WorldWideScience

Sample records for atomistic molecular simulation

  1. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable...

  2. Atomistic Molecular Dynamics Simulations of Shock Compressed Quartz

    CERN Document Server

    Farrow, Matthew R

    2011-01-01

    Atomistic non-equilibrium molecular dynamics (NEMD) simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer and van Santen to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geom- etry optimised system of a polar slab in a 3-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under repres...

  3. Parallel Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    HEFFELFINGER,GRANT S.

    2000-01-18

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

  4. Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann-Molecular Dynamics Simulations of Dense Fluids

    Science.gov (United States)

    Dupuis, A.; Koumoutsakos, P.

    We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  6. Hypercrosslinked polystyrene networks: An atomistic molecular dynamics simulation combined with a mapping/reverse mapping procedure

    Energy Technology Data Exchange (ETDEWEB)

    Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R. [A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova Str. 28, 119991 Moscow (Russian Federation)

    2014-04-07

    An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.

  7. 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.

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

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    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 pos......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...... 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...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  9. Atomistic simulations of nanoindentation

    Directory of Open Access Journals (Sweden)

    Izabela Szlufarska

    2006-05-01

    Full Text Available Our understanding of mechanics is pushed to its limit when the functionality of devices is controlled at the nanometer scale. A fundamental understanding of nanomechanics is needed to design materials with optimum properties. Atomistic simulations can bring an important insight into nanostructure-property relations and, when combined with experiments, they become a powerful tool to move nanomechanics from basic science to the application area. Nanoindentation is a well-established technique for studying mechanical response. We review recent advances in modeling (atomistic and beyond of nanoindentation and discuss how they have contributed to our current state of knowledge.

  10. Atomistic simulations of fracture

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1997-12-31

    Embedded atom interaction potentials are used to simulate the atomistic aspects of the fracture process. Simulations are presented for the behavior of cracks in pure metals and intermetallics, near the Griffith condition. The materials considered include Fe, Cu, Ni as well as Fe, Ni, Co, and Ti aluminides. The work focuses on the comparative study of fracture behavior in the different materials. The role of the atomic relaxation at the crack tip and of lattice trapping phenomena is analyzed.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Science.gov (United States)

    Papaleo, Elena

    2015-01-01

    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.

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

    KAUST Repository

    French, William R.

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jianfeng Wang

    2009-01-01

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

  15. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    Science.gov (United States)

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Summary Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  16. Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena.

    Science.gov (United States)

    Prasad, Manish; Sinno, Talid

    2004-11-01

    An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.

  17. Atomistic Simulations of Bicelle Mixtures

    OpenAIRE

    Jiang, Yong; Wang, Hao; Kindt, James T.

    2010-01-01

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironmen...

  18. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-12-01

    Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations.

  19. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.

    Science.gov (United States)

    Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R; Shalashilin, Dmitrii V

    2014-08-06

    In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

  20. Atomistic Simulations of Nanotube Fracture

    CERN Document Server

    Belytschko, T; Schatz, G; Ruoff, R S

    2002-01-01

    The fracture of carbon nanotubes is studied by atomistic simulations. The fracture behavior is found to be almost independent of the separation energy and to depend primarily on the inflection point in the interatomic potential. The rangle of fracture strians compares well with experimental results, but predicted range of fracture stresses is marketly higher than observed. Various plausible small-scale defects do not suffice to bring the failure stresses into agreement with available experimental results. As in the experiments, the fracture of carbon nanotubes is predicted to be brittle. The results show moderate dependence of fracture strength on chirality.

  1. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

    Science.gov (United States)

    Reif, Maria M; Oostenbrink, Chris

    2014-01-30

    The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.

  2. 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.

  3. Atomistic Monte Carlo Simulation of Lipid Membranes

    Directory of Open Access Journals (Sweden)

    Daniel Wüstner

    2014-01-01

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

  4. Atomistic simulations of bicelle mixtures.

    Science.gov (United States)

    Jiang, Yong; Wang, Hao; Kindt, James T

    2010-06-16

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets.

  5. 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......, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential...... of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol....

  6. 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.

  7. 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 sta......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...

  8. Atomistic simulation of solid-liquid coexistence for molecular systems: application to triazole and benzene.

    Science.gov (United States)

    Eike, David M; Maginn, Edward J

    2006-04-28

    A method recently developed to rigorously determine solid-liquid equilibrium using a free-energy-based analysis has been extended to analyze multiatom molecular systems. This method is based on using a pseudosupercritical transformation path to reversibly transform between solid and liquid phases. Integration along this path yields the free energy difference at a single state point, which can then be used to determine the free energy difference as a function of temperature and therefore locate the coexistence temperature at a fixed pressure. The primary extension reported here is the introduction of an external potential field capable of inducing center of mass order along with secondary orientational order for molecules. The method is used to calculate the melting point of 1-H-1,2,4-triazole and benzene. Despite the fact that the triazole model gives accurate bulk densities for the liquid and crystal phases, it is found to do a poor job of reproducing the experimental crystal structure and heat of fusion. Consequently, it yields a melting point that is 100 K lower than the experimental value. On the other hand, the benzene model has been parametrized extensively to match a wide range of properties and yields a melting point that is only 20 K lower than the experimental value. Previous work in which a simple "direct heating" method was used actually found that the melting point of the benzene model was 50 K higher than the experimental value. This demonstrates the importance of using proper free energy methods to compute phase behavior. It also shows that the melting point is a very sensitive measure of force field quality that should be considered in parametrization efforts. The method described here provides a relatively simple approach for computing melting points of molecular systems.

  9. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations

    Science.gov (United States)

    Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue

    2016-05-01

    Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.

  10. Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential.

    Science.gov (United States)

    Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

    2016-01-14

    To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.

  11. Atomistic computer simulations a practical guide

    CERN Document Server

    Brazdova, Veronika

    2013-01-01

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

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

    Science.gov (United States)

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

    2012-07-01

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

  13. Coupling atomistic and continuum length scales in heteroepitaxial systems: Multiscale molecular-dynamics/finite-element simulations of strain relaxation in Si/ Si3 N4 nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2005-09-01

    A hybrid atomistic-continuum simulation approach has been implemented to study strain relaxation in lattice-mismatched Si/Si3N4 nanopixels on a Si(111) substrate. We couple the molecular-dynamics (MD) and finite-element simulation approaches to provide an atomistic description near the interface and a continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are validated against full multimillion-atom MD simulations. We find that strain relaxation in Si/Si3N4 nanopixels may occur through the formation of a network of interfacial domain boundaries reminiscent of interfacial misfit dislocations. They result from the nucleation of domains of different interfacial bonding at the free edges and corners of the nanopixel, and subsequent to their creation they propagate inwards. We follow the motion of the domain boundaries and estimate a propagation speed of about ˜2.5×103m/s . The effects of temperature, nanopixel architecture, and film structure on strain relaxation are also investigated. We find: (i) elevated temperature increases the interfacial domain nucleation rates; (ii) a thin compliant Si layer between the film and the substrate plays a beneficial role in partially suppressing strain relaxation; and (iii) additional control over the interface morphology may be achieved by varying the film structure.

  14. Atomistic simulation of Voronoi-based coated nanoporous metals

    Science.gov (United States)

    Onur Yildiz, Yunus; Kirca, Mesut

    2017-02-01

    In this study, a new method developed for the generation of periodic atomistic models of coated and uncoated nanoporous metals (NPMs) is presented by examining the thermodynamic stability of coated nanoporous structures. The proposed method is mainly based on the Voronoi tessellation technique, which provides the ability to control cross-sectional dimension and slenderness of ligaments as well as the thickness of coating. By the utilization of the method, molecular dynamic (MD) simulations of randomly structured NPMs with coating can be performed efficiently in order to investigate their physical characteristics. In this context, for the purpose of demonstrating the functionality of the method, sample atomistic models of Au/Pt NPMs are generated and the effects of coating and porosity on the thermodynamic stability are investigated by using MD simulations. In addition to that, uniaxial tensile loading simulations are performed via MD technique to validate the nanoporous models by comparing the effective Young’s modulus values with the results from literature. Based on the results, while it is demonstrated that coating the nanoporous structures slightly decreases the structural stability causing atomistic configurational changes, it is also shown that the stability of the atomistic models is higher at lower porosities. Furthermore, adaptive common neighbour analysis is also performed to identify the stabilized atomistic structure after the coating process, which provides direct foresights for the mechanical behaviour of coated nanoporous structures.

  15. NiTi superelasticity via atomistic simulations

    Science.gov (United States)

    Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin

    2015-12-01

    The NiTi shape memory alloys (SMAs) are promising candidates for the next-generation multifunctional materials. These materials are superelastic i.e. they can fully recover their original shape even after fairly large inelastic deformations once the mechanical forces are removed. The superelasticity reportedly stems from atomic scale crystal transformations. However, very few computer simulations have emerged, elucidating the transformation mechanisms at the discrete lattice level, which underlie the extraordinary strain recoverability. Here, we conduct breakthrough molecular dynamics modelling on the superelastic behaviour of the NiTi single crystals, and unravel the atomistic genesis thereof. The deformation recovery is clearly traced to the reversible transformation between austenite and martensite crystals through simulations. We examine the mechanistic origin of the tension-compression asymmetries and the effects of pressure/temperature/strain rate variation isolatedly. Hence, this work essentially brings a new dimension to probing the NiTi performance based on the mesoscale physics under more complicated thermo-mechanical loading scenarios.

  16. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

    DEFF Research Database (Denmark)

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia

    2016-01-01

    In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present ...... (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3]....

