage V. This differential, a consequence of the direct formation of interstitial clusters in cascades and the relative thermal stability of vacancy and interstitial clusters during subsequent annealing, is the basis for the production bias mechanism of void swelling. (orig.)

Molecular Simulations and Theoretical Predictions for Adsorption and Diffusion of CH{sub 4}/H{sub 2} and CO{sub 2}/CH{sub 4} Mixtures in ZIFs

Energy Technology Data Exchange (ETDEWEB)

Liu, Jinchen; Keskin, Seda; Sholl, David S; Johnson, J. Karl

2011-05-01

Adsorption and diffusion of CO{sub 2}/CH{sub 4} and CH{sub 4}/H{sub 2} mixtures were computed in zeolite imidazolate frameworks (ZIFs), ZIF-68 and ZIF-70, using atomically detailed simulations. Adsorption selectivity, diffusion selectivity, and membrane selectivity of ZIFs were calculated based on the results of atomistic simulations. Mixture adsorption isotherms predicted by the ideal adsorbed solution theory agree well with the results of molecular simulations for both ZIFs. Mixture diffusivity calculations indicate that diffusion of CH{sub 4} is increased with increasing concentration of H{sub 2} in the CH{sub 4}/H{sub 2} mixture, while the diffusivity of H{sub 2} decreases with increasing CH{sub 4} concentration. In contrast, the diffusivity of CH{sub 4} is essentially independent of the concentration of CO{sub 2} in the CO{sub 2}/CH{sub 4} mixture, while CO{sub 2} diffusivity decreases with increased CH{sub 4} loading, even though the diffusivity of CH{sub 4} is substantially larger than that of CO{sub 2}. This unusual behavior can be explained in terms of differences in adsorption site preferences due to charge–quadrupole interactions.

Comparison of coarse-grained (MARTINI) and atomistic molecular ...

Indian Academy of Sciences (India)

Rajat Desikan

as the root mean square deviation (RMSD) histograms and the inner pore radius profiles from ... ever coarse-grained simulations of membrane-proteins ..... from the MARTINI simulations show greater fluctuations than the all-atom simulations.

Molecular simulation of the thermophysical properties of N-functionalized alkylimidazoles.

Science.gov (United States)

Turner, C Heath; Cooper, Alex; Zhang, Zhongtao; Shannon, Matthew S; Bara, Jason E

2012-06-07

Molecular simulations are used to probe the thermophysical properties of a series of N-functionalized alkylimidazoles, ranging from N-methylimidazole to N-heptylimidazole. These compounds have been previously synthesized, and their solvation properties have been shown to be potentially useful for CO(2) capture from industrial sources. In this work, we use first-principles calculations to fit electrostatic charges to the molecular models, which are then used to perform a series of molecular dynamics simulations. Over a range of different temperatures, we benchmark the simulated densities and heat capacities against experimental measurements. Also, we predict the Henry's constants for CO(2) absorption and probe the solvents' structures using molecular simulation techniques, such as fractional free volume analysis and void distributions. We find that our simulations are able to closely reproduce the experimental benchmarks and add additional insight into the molecular structure of these fluids, with respect to their observed solvent properties.

The simulation approach to lipid-protein interactions.

Science.gov (United States)

Paramo, Teresa; Garzón, Diana; Holdbrook, Daniel A; Khalid, Syma; Bond, Peter J

2013-01-01

The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

Science.gov (United States)

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-01

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

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.

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

Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

Science.gov (United States)

Hu, Hao; Liu, Haiyan

2013-05-30

Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

Transitional grain boundary structures and the influence on thermal, mechanical and energy properties from molecular dynamics simulations

International Nuclear Information System (INIS)

Burbery, N.J.; Das, R.; Ferguson, W.G.

2016-01-01

The thermo-kinetic characteristics that dictate the activation of atomistic crystal defects significantly influence the mechanical properties of crystalline materials. Grain boundaries (GBs) primarily influence the plastic deformation of FCC metals through their interaction with mobile dislocation defects. The activation thresholds and atomic mechanisms that dictate the thermo-kinetic properties of grain boundaries have been difficult to study due to complex and highly variable GB structure. This paper presents a new approach for modelling GBs which is based on a systematic structural analysis of metastable and stable GBs. GB structural transformation accommodates defect interactions at the interface. The activation energy for such structural transformations was evaluated with nudged elastic band analysis of bi-crystals with several metastable 0 K grain boundary structures in pure FCC Aluminium (Al). The resultant activation energy was used to evaluate the thermal stability of the metastable grain boundary structures, with predictions of transition time based on transition state theory. The predictions are in very good agreement with the minimum time for irreversible structure transformation at 300 K obtained with molecular dynamics simulations. Analytical methods were used to evaluate the activation volume, which in turn was used to predict and explain the influence of stress and strain rate on the thermal and mechanical properties. Results of molecular dynamics simulations show that the GB structure is more closely related to the elastic strength at 0 K than the GB energy. Furthermore, the thermal instability of the GB structure directly influences the relationship between bi-crystal strength, temperature and strain rate. Hence, theoretically consistent models are established on the basis of activation criteria, and used to make predictions of temperature-dependent yield stress at a low strain rate, in agreement with experimental results.

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