  17. Phase separation in H2O:N2 mixture - molecular dynamics simulations using atomistic force fields

    Energy Technology Data Exchange (ETDEWEB)

    Maiti, A; Gee, R; Bastea, S; Fried, L

    2006-09-25

    A class II atomistic force field with Lennard-Jones 6-9 nonbond interactions is used to investigate equations of state (EOS) for important high explosive detonation products N{sub 2} and H{sub 2}O in the temperature range 700-2500 K and pressure range 0.1-10 GPa. A standard 6th order parameter-mixing scheme is then employed to study a 2:1 (molar) H{sub 2}O:N{sub 2} mixture, to investigate in particular the possibility of phase-separation under detonation conditions. The simulations demonstrate several important results, including: (1) the accuracy of computed EOS for both N{sub 2} and H{sub 2}O over the entire range of temperature and pressure considered; (2) accurate mixing-demixing phase boundary as compared to experimental data; and (3) the departure of mixing free energy from that predicted by ideal mixing law. The results provide comparison and guidance to state-of-the-art chemical kinetic models.

  18. 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

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a co...

  19. The notion of a plastic material spin in atomistic simulations

    Science.gov (United States)

    Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

    2016-12-01

    A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

  20. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.

    Science.gov (United States)

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

    Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

  1. 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

    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...... 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...... process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5-1 micros). Together with lipids binding in matching positions...

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    -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......Cytochrome (cyt) bc(1) is a multi-subunit membrane protein complex that is a vital component of the respiratory and photosynthetic electron transfer chains both in bacteria and eukaryotes. Although the complex's dimer structure has been solved using X-ray crystallography, it has not yet been...... 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...

  3. Atomistic simulations of nanoscale electrokinetic transport

    Science.gov (United States)

    Liu, Jin; Wang, Moran; Chen, Shiyi; Robbins, Mark

    2011-11-01

    An efficient and accurate algorithm for atomistic simulations of nanoscale electrokinetic transport will be described. The long-range interactions between charged molecules are treated using the Particle-Particle Particle-Mesh method and the Poisson equation for the electric potential is solved using an efficient multi-grid method in physical space. Using this method, we investigate two important applications in electrokinetic transport: electroosmotic flow in rough channels and electowetting on dielectric (EWOD). Simulations of electroosmotic and pressure driven flow in exactly the same geometries show that surface roughness has a much more pronounced effect on electroosmotic flow. Analysis of local quantities shows that this is because the driving force in electroosmotic flow is localized near the wall where the charge density is high. In atomistic simulations of EWOD, we find the contact angle follows the continuum theory at low voltages and always saturates at high voltages. Based on our results, a new mechanism for saturation is identified and possible techniques for controlling saturation are proposed. This work is supported by the National Science Foundation under Grant No. CMMI 0709187.

  4. Atomistic simulations of the Fe K-edge EXAFS in FeF3 using molecular dynamics and reverse Monte Carlo methods

    Science.gov (United States)

    Jonane, Inga; Timoshenko, Janis; Kuzmin, Alexei

    2016-10-01

    Atomistic simulations of the experimental Fe K-edge extended x-ray absorption fine structure (EXAFS) of rhombohedral (space group R\\bar{3}c) FeF3 at T = 300 K were performed using classical molecular dynamics and reverse Monte Carlo (RMC) methods. The use of two complementary theoretical approaches allowed us to account accurately for thermal disorder effects in EXAFS and to validate the developed force-field model, which was constructed as a sum of two-body Buckingham-type (Fe-F and F-F), three-body harmonic (Fe-F-Fe) and Coulomb potentials. We found that the shape of the Fe K-edge EXAFS spectrum of FeF3 is a more sensitive probe for the determination of potential parameters than the values of structural parameters (a, c, x(F)) available from diffraction studies. The best overall agreement between the experimental and theoretical EXAFS spectra calculated using ab initio multiple-scattering approach was obtained for the iron effective charge q(Fe) = 1.71. The RMC method coupled with the evolutionary algorithm was used for more elaborate analysis of the EXAFS data. The obtained results suggest that our force-field model slightly underestimates the amplitude of thermal vibrations of fluorine atoms in the direction perpendicular to the Fe-F bonds.

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

    Science.gov (United States)

    Kotsalis, E. M.; Walther, J. H.; Koumoutsakos, P.

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system 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 of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

  6. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2007-01-12

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process. We also discuss a technique for optimizing the calculation of fine-scale information on the fly for use in a coarse-scale simulation, and discuss the specific case of a fine-scale model that calculates void growth explicitly feeding into a coarse-scale mechanics model to study damage localization.

  7. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2005-12-31

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process.

  8. 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

    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...... 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...

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

    Science.gov (United States)

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

    2014-02-01

    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.

  10. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si{sub 3}N

    Energy Technology Data Exchange (ETDEWEB)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-20

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  11. Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Wijesinghe, S; Hornung, R; Garcia, A; Hadjiconstantinou, N

    2004-04-15

    We present an adaptive mesh and algorithmic refinement (AMAR) scheme for modeling multi-scale hydrodynamics. The AMAR approach extends standard conservative adaptive mesh refinement (AMR) algorithms by providing a robust flux-based method for coupling an atomistic fluid representation to a continuum model. The atomistic model is applied locally in regions where the continuum description is invalid or inaccurate, such as near strong flow gradients and at fluid interfaces, or when the continuum grid is refined to the molecular scale. The need for such ''hybrid'' methods arises from the fact that hydrodynamics modeled by continuum representations are often under-resolved or inaccurate while solutions generated using molecular resolution globally are not feasible. In the implementation described herein, Direct Simulation Monte Carlo (DSMC) provides an atomistic description of the flow and the compressible two-fluid Euler equations serve as our continuum-scale model. The AMR methodology provides local grid refinement while the algorithm refinement feature allows the transition to DSMC where needed. The continuum and atomistic representations are coupled by matching fluxes at the continuum-atomistic interfaces and by proper averaging and interpolation of data between scales. Our AMAR application code is implemented in C++ and is built upon the SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) framework developed at Lawrence Livermore National Laboratory. SAMRAI provides the parallel adaptive gridding algorithm and enables the coupling between the continuum and atomistic methods.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ogawa, Hiroshi, E-mail: h.ogawa@aist.go.jp

    2015-10-05

    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.

  13. 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

  14. A robust, coupled approach for atomistic-continuum simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Aubry, Sylvie; Webb, Edmund Blackburn, III (Sandia National Laboratories, Albuquerque, NM); Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John (Sandia National Laboratories, Albuquerque, NM); Kimmer, Christopher J.

    2004-09-01

    This report is a collection of documents written by the group members of the Engineering Sciences Research Foundation (ESRF), Laboratory Directed Research and Development (LDRD) project titled 'A Robust, Coupled Approach to Atomistic-Continuum Simulation'. Presented in this document is the development of a formulation for performing quasistatic, coupled, atomistic-continuum simulation that includes cross terms in the equilibrium equations that arise due to kinematic coupling and corrections used for the calculation of system potential energy to account for continuum elements that overlap regions containing atomic bonds, evaluations of thermo-mechanical continuum quantities calculated within atomistic simulations including measures of stress, temperature and heat flux, calculation used to determine the appropriate spatial and time averaging necessary to enable these atomistically-defined expressions to have the same physical meaning as their continuum counterparts, and a formulation to quantify a continuum 'temperature field', the first step towards constructing a coupled atomistic-continuum approach capable of finite temperature and dynamic analyses.

  15. 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.

  16. Scoring multipole electrostatics in condensed-phase atomistic simulations.

    Science.gov (United States)

    Bereau, Tristan; Kramer, Christian; Monnard, Fabien W; Nogueira, Elisa S; Ward, Thomas R; Meuwly, Markus

    2013-05-09

    Permanent multipoles (MTPs) embody a natural extension to common point-charge (PC) representations in atomistic simulations. In this work, we propose an alternative to the computationally expensive MTP molecular dynamics simulations by running a simple PC simulation and later reevaluate-"score''-all energies using the more detailed MTP force field. The method, which relies on the assumption that the PC and MTP force fields generate closely related phase spaces, is accomplished by enforcing identical sets of monopoles between the two force fields-effectively highlighting the higher MTP terms as a correction to the PC approximation. We first detail our consistent parametrization of the electrostatics and van der Waals interactions for the two force fields. We then validate the method by comparing the accuracy of protein-ligand binding free energies from both PC and MTP-scored representations with experimentally determined binding constants obtained by us. Specifically, we study the binding of several arylsulfonamide ligands to human carbonic anhydrase II. We find that both representations yield an accuracy of 1 kcal/mol with respect to experiment. Finally, we apply the method to rank the energetic contributions of individual atomic MTP coefficients for molecules solvated in water. All in all, MTP scoring is a computationally appealing method that can provide insight into the multipolar electrostatic interactions of condensed-phase systems.

  17. 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,

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

    NARCIS (Netherlands)

    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 coa

  19. Atomistic simulations of jog migration on extended screw dislocations

    DEFF Research Database (Denmark)

    Vegge, T.; Leffers, T.; Pedersen, O.B.;

    2001-01-01

    We have performed large-scale atomistic simulations of the migration of elementary jogs on dissociated screw dislocations in Cu. The local crystalline configurations, transition paths. effective masses. and migration barriers for the jogs are determined using an interatomic potential based on the...

  20. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. I. Structural modeling

    Science.gov (United States)

    Kim, Nayong; Kim, Yongman; Tsotsis, Theodore T.; Sahimi, Muhammad

    2005-06-01

    An atomistic model of layered double hydroxides, an important class of nanoporous materials, is presented. These materials have wide applications, ranging from adsorbents for gases and liquid ions to nanoporous membranes and catalysts. They consist of two types of metallic cations that are accommodated by a close-packed configuration of OH- and other anions in a positively charged brucitelike layer. Water and various anions are distributed in the interlayer space for charge compensation. A modified form of the consistent-valence force field, together with energy minimization and molecular dynamics simulations, is utilized for developing an atomistic model of the materials. To test the accuracy of the model, we compare the vibrational frequencies, x-ray diffraction patterns, and the basal spacing of the material, computed using the atomistic model, with our experimental data over a wide range of temperature. Good agreement is found between the computed and measured quantities.

  1. Atomistic Simulation of Non-Equilibrium Phenomena in Hypersonic Flows

    Science.gov (United States)

    Norman, Paul Erik

    The goal of this work is to model the heterogeneous recombination of atomic oxygen on silica surfaces, which is of interest for accurately predicting the heating on vehicles traveling at hypersonic speeds. This is accomplished by creating a finite rate catalytic model, which describes recombination with a set of elementary gas-surface reactions. Fundamental to a description of surface catalytic reactions are the in situ chemical structures on the surface where recombination can occur. Using molecular dynamics simulations with the Reax GSISiO potential, we find that the chemical sites active in direct gas-phase reactions on silica surfaces consist of a small number of specific structures (or defects). The existence of these defects on real silica surfaces is supported by experimental results and the structure and energetics of these defects have been verified with quantum chemical calculations. The reactions in the finite rate catalytic model are based on the interaction of molecular and atomic oxygen with these defects. Trajectory calculations are used to find the parameters in the forward rate equations, while a combination of detailed balance and transition state theory are used to find the parameters in the reverse rate equations. The rate model predicts that the oxygen recombination coefficient is relatively constant at T (300-1000 K), in agreement with experimental results. At T > 1000 K the rate model predicts a drop off in the oxygen recombination coefficient, in disagreement with experimental results, which predict that the oxygen recombination coefficient increases with temperature. A discussion of the possible reasons for this disagreement, including non-adiabatic collision dynamics, variable surface site concentrations, and additional recombination mechanisms is presented. This thesis also describes atomistic simulations with Classical Trajectory Calculation Direction Simulation Monte Carlo (CTC-DSMC), a particle based method for modeling non

  2. Predicting dislocation climb: Classical modeling versus atomistic simulations

    OpenAIRE

    Clouet, Emmanuel

    2011-01-01

    International audience; The classical modeling of dislocation climb based on a continuous description of vacancy diffusion is compared to recent atomistic simulations of dislocation climb in body-centered cubic iron under vacancy supersaturation [Phys. Rev. Lett. 105 095501 (2010)]. A quantitative agreement is obtained, showing the ability of the classical approach to describe dislocation climb. The analytical model is then used to extrapolate dislocation climb velocities to lower dislocation...

  3. State Representation Approach for Atomistic Time-Dependent Transport Calculations in Molecular Junctions.

    Science.gov (United States)

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

    We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville-von-Neumann equation approach of Sánchez et al. [J. Chem. Phys. 2006, 124, 214708] and Subotnik et al. [J. Chem. Phys. 2009, 130, 144105]. A key ingredient of our approach is a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to uniquely define the bias voltage across the system while maintaining a proper thermal electronic distribution within the finite lead models. Furthermore, it allows us to investigate complex molecular junctions, including multilead configurations. A heuristic derivation of our working equation leads to explicit expressions for the damping and driving terms, which serve as appropriate electron sources and sinks that effectively "open" the finite model system. Although the method does not forbid it, in practice we find neither violation of Pauli's exclusion principles nor deviation from density matrix positivity throughout our numerical simulations of various tight-binding model systems. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic molecular junction models.

  4. Perspective: Machine learning potentials for atomistic simulations

    Science.gov (United States)

    Behler, Jörg

    2016-11-01

    Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of the investigated problems, there is a constantly increasing need for simulations of more realistic, i.e., larger, model systems with improved accuracy. In many cases, the availability of sufficiently efficient interatomic potentials providing reliable energies and forces has become a serious bottleneck for performing these simulations. To address this problem, currently a paradigm change is taking place in the development of interatomic potentials. Since the early days of computer simulations simplified potentials have been derived using physical approximations whenever the direct application of electronic structure methods has been too demanding. Recent advances in machine learning (ML) now offer an alternative approach for the representation of potential-energy surfaces by fitting large data sets from electronic structure calculations. In this perspective, the central ideas underlying these ML potentials, solved problems and remaining challenges are reviewed along with a discussion of their current applicability and limitations.

  5. Methods for atomistic abrasion simulations of laterally periodic polycrystalline substrates with fractal surfaces

    Science.gov (United States)

    Eder, S. J.; Bianchi, D.; Cihak-Bayr, U.; Gkagkas, K.

    2017-03-01

    In this work we discuss a method to generate laterally periodic polycrystalline samples with fractal surfaces for use in molecular dynamics simulations of abrasion. We also describe a workflow that allows us to produce random lateral distributions of simple but realistically shaped hard abrasive particles with Gaussian size distribution and random particle orientations. We evaluate some on-the-fly analysis and visualization possibilities that may be applied during a molecular dynamics simulation to considerably reduce the post-processing effort. Finally, we elaborate on a parallelizable post-processing approach to evaluating and visualizing the surface topography, the grain structure and orientation, as well as the temperature distribution in large atomistic systems.

  6. 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.

  7. First principles molecular dynamics simulation of a task-specific ionic liquid based on silver-olefin complex: atomistic insight into separation process

    CERN Document Server

    Jiang, De-en

    2008-01-01

    First principles molecular dynamics based on density functional theory is applied to a hypothetical ionic liquid whose cations and anions are silver-ethylene complex [Ag(C2H4)2+] and tetrafluoroborate [BF4-], respectively. This ionic liquid represents a group of task-specific silver complex-based ionic liquids synthesized recently. Molecular dynamics simulations at two temperatures are performed for five picoseconds. Events of association, dissociation, exchange, and recombination of ethylene with silver cation are observed. A mechanism of ethylene transfer similar to the Grotthus type of proton transfer in water is identified, where a silver cation accepts one ethylene molecule and donates another to a neighboring silver cation. This mechanism may contribute to fast transport of olefins through ionic liquid membranes based on silver complexes for olefin/paraffin separation.

  8. First principles molecular dynamics simulation of a task-specific ionic liquid based on silver-olefin complex: atomistic insights into a separation process.

    Science.gov (United States)

    Jiang, De-en; Dai, Sheng

    2008-08-21

    First principles molecular dynamics based on density functional theory is applied to a hypothetical ionic liquid whose cations and anions are silver-ethylene complex [Ag(C2H4)2+] and tetrafluoroborate [BF4-], respectively. This ionic liquid represents a group of task-specific silver complex-based ionic liquids synthesized recently. Molecular dynamics simulations at two temperatures are performed for five picoseconds. Events of association, dissociation, exchange, and recombination of ethylene with silver cation are found. A mechanism of ethylene transfer similar to the Grotthus type of proton transfer in water is identified, where a silver cation accepts one ethylene molecule and donates another to a neighboring silver cation. This mechanism may contribute to fast transport of olefins through ionic liquid membranes based on silver complexes for olefin/paraffin separation.

  9. Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments.

    Science.gov (United States)

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  10. The atomistic mechanism of hcp-to-bcc martensitic transformation in the Ti-Nb system revealed by molecular dynamics simulations.

    Science.gov (United States)

    Li, Yang; Li, JiaHao; Liu, BaiXin

    2015-02-14

    Applying the constructed Ti-Nb potentials, molecular dynamics simulations were conducted to investigate the martensitic transformation of Ti100-xNbx alloys (x = 5, 10…25) from the α' phase (hcp) to the β phase (bcc). It is found that the transformation involved four phases, i.e. α', α'', fco (face-centered orthorhombic), and β phases. The structures of the obtained phases exhibit consistency with experimental data, verifying the validity of atomic simulations. The simulations not only revealed the processes of atomic displacements during the transformation, but also elucidated the underlying mechanism of the martensitic transformation at the atomic level. The martensitic transformation incorporates three types of coinstantaneous deformations i.e. slide, shear as well as extension, and the subsequent lattice constant relaxation. Furthermore, according to the proposed mechanism, the crystallographic correlation between the initial α' phase and the final β phase has been deduced. The simulation results provide a clear landscape on the martensitic transformation mechanism, facilitating our comprehensive understanding on the phase transition in the Ti-Nb system.

  11. Influence of specific intermolecular interactions on the thermal and dielectric properties of bulk polymers: atomistic molecular dynamics simulations of Nylon 6.

    Science.gov (United States)

    Lukasheva, N V; Tolmachev, D A; Nazarychev, V M; Kenny, J M; Lyulin, S V

    2017-01-04

    Specific intermolecular interactions, in particular H-bonding, have a strong influence on the structural, thermal and relaxation characteristics of polymers. We report here the results of molecular dynamics simulations of Nylon 6 which provides an excellent example for the investigation of such an influence. To demonstrate the effect of proper accounting for H-bonding on bulk polymer properties, the AMBER99sb force field is used with two different parametrization approaches leading to two different sets of partial atomic charges. The simulations allowed the study of the thermal and dielectric properties in a wide range of temperatures and cooling rates. The feasibility of the use of the three methods for the estimation of the glass transition temperature not only from the temperature dependence of structural characteristics such as density, but also by using the electrostatic energy and dielectric constant is demonstrated. The values of glass transition temperatures obtained at different cooling rates are practically the same for the three methods. By proper accounting for partial charges in the simulations, a reasonable agreement between the results of our simulations and experimental data for the density, thermal expansion coefficient, static dielectric constant and activation energy of γ and β relaxations is obtained demonstrating the validity of the modeling approach reported.

  12. Rotational viscosity of a liquid crystal mixture:a fully atomistic molecular dynamics study

    Institute of Scientific and Technical Information of China (English)

    Zhang Ran; Peng Zeng-Hui; Liu Yong-Gang; Zheng Zhi-Gang; Xuan Li

    2009-01-01

    Fully atomistic molecular dynamics(MD)simulations at 293, 303 and 313 K have been performed for the four. component liquid crystal mixture, E7, using the software package Material Studio. Order parameters and orientational time correlation functions(TCFs)were calculated from MD trajectories. The rotational viscosity coefficients(RVCs)of the mixture were ca]culated using the Nemtsov-Zakharov and Fialkowski methods based on statistical-mechanical approaches. Temperature dependences of RVC and density were discussed in detall. Reasonable agreement between the simulated and experimental values was found.

  13. Coupling-of-length-scale approach for multiscale atomistic-continuum simulations: Atomistically-induced stress distributions in Si/Si_3N4 nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George; Madhukar, Anupam

    2001-03-01

    A hybrid molecular-dynamics and finite-element simulation approach has been used to investigate stress distributions in Si(111) nanopixels covered with both crystalline and amorphous Si_3N4 thin films. Surfaces, lattice-mismatched interfaces, edges, and corners create stress fields on the order of 1 GPa inside the Si substrate with patterns that cannot be reproduced by a continuum approach alone. For these atomistically-induced inhomogeneouse stresses, the hybrid simulation approach provides an excellent agreement with the standard molecular dynamics, with considerably less computational costs.

  14. Nuclear wasteform materials: Atomistic simulation case studies

    Energy Technology Data Exchange (ETDEWEB)

    Chroneos, A., E-mail: alex.chroneos@open.ac.uk [Materials Engineering, The Open University, Milton Keynes MK7 6AA (United Kingdom); Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Institute of Materials Science, NCSR Demokritos, GR-15310 Athens (Greece); Rushton, M.J.D. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Jiang, C. [State Key Laboratory of Powder Metallurgy, Central South University, Changsha 410083 (China); Tsoukalas, L.H. [Department of Nuclear Engineering, Purdue University, West Lafayette, IN 47907 (United States)

    2013-10-15

    Ever increasing global energy demand combined with a requirement to reduce CO{sub 2} emissions has rekindled an interest in nuclear power generation. In order that nuclear energy remains publicly acceptable and therefore a sustainable source of power it is important that nuclear waste is dealt with in a responsible manner. To achieve this, improved materials for the long-term immobilisation of waste should be developed. The extreme conditions experienced by nuclear wasteforms necessitate the detailed understanding of their properties and the mechanisms acting within them at the atomic scale. This latter issue is the focus of the present review. Atomic scale simulation techniques can accelerate the development of new materials for nuclear wasteform applications and provide detailed information on their physical properties that cannot be easily accessed by experiment. The present article introduces examples of how atomic scale, computational modelling techniques have led to an improved understanding of current nuclear wasteform materials and also suggest how they may be used in the development of new wasteforms.

  15. Atomistic simulation of the structural and elastic properties of magnesite

    Indian Academy of Sciences (India)

    ZI-JIANG LIU; XIAO-WEI SUN; TING SONG; YUAN GUO; CAI-RONG ZHANG; ZHENG-RONG ZHANG

    2016-09-01

    Atomistic simulation was carried out to study the structural and elastic properties of MgCO$_3$ magnesite within the pressure range of the Earth’s mantle based on a novel force field. The lattice parameters and elasticconstants as a function of pressure up to 150 GPa are calculated. The results are in good agreement with the available experimental data and previous theoretical results, showing no phase transition over the pressure range of interest. We also found that magnesite exhibits a strong anisotropy throughout the lower mantle and that the nature of the anisotropy changes significantly with depth.

  16. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si3N4 Nanopixels

    Science.gov (United States)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-01

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  17. Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

    Science.gov (United States)

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

    2006-01-01

    A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

  18. 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.

  19. Atomistic simulation of static magnetic properties of bit patterned media

    Science.gov (United States)

    Arbeláez-Echeverri, O. D.; Agudelo-Giraldo, J. D.; Restrepo-Parra, E.

    2016-09-01

    In this work we present a new design of Co based bit pattern media with out-of-plane uni-axial anisotropy induced by interface effects. Our model features the inclusion of magnetic impurities in the non-magnetic matrix. After the material model was refined during three iterations using Monte Carlo simulations, further simulations were performed using an atomistic integrator of Landau-Lifshitz-Gilbert equation with Langevin dynamics to study the behavior of the system paying special attention to the super-paramagnetic limit. Our model system exhibits three magnetic phase transitions, one due to the magnetically doped matrix material and the weak magnetic interaction between the nano-structures in the system. The different magnetic phases of the system as well as the features of its phase diagram are explained.

  20. A dynamic atomistic-continuum method for the simulation of crystalline materials

    CERN Document Server

    Huang Zhon Gy

    2002-01-01

    We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics in crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away from defects and interfaces. We propose a new class of matching conditions between the atomistic and the continuum regions. These conditions ensure the accurate passage of large-scale information between the atomistic and the continuum regions and at the same time minimize the reflection of phonons at the atomistic-continuum interface. They can be made adaptive by choosing appropriate weight functions. We present applications to dislocation dynamics, friction between two-dimensional crystal surfaces, and fracture dynamics. We compare results of the coupled method and of the detailed atomistic model.

  1. Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    McCarty, Keven F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Zhou, Xiaowang [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ward, Donald K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schultz, Peter A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Foster, Michael E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bartelt, Norman Charles [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expand the number of potential types of graphene electronic devices.

  2. A hybrid atomistic electrodynamics-quantum mechanical approach for simulating surface-enhanced Raman scattering.

    Science.gov (United States)

    Payton, John L; Morton, Seth M; Moore, Justin E; Jensen, Lasse

    2014-01-21

    Surface-enhanced Raman scattering (SERS) is a technique that has broad implications for biological and chemical sensing applications by providing the ability to simultaneously detect and identify a single molecule. The Raman scattering of molecules adsorbed on metal nanoparticles can be enhanced by many orders of magnitude. These enhancements stem from a twofold mechanism: an electromagnetic mechanism (EM), which is due to the enhanced local field near the metal surface, and a chemical mechanism (CM), which is due to the adsorbate specific interactions between the metal surface and the molecules. The local field near the metal surface can be significantly enhanced due to the plasmon excitation, and therefore chemists generally accept that the EM provides the majority of the enhancements. While classical electrodynamics simulations can accurately simulate the local electric field around metal nanoparticles, they offer few insights into the spectral changes that occur in SERS. First-principles simulations can directly predict the Raman spectrum but are limited to small metal clusters and therefore are often used for understanding the CM. Thus, there is a need for developing new methods that bridge the electrodynamics simulations of the metal nanoparticle and the first-principles simulations of the molecule to facilitate direct simulations of SERS spectra. In this Account, we discuss our recent work on developing a hybrid atomistic electrodynamics-quantum mechanical approach to simulate SERS. This hybrid method is called the discrete interaction model/quantum mechanics (DIM/QM) method and consists of an atomistic electrodynamics model of the metal nanoparticle and a time-dependent density functional theory (TDDFT) description of the molecule. In contrast to most previous work, the DIM/QM method enables us to retain a detailed atomistic structure of the nanoparticle and provides a natural bridge between the electronic structure methods and the macroscopic

  3. Quantum-based Atomistic Simulation of Transition Metals

    Energy Technology Data Exchange (ETDEWEB)

    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

    2005-08-29

    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.

  4. Shock Hugoniot behavior of single crystal titanium using atomistic simulations

    Science.gov (United States)

    Mackenchery, Karoon; Dongare, Avinash

    2017-01-01

    Atomistic shock simulations are performed for single crystal titanium using four different interatomic potentials at impact velocities ranging from 0.5 km/s to 2.0 km/s. These potentials comprise of three parameterizations in the formulation of the embedded atom method and one formulation of the modified embedded atom method. The capability of the potentials to model the shock deformation and failure behavior is investigated by computing the shock hugoniot response of titanium and comparing to existing experimental data. In addition, the capability to reproduce the shock induced alpha (α) to omega (ω) phase transformation seen in Ti is investigated. The shock wave structure is discussed and the velocities for the elastic, plastic and the α-ω phase transformation waves are calculated for all the interatomic potentials considered.

  5. Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation.

    Science.gov (United States)

    Zahariev, Tsvetan K; Slavchov, Radomir I; Tadjer, Alia V; Ivanova, Anela N

    2014-04-15

    Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems.

  6. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

    Science.gov (United States)

    Pande, Vijay S; Baker, Ian; Chapman, Jarrod; Elmer, Sidney P; Khaliq, Siraj; Larson, Stefan M; Rhee, Young Min; Shirts, Michael R; Snow, Christopher D; Sorin, Eric J; Zagrovic, Bojan

    2003-01-01

    Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.

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

    Science.gov (United States)

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

    2011-01-01

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

  8. Atomistic Simulations of Uranium Incorporation into Iron (Hydr)Oxides

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Felmy, Andrew R.; Ilton, Eugene S.

    2011-04-29

    Atomistic simulations were carried out to characterize the coordination environments of U incorporated in three Fe-(hydr)oxide minerals: goethite, magnetite, and hematite. The simulations provided information on U-O and U-Fe distances, coordination numbers, and lattice distortion for U incorporated in different sites (e.g., unoccupied versus occupied sites, octahedral versus tetrahedral) as a function of the oxidation state of U and charge compensation mechanisms (i.e., deprotonation, vacancy formation, or reduction of Fe(III) to Fe(II)). For goethite, deprotonation of first shell hydroxyls enables substitution of U for Fe(III) with a minimal amount of lattice distortion, whereas substitution in unoccupied octahedral sites induced appreciable distortion to 7-fold coordination regardless of U oxidation states and charge compensation mechanisms. Importantly, U-Fe distances of ~3.6 Å were associated with structural incorporation of U and cannot be considered diagnostic of simple adsorption to goethite surfaces. For magnetite, the octahedral site accommodates U(V) or U(VI) with little lattice distortion. U substituted for Fe(III) in hematite maintained octahedral coordination in most cases. In general, comparison of the simulations with available experimental data provides further evidence for the structural incorporation of U in iron (hydr)oxide minerals.

  9. Nano sculpt: A methodology for generating complex realistic configurations for atomistic simulations.

    Science.gov (United States)

    Prakash, A; Hummel, M; Schmauder, S; Bitzek, E

    2016-01-01

    Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nano sculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data.

  10. 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; Biegel, Bryan (Technical Monitor)

    2002-01-01

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

  11. Fracture toughness from atomistic simulations: Brittleness induced by emission of sessile dislocations

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1998-08-04

    Using atomistic simulations of crack response for intermetallic materials the author shows that when the emitted dislocations are sessile and stay in the immediate vicinity of the crack tip the emitted dislocations can actually lead to brittle failure. She present the results of an atomistic simulation study of the simultaneous dislocation emission and crack propagation process in this class of materials. She used a molecular statics technique with embedded atom (EAM) potentials developed for NiAl. The crystal structure of NiAl is the CsCl type (B2) with a lattice parameter of 0.287 nm, which is reproduced by the potential together with the cohesive energy and elastic constants. The compound stays ordered up to the melting point, indicating a strong tendency towards chemical ordering with a relatively high energy of the antiphase boundary (APB). As a result of this relatively large energy the dislocations of 1/2<111> type Burgers vectors imply a high energy and the deformation process occurs via the larger <100> type dislocations.

  12. Atomistic-Continuum Hybrid Simulation of Heat Transfer between Argon Flow and Copper Plates

    CERN Document Server

    Mao, Yijin; Chen, C L

    2016-01-01

    A simulation work aiming to study heat transfer coefficient between argon fluid flow and copper plate is carried out based on atomistic-continuum hybrid method. Navier-Stokes equations for continuum domain are solved through the Pressure Implicit with Splitting of Operators (PISO) algorithm, and the atom evolution in molecular domain is solved through the Verlet algorithm. The solver is validated by solving Couette flow and heat conduction problems. With both momentum and energy coupling method applied, simulations on convection of argon flows between two parallel plates are performed. The top plate is kept as a constant velocity and has higher temperature, while the lower one, which is modeled with FCC copper lattices, is also fixed but has lower temperature. It is found that, heat transfer between argon fluid flow and copper plate in this situation is much higher than that at macroscopic when the flow is fully developed.

  13. Linking Atomistic and Mesoscale Simulations of Water Soluble Polymers

    Science.gov (United States)

    Jones, J. L.

    2003-03-01

    There exist a range of techniques for studying surfactants and polymers in the mesoscale regime. One of the challenges is to link mesoscale theories and simulations to other calculation methods which address different length scales of the system. We introduce some mesoscale methods of calculation for polymers and surfactants and then present a case study of where mesoscale modelling is used for mechanistic understanding, by linking the method to high throughput in-silico screening methods. We look at the adsorption onto silica of ethylene oxide (EO)/ propylene oxide (PO) block copolymers (lutrols) which have been modified by end-grafting of short, cationic dimethylamino ethyl methacrylate (DMAEMA)chains. Given that the silica surface is negatively charged, it is remarkable that in some circumstances, polymers with longercationic chains have a lower adsorption. The effect is attributed to a competition between strong adsorption of the cationic DMAEMA groups driven by electrostatics, and weaker adsorption of the more numerous EO groups. This then raises the question of how we produce the values for the mesoscale parameters in these models and in the second part of the talk we describe a calculation method for doing this for water soluble polymers. The most promising route, but notoriously costly, is based on free energy calculations at the atomistic level. Free energy calculations are computationally intensive in general, but in an aqueous system one is also faced with the additional problem of using complex continuum models and/or accurate interaction potentials for water. Here we show how potential of mean force (PMF)calculations offer a practical alternative which avoids these drawbacks, though one is still faced with extremely long simulations.

  14. Atomistic simulations of fracture in the B2 phase of the Nb-Ti-Al system

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Computer Simulation Lab.

    1998-06-30

    Atomistic simulations of the crack tip configuration in the B2 phase of Nb-rich alloys in the Nb-Ti-Al are presented. The alloy compositions studied are Nb-16Al-16Ti and Nb-16Al-33Ti. The simulations were carried out using molecular statics and empirical embedded atom method (EAM) potentials for the ternary system developed in previous work. The behavior of a semi-infinite crack was studied under mode I loading for different crack tip geometries. The crack was embedded in a simulation cell with periodic boundary conditions along the direction parallel to the crack front and fixed boundary conditions along the periphery of the simulation cell. The quasi-static simulations were carried out using a molecular statics relaxation technique to obtain the minimum energy configuration of the atoms starting from their initial elastic positions, under increasingly higher stress intensities. The competition between dislocation emission and cleavage was studied in these alloys as a function of Ti content. Cracks along {l_brace}110{r_brace}-type planes with crack fronts oriented along different directions were studied. The alloys showed increased ductility with increased Ti content. The simulations show more ductile behavior than other intermetallics, due to easier dislocation emission processes at the crack tip. (orig.) 30 refs.

  15. 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.

  16. Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics

    OpenAIRE

    Vila Verde, A.; Beltramo, Peter J.; Maranas, Janna K.

    2011-01-01

    We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala 10 , Ser 10 , Thr 10 , Arg 10 , Lys 10 , and Gln 10 ], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movemen...

  17. Atomistic Simulations of Functional Au-144(SR)(60) Gold Nanoparticles in Aqueous Environment

    DEFF Research Database (Denmark)

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

    2012-01-01

    Charged monolayer-protected gold nanoparticles (AuNPs) have been studied in aqueous solution by performing atomistic molecular dynamics simulations at physiological temperature (310 K). Particular attention has been paid to electrostatic properties that modulate the formation of a complex comprised...... of the nanoparticle together with surrounding ions and water. We focus on Au-144 nanoparticles that comprise a nearly spherical Au core (diameter similar to 2 nm), a passivating Au-S interface, and functionalized alkanethiol chains. Cationic and anionic AuNPs have been modeled with amine and carboxyl terminal groups...... potential displays a minimum for AuNP- at 1.9 nm from the center of the nanoparticle, marking a preferable location for Na+, while the AuNP+ potential (affecting the distribution of Cl-) rises almost monotonically with a local maximum. Comparison to Debye-Huckel theory shows very good agreement for radial...

  18. A Spectral Multiscale Method for Wave Propagation Analysis: Atomistic-Continuum Coupled Simulation

    CERN Document Server

    Patra, Amit K; Ganguli, Ranjan

    2014-01-01

    In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a ...

  19. Identifying early stage precipitation in large-scale atomistic simulations of superalloys

    Science.gov (United States)

    Schmidt, Eric; Bristowe, Paul D.

    2017-04-01

    A method for identifying and classifying ordered phases in large chemically and thermally disordered atomistic models is presented. The method uses Steinhardt parameters to represent local atomic configurations and develops probability density functions to classify individual atoms using naïve Bayes. The method is applied to large molecular dynamics simulations of supersaturated Ni-20 at% Al solid solutions in order to identify the formation of embryonic γ‧-Ni3Al. The composition and temperatures are chosen to promote precipitation, which is observed in the form of ordering and is found to occur more likely in regions with above average Al concentration producing ‘clusters’ of increasing size. The results are interpreted in terms of a precipitation mechanism in which the solid solution is unstable with respect to ordering and potentially followed by either spinodal decomposition or nucleation and growth.

  20. Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface

    Science.gov (United States)

    He, Xibing; Guvench, Olgun; MacKerell, Alexander D.; Klein, Michael L.

    2010-01-01

    Molecular Dynamics simulations with the CHARMM atomistic force field have been used to study monolayers of a series of linear alkylbenzene sulfonates (LAS) at the water/air interface. Both the numbers of carbon atoms in the LAS alkyl tail (1 to 11), and the position of attachment of the benzene ring on the alkyl chain have been varied. Totally 36 LAS homologues and isomers have been investigated. The surface tensions of the systems and the average tilt angles of the LAS molecules are found to be related to both the length and the degree of branching of the alkyl tails, whereas the solubility and mobility are mostly determined by the tail length. PMID:20614916

  1. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

    Science.gov (United States)

    Rzepiela, Andrzej J; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J

    2011-06-14

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1:1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein

  2. Predictive atomistic simulations of electronic properties of realistic nanoscale devices: A multiscale modeling approach

    Science.gov (United States)

    Vedula, Ravi Pramod Kumar

    profiles, inherent in strain-engineered Ge nanofins, on their transport properties. Fully atomistic simulations, involving a combination molecular dynamics simulations with first-principles based force-fields and semi-empirical tight binding calculations, coupled with linearized Boltzmann model are used to calculate the hole transport properties of realistic Ge nanofins (heights 5-15nm and widths 5nm-40nm). Our simulations predict the technological limit of phonon limited hole mobility improvement in Ge channel PMOS devices (Hengineer high performance uniaxial devices conducive to the existing top-down fabrication approaches. From these calculations, we demonstrate that realistic modeling of the devices requires a reduction in the empiricism of fitting parameters and incorporation of new multi-scale, multi-resolution approach spanning across various spatial and temporal scales. Such physics based predictive multiscale models facilitate an integrated approach for rapid development and pave the way for designing new advanced materials and devices.

  3. Interfacial Phenomena: Linking Atomistic and Molecular Level Processes

    Energy Technology Data Exchange (ETDEWEB)

    Jay A Brandes

    2009-09-23

    This was a grant to support travel for scientists to present data and interact with others in their field. Specifically, speakers presented their data in a session entitled “Interfacial Phenomena: Linking Atomistic and Macroscopic Properties: Theoretical and Experimental Studies of the Structure and Reactivity of Mineral Surfaces”. The session ran across three ½ day periods, March 30-31 2004. The session’s organizers were David J. Wesolowski andGordon E. Brown Jr. There were a total of 30 talks presented.

  4. Unravelling Mg2+-RNA binding with atomistic molecular dynamics.

    Science.gov (United States)

    Cunha, Richard A; Bussi, Giovanni

    2017-02-01

    Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg(2+) on a RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases. Based on this, we simulate a carefully chosen set of models that allows us to quantify the effects of competition with monovalent cations, RNA flexibility, and RNA hybridization. Our simulations reproduce the decrease and increase of Mg(2+) affinity due to ion competition and hybridization respectively, and predict that RNA flexibility has a site dependent effect. This suggests a non trivial interplay between RNA conformational entropy and divalent cation binding.

  5. Voltage equilibration for reactive atomistic simulations of electrochemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Onofrio, Nicolas; Strachan, Alejandro, E-mail: strachan@purdue.edu [School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47906 (United States)

    2015-08-07

    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.

  6. 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 ...

  7. Origin of unrealistic blunting during atomistic fracture simulations based on MEAM potentials

    Science.gov (United States)

    Ko, Won-Seok; Lee, Byeong-Joo

    2014-06-01

    Atomistic simulations based on interatomic potentials have frequently failed to correctly reproduce the brittle fracture of materials, showing an unrealistic blunting. We analyse the origin of the unrealistic blunting during atomistic simulations by modified embedded-atom method (MEAM) potentials for experimentally well-known brittle materials such as bcc tungsten and diamond silicon. The radial cut-off which has been thought to give no influence on MEAM calculations is found to have a decisive effect on the crack propagation behaviour. Extending both cut-off distance and truncation range can prevent the unrealistic blunting, reproducing many well-known fracture behaviour which have been difficult to reproduce. The result provides a guideline for future atomistic simulations that focus on various fracture-related phenomena including the failure of metallic-covalent bonding material systems using MEAM potentials.

  8. Thermal stability of silicon nanowires:atomistic simulation study

    Institute of Scientific and Technical Information of China (English)

    Liu Wen-Liang; Zhang Kai-Wang; Zhong Jian-Xin

    2009-01-01

    Using the Stillinger-Weber (SW) potential model, we investigate the thermal stability of pristine silicon nanowires based on classical molecular dynamics (MD) simulations. We explore the structural evolutions and the Lindemann indices of silicon nanowires at different temperatures in order to unveil atomic-level melting behaviour of silicon nanowires.The simulation results show that silicon nanowires with surface reconstructions have higher thermal stability than those without surface reconstructions, and that silicon nanowires with perpendicular dimmer rows on the two (100) surfaces have somewhat higher thermal stability than nanowires with parallel dimmer rows on the two (100) surfaces. Furthermore, the melting temperature of silicon nanowires increases as their diameter increases and reaches a saturation value close to the melting temperature of bulk silicon. The value of the Lindemann index for melting silicon nanowires is 0.037.

  9. Atomistic Simulations of Material Properties under Extreme Conditions

    Science.gov (United States)

    An, Qi

    Extreme conditions involve low or high temperatures (> 1500 K), high pressures (> 30 MPa), high strains or strain rates, high radiation fluxes (> 100 dpa), and high electromagnetic fields (> 15T). Material properties under extreme conditions can be extremely different from those under normal conditions. Understanding material properties and performance under extreme conditions, including their dynamic evolution over time, plays an essential role in improving material properties and developing novel materials with desired properties. To understand material properties under extreme conditions, we use molecular dynamics (MD) simulations with recently developed reactive force fields (ReaxFF) and traditional embedded atom methods (EAM) potentials to examine various materials (e.g., energetic materials and binary liquids) and processes. The key results from the simulations are summarized below. Anisotropic sensitivity of RDX crystals: Based on the compress-and-shear reactive dynamics (CS-RD) simulations of cyclotrimethylene trinitramine (RDX) crystals, we predict that for mechanical shocks between 3 and 7 GPa, RDX is the most sensitive to shocks perpendicular to the (100) and (210) planes, while it is insensitive to those perpendicular to the (120), (111), and (110) planes. The simulations demonstrate that the molecular origin of anisotropic shock sensitivity is the steric hindrance to shearing of adjacent slip planes. Mechanisms of hotspot formation in polymer bonded explosives (PBXs): The simulations of a realistic model of PBXs reveal that hotspots may form at the nonplanar interfaces where shear relaxation leads to a dramatic temperature increase that persists long after the shock front has passed the interface. For energetic materials this temperature increase is coupled to chemical reactions that eventually lead to detonation. We show that decreasing the density of the binder eliminates the hotspots or reduces the sensitivity. Cavitation in binary metallic liquids

  10. Atomistic simulation for deforming complex alloys with application toward TWIP steel and associated physical insights

    Science.gov (United States)

    Wang, Peng; Xu, Shaofeng; Liu, Jiabin; Li, Xiaoyan; Wei, Yujie; Wang, Hongtao; Gao, Huajian; Yang, Wei

    2017-01-01

    The interest in promoting deformation twinning for plasticity is mounting for advanced materials. In contrast to disordered grain boundaries, highly organized twin boundaries are beneficial to promoting strength-ductility combination. Twinning deformation typically involves the kinetics of stacking faults, its interplay with dislocations, as well as the interactions between dislocations and twin boundaries. While the latter has been intensively studied, the dynamics of stacking faults has been rarely touched upon. In this work, we report new physical insights on the stacking fault dynamics in twin induced plasticity (TWIP) steels. The atomistic simulation is made possible by a newly introduced approach: meta-atom molecular dynamics simulation. The simulation suggests that the stacking fault interactions are dominated by dislocation reactions that take place spontaneously, different from the existing mechanisms. Whether to generate a single stacking fault, or a twinning partial and a trailing partial dislocation, depends upon a unique parameter, namely the stacking fault energy. The latter in turn determines the deformation twinning characteristics. The complex twin-slip and twin-dislocation interactions demonstrate the dual role of deformation twins as both the dislocation barrier and dislocation storage. This duality contributes to the high strength and high ductility of TWIP steels.

  11. A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nomura, K; Seymour, R; Wang, W; Kalia, R; Nakano, A; Vashishta, P; Shimojo, F; Yang, L H

    2009-02-17

    A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based on hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).

  12. Atomistic simulation of laser ablation of gold : Effect of pressure relaxation

    NARCIS (Netherlands)

    Norman, G. E.; Starikov, S. V.; Stegailov, V. V.

    2012-01-01

    The process of ablation of a gold target by femto- and picosecond laser radiation pulses has been studied by numerical simulations using an atomistic model with allowance for the electron subsystem and the dependence of the ion-ion interaction potential on the electron temperature. Using this potent

  13. Hybrid simulations : combining atomistic and coarse-grained force fields using virtual sites

    NARCIS (Netherlands)

    Rzepiela, Andrzej J.; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J.

    2011-01-01

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. I

  14. A fast mollified impulse method for biomolecular atomistic simulations

    Science.gov (United States)

    Fath, L.; Hochbruck, M.; Singh, C. V.

    2017-03-01

    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.

  15. 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.

  16. Understanding materials behavior from atomistic simulations: Case study of al-containing high entropy alloys and thermally grown aluminum oxide

    Science.gov (United States)

    Yinkai Lei

    Atomistic simulation refers to a set of simulation methods that model the materials on the atomistic scale. These simulation methods are faster and cheaper alternative approaches to investigate thermodynamics and kinetics of materials compared to experiments. In this dissertation, atomistic simulation methods have been used to study the thermodynamic and kinetic properties of two material systems, i.e. the entropy of Al-containing high entropy alloys (HEAs) and the vacancy migration energy of thermally grown aluminum oxide. (Abstract shortened by ProQuest.).

  17. 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.

  18. Atomistic simulation of the structure and elastic properties of gold nanowires

    Science.gov (United States)

    Diao, Jiankuai; Gall, Ken; Dunn, Martin L.

    2004-09-01

    We performed atomistic simulations to study the effect of free surfaces on the structure and elastic properties of gold nanowires aligned in the and crystallographic directions. Computationally, we formed a nanowire by assembling gold atoms into a long wire with free sides by putting them in their bulk fcc lattice positions. We then performed a static relaxation on the assemblage. The tensile surface stresses on the sides of the wire cause the wire to contract along the length with respect to the original fcc lattice, and we characterize this deformation in terms of an equilibrium strain versus the cross-sectional area. While the surface stress causes wires of both orientations and all sizes to increasingly contract with decreasing cross-sectional area, when the cross-sectional area of a nanowire is less than 1.83 nm×1.83 nm, the wire undergoes a phase transformation from fcc to bct, and the equilibrium strain increases by an order of magnitude. We then applied a uniform uniaxial strain incrementally to 1.2% to the relaxed nanowires in a molecular statics framework. From the simulation results we computed the effective axial Young's modulus and Poisson's ratios of the nanowire as a function of cross-sectional area. We used two approaches to compute the effective elastic moduli, one based on a definition in terms of the strain derivative of the total energy and another in terms of the virial stress often used in atomistic simulations. Both give quantitatively similar results, showing an increase in Young's modulus with a decrease of cross-sectional area in the nanowires that do not undergo a phase transformation. Those that undergo a phase transformation experience an increase of about a factor of three of Young's modulus. The Poisson's ratio of the wires that do not undergo a phase transformation show little change with the cross-sectional area. Those wires that undergo a phase transformation experience an increase of about 10% in Poisson's ratio. The wires show

  19. Simulations of boundary migration during recrystallization using molecular dynamics

    DEFF Research Database (Denmark)

    Godiksen, Rasmus Brauner; Trautt, Z.T.; Upmanyu, M.

    2007-01-01

    We have applied an atomistic simulation methodology based on molecular dynamics to study grain boundary migration in crystalline materials, driven by the excess energy of dislocation arrangements. This method is used to simulate recrystallization in metals. The simulations reveal that the migration...

  20. Molecular recognition effects in atomistic models of imprinted polymers.

    Science.gov (United States)

    Dourado, Eduardo M A; Herdes, Carmelo; van Tassel, Paul R; Sarkisov, Lev

    2011-01-01

    In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  1. Molecular Recognition Effects in Atomistic Models of Imprinted Polymers

    Directory of Open Access Journals (Sweden)

    Carmelo Herdes

    2011-07-01

    Full Text Available In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  2. 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.

  3. Dynamic Deformation of Thermosetting Polymers---All Atomistic Simulations

    Science.gov (United States)

    Tsige, Mesfin; Shenogina, Natalia; Mukhopadhyay, Sharmila; Patnaik, Soumya

    2013-03-01

    We are using all-atom molecular dynamics simulations to investigate the interconnection between structural and mechanical properties of highly cross-linked polymer networks. In this study we focused on the widely used resin-hardener system composed of DGEBA epoxy oligomers and aromatic amine hardener DETDA. Accurate cross-linked models were developed using the effective cross-linking procedure that enables to generate thermoset structures with realistic structural characteristics. These models were used to examine the elastic properties of thermosetting networks with various degrees of curing and length of resin strands both in glassy and rubbery states. In our recent study we employed static deformation approach to estimate potential energy contribution to the mechanical response. In the present work we are using dynamic deformation approach which takes into account both potential energy and thermal motions in the structure. Uniaxial, volumetric and shear dynamic deformation modes were used to obtain Young's, bulk, shear moduli and Poisson's ratio directly. We also calculated elastic constants using formulae of linear elasticity and analyzed the results obtained by direct deformation and interconversion methods. The elastic properties determined from these two approaches are in good agreement with each other and also with experimental data.

  4. 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

    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......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...

  5. 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...

  6. 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.

  7. Features of structure and phase transitions in pure uranium and U-Mo alloys: atomistic simulation

    Science.gov (United States)

    Kolotova, L. N.; Kuksin, A. Yu; Smirnova, D. E.; Starikov, S. V.; Tseplyaev, V. I.

    2016-11-01

    We study structural properties of cubic and tetragonal phases of U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. For pure uranium and U-Mo alloys at low temperatures we observe body-centered tetragonal (bct) structure, which is similar to the metastable γ°-phase found in the experiments. At higher temperatures bct structure transforms to a quasi body-centered cubic (q-bcc) phase that exhibits cubic symmetry just on the scale of several interatomic spacings or when averaged over time. Instantaneous pair distribution function (PDF) differs from PDF for the time-averaged atomic coordinates corresponding to the bcc lattice. The local positions of uranium atoms in q-bcc lattice correspond to the bct structure, which is energetically favourable due to formation of short U-U bonds. Transition from bct to q-bcc could be considered as ferro-to paraelastic transition of order-disorder type. The temperature of transition depends on Mo concentration. For pure uranium it is equal to about 700 K, which is well below than the upper boundary of the stability region of the α-U phase. Due to this reason, bct phase is observed only in uranium alloys containing metals with low solubility in α-U.

  8. Analytical potential for atomistic simulations of silicon, carbon, and silicon carbide

    Science.gov (United States)

    Erhart, Paul; Albe, Karsten

    2005-01-01

    We present an analytical bond-order potential for silicon, carbon, and silicon carbide that has been optimized by a systematic fitting scheme. The functional form is adopted from a preceding work [Phys. Rev. B 65, 195124 (2002)] and is built on three independently fitted potentials for SiSi , CC , and SiC interaction. For elemental silicon and carbon, the potential perfectly reproduces elastic properties and agrees very well with first-principles results for high-pressure phases. The formation enthalpies of point defects are reasonably reproduced. In the case of silicon stuctural features of the melt agree nicely with data taken from literature. For silicon carbide the dimer as well as the solid phases B1, B2, and B3 were considered. Again, elastic properties are very well reproduced including internal relaxations under shear. Comparison with first-principles data on point defect formation enthalpies shows fair agreement. The successful validation of the potentials for configurations ranging from the molecular to the bulk regime indicates the transferability of the potential model and makes it a good choice for atomistic simulations that sample a large configuration space.

  9. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. II. Adsorption and diffusion

    Science.gov (United States)

    Kim, Nayong; Harale, Aadesh; Tsotsis, Theodore T.; Sahimi, Muhammad

    2007-12-01

    Nanoporous layered double hydroxide (LDH) materials have wide applications, ranging from being good adsorbents for gases (particularly CO2) and liquid ions to membranes and catalysts. They also have applications in medicine, environmental remediation, and electrochemistry. Their general chemical composition is [M1-xIIMxIII(OH-)2]x+[Xn/mm -•nH2O], where M represents a metallic cation (of valence II or III), and Xn/mm - is an m-valence inorganic, or heteropolyacid, or organic anion. We study diffusion and adsorption of CO2 in a particular LDH with MII=Mg, MIII=Al, and x ≃0.71, using an atomistic model developed based on energy minimization and molecular dynamics simulations, together with a modified form of the consistent-valence force field. The adsorption isotherms and self-diffusivity of CO2 in the material are computed over a range of temperature, using molecular simulations. The computed diffusivities are within one order of magnitude of the measured ones at lower temperatures, while agreeing well with the data at high temperatures. The measured and computed adsorption isotherms agree at low loadings, but differ by about 25% at high loadings. Possible reasons for the differences between the computed properties and the experimental data are discussed, and a model for improving the accuracy of the computed properties is suggested. Also studied are the material's hydration and swelling properties. As water molecules are added to the pore space, the LDH material swells to some extent, with the hydration energy exhibiting interesting variations with the number of the water molecules added. The implications of the results are discussed.

  10. Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

    Science.gov (United States)

    2017-01-01

    Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor–acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)–phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device. PMID:28209056

  11. Study of Nanowires Using Molecular Dynamics Simulations

    OpenAIRE

    Monk, Joshua D

    2007-01-01

    In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...

  12. Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

    Science.gov (United States)

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

    Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

  13. Atomistic simulation of grain boundary structure in a series of B2 intermetallics

    Energy Technology Data Exchange (ETDEWEB)

    Mutasa, B. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Engineering; Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Engineering

    1996-08-01

    Using molecular statics and interatomic potentials of the embedded atom type, the relaxed atomistic grain boundary structures in B2 aluminides were investigated in order to study trends in a series of B2 compounds. The compounds studied: FeAl, NiAl and CoAl show increasing anti-phase boundary energies. The atomistic structure of the {Sigma}=5(310)[100] and {Sigma}=5(210)[100] symmetrical tilt grain boundaries in these compounds was studied considering possible variations of local chemical composition on grain boundary energetics. The structures obtained for the three alloys are very similar. A discussion of the trends in energetics across this series of compounds is entered into. (orig.)

  14. Role of Ionic Clusters in Dynamics of Ionomer Melts: From Atomistic to Coarse Grained Simulations

    Science.gov (United States)

    Agrawal, Anupriya

    Ionomers, polymers decorated with ionizable groups, have found application in numerous technologies where ionic transport is required. The ionic groups associate into random clusters resulting in substantial effect on structure, dynamics and transport of these materials. The effects of topology, size and dynamics of these aggregates however remain an open question. Here we probe cluster formation correlated with polymer dynamics through a model system of randomly sulfonated polystyrene (SPS) melts with molecular dynamics (MD) simulations over a broad time and length scales ranging from that within the ionic clusters through polymer segmental dynamics to the motion of the entire molecules. The cluster evolution was probed by fully atomistic studies. We find ladder-like aggregates that transform to globule-like with increasing the dielectric constant of media for sodium neutralized SPS. With increasing dielectric constant, the size of the aggregates decrease and their number increases. Concurrently, the mobility of the polymer increases. The counterion radius and valency affect both morphology and dynamics as is evident in the calculated static and dynamic structure factors. It is further manifested in the results of viscosity obtained through non-equilibrium molecular dynamics technique. Finally, to access larger length scales a three bead coarse-grained model to describe sulfonated styrene that we have developed will be discussed in view of the outstanding challenges in ionic polymers. Supported in part by DOE Grant No. DE-SC007908. This work was carried out in collaboration with Dvora Perahia and Gary Grest while I was a postdoc at Clemson University. I gratefully acknowledge both of them for their support and encouragement.

  15. Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures

    Directory of Open Access Journals (Sweden)

    Aruna Prakash

    2017-01-01

    Full Text Available Single-crystal Ni-base superalloys, consisting of a two-phase γ/ γ ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/ γ ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ ′ particles with planar γ/ γ ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions.

  16. Atomistic electrodynamics simulations of bare and ligand-coated nanoparticles in the quantum size regime.

    Science.gov (United States)

    Chen, Xing; Moore, Justin E; Zekarias, Meserret; Jensen, Lasse

    2015-11-10

    The optical properties of metallic nanoparticles with nanometre dimensions exhibit features that cannot be described by classical electrodynamics. In this quantum size regime, the near-field properties are significantly modified and depend strongly on the geometric arrangements. However, simulating realistically sized systems while retaining the atomistic description remains computationally intractable for fully quantum mechanical approaches. Here we introduce an atomistic electrodynamics model where the traditional description of nanoparticles in terms of a macroscopic homogenous dielectric constant is replaced by an atomic representation with dielectric properties that depend on the local chemical environment. This model provides a unified description of bare and ligand-coated nanoparticles, as well as strongly interacting nanoparticle dimer systems. The non-local screening owing to an inhomogeneous ligand layer is shown to drastically modify the near-field properties. This will be important to consider in optimization of plasmonic nanostructures for near-field spectroscopy and sensing applications.

  17. 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

  18. Atomistic Simulation Study of Vacancy Clusters in Copper.

    Science.gov (United States)

    1985-01-01

    found to be very mobile with migration energies of 0.56 and 0.39 eV, respectively, compared to previously calculated single and divacancy migration...CF 1985 Massachusetts Institute of Techonology Signature of Author Department of Nuclear Engineering December 4, 1985 C e r t i f i e d b y S i d n...using molecular statics with an interatomic potential recently derived from first principles. Tri- and tetravacancies are found to be very mobile with

  19. Towards Novel Energy Solutions - an Electronic/Atomistic Simulation Approach

    Science.gov (United States)

    Dong, Rui

    This thesis focuses on computer modeling and multi-scale simulations of new materials that can potentially be used in novel energy applications, i.e., the dye molecules in dye-sensitizedsolar- cells and polymers for the capacitive energy storage. The aim is to understand physical properties of existing materials and then to find ways to improve them. (Abstract shortened by ProQuest.).

  20. Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks.

    Science.gov (United States)

    Zhang, Haiyang; Lv, Yongqin; Tan, Tianwei; van der Spoel, David

    2016-01-28

    Fabrication of metal-organic frameworks (MOFs) with large apertures triggers a brand-new research area for selective encapsulation of biomolecules within MOF nanopores. The underlying inclusion mechanism is yet to be clarified however. Here we report a molecular dynamics study on the mechanism of protein encapsulation in MOFs. Evaluation for the binding of amino acid side chain analogues reveals that van der Waals interaction is the main driving force for the binding and that guest size acts as a key factor predicting protein binding with MOFs. Analysis on the conformation and thermodynamic stability of the miniprotein Trp-cage encapsulated in a series of MOFs with varying pore apertures and surface chemistries indicates that protein encapsulation can be achieved via maintaining a polar/nonpolar balance in the MOF surface through tunable modification of organic linkers and Mg-O chelating moieties. Such modifications endow MOFs with a more biocompatible confinement. This work provides guidelines for selective inclusion of biomolecules within MOFs and facilitates MOF functions as a new class of host materials and molecular chaperones.

  1. Dislocation pinning effects on fracture behavior: Atomistic and dislocation dynamics simulations

    Science.gov (United States)

    Noronha, S. J.; Farkas, D.

    2002-10-01

    We introduce an approach in which results from atomistic simulations are combined with discrete dislocation dynamics simulations of crack-tip plasticity. The method is used to study the effects of dislocation pinning due to grain boundaries or secondary particles on the fracture behavior of aluminum. We find that the fracture resistance is reduced with decreasing pinning distance. The results show that the pinning of the dislocations causes a net decrease in the shear stress projected on the slip plane, preventing further dislocation emission. Semibrittle cleavage occurs after a certain number of dislocations is emitted.

  2. 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.

  3. 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.

  4. Ultrafast laser melting of Au nanoparticles: atomistic simulations

    Science.gov (United States)

    Wang, Ningyu; Rokhlin, S. I.; Farson, D. F.

    2011-10-01

    In spite of the technological importance of laser modification and processing of nanoparticles, the interaction of laser energy with nanoparticles is not well understood. In this work, integrated molecular dynamics (MD) and two-temperature (TTM) computational models have been developed to study ultrafast laser interaction with free Au nanoparticles with sizes 2.44-6.14 nm. At low intensity, when surface premelting and solid-liquid phase transition dominate, a nonhomogeneous surface premelting mechanism was identified. The appearance of a contiguous surface liquid layer (complete surface premelting) is size dependent and is not related to surface premelting history. The effects of temporary superheating and stable supercooling of nanoparticles were found and examined.

  5. Atomistic Simulation of He Clustering and Defects Produced in Ni

    Institute of Scientific and Technical Information of China (English)

    LIU Ti-Jiang; WANG Yue-Xia; PAN Zheng-Ying; JIANG Xiao-Mei; ZHOU Liang; ZHU Jing

    2006-01-01

    @@ Using the molecular dynamics method, the stability of small He-vacancy clusters is studied under the condition of the high He and low vacancy densities. The result shows that there is a competition between He atoms detrapped and self-interstitial atoms (SIAs) emitted during the clustering of He atoms. When the He number is above a critical value of 9, the SIA emission is predominant. The SIA emission can result in deep capture of He atoms since the binding energy of He to a He-vacancy cluster is increased with the number of SIAs created. The cluster thus grows up. In addition, more SIAs are created when the temperature is elevated. The average volume of a He atom is increased. The cluster expansion takes place at high temperature.

  6. Using atomistic simulations to model cadmium telluride thin film growth

    Science.gov (United States)

    Yu, Miao; Kenny, Steven D.

    2016-03-01

    Cadmium telluride (CdTe) is an excellent material for low-cost, high efficiency thin film solar cells. It is important to conduct research on how defects are formed during the growth process, since defects lower the efficiency of solar cells. In this work we use computer simulation to predict the growth of a sputter deposited CdTe thin film. On-the-fly kinetic Monte Carlo technique is used to simulate the CdTe thin film growth on the (1 1 1) surfaces. The results show that on the (1 1 1) surfaces the growth mechanisms on surfaces which are terminated by Cd or Te are quite different, regardless of the deposition energy (0.1∼ 10 eV). On the Te-terminated (1 1 1) surface the deposited clusters first form a single mixed species layer, then the Te atoms in the mixed layer moved up to form a new layer. Whilst on the Cd-terminated (1 1 1) surface the new Cd and Te layers are formed at the same time. Such differences are probably caused by stronger bonding between ad-atoms and surface atoms on the Te layer than on the Cd layer.

  7. Analysis of Boundary Conditions for Crystal Defect Atomistic Simulations

    Science.gov (United States)

    Ehrlacher, V.; Ortner, C.; Shapeev, A. V.

    2016-12-01

    Numerical simulations of crystal defects are necessarily restricted to finite computational domains, supplying artificial boundary conditions that emulate the effect of embedding the defect in an effectively infinite crystalline environment. This work develops a rigorous framework within which the accuracy of different types of boundary conditions can be precisely assessed. We formulate the equilibration of crystal defects as variational problems in a discrete energy space and establish qualitatively sharp regularity estimates for minimisers. Using this foundation we then present rigorous error estimates for (i) a truncation method (Dirichlet boundary conditions), (ii) periodic boundary conditions, (iii) boundary conditions from linear elasticity, and (iv) boundary conditions from nonlinear elasticity. Numerical results confirm the sharpness of the analysis.

  8. 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

  9. Atomistic Simulations of Mass and Thermal Transport in Oxide Nuclear Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Anders D. [Los Alamos National Laboratory; Uberuaga, Blas P. [Los Alamos National Laboratory; Du, Shiyu [Los Alamos National Laboratory; Liu, Xiang-Yang [Los Alamos National Laboratory; Nerikar, Pankaj [IBM; Stanek, Christopher R. [Los Alamos National Laboratory; Tonks, Michael [Idaho National Laboratory; Millet, Paul [Idaho National Laboratory; Biner, Bulent [Idaho National Laboratory

    2012-06-04

    boundaries derived from separate atomistic calculations, we simulate Xe redistribution for a few simple microstructures using finite element methods (FEM), as implemented in the MOOSE framework from Idaho National Laboratory. Thermal transport together with the power distribution determines the temperature distribution in the fuel rod and it is thus one of the most influential properties on nuclear fuel performance. The fuel thermal conductivity changes as function of time due to microstructure evolution (e.g. fission gas redistribution) and compositional changes. Using molecular dynamics simulations we have studied the impact of different types of grain boundaries and fission gas bubbles on UO{sub 2} thermal conductivity.

  10. 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.

  11. Investigations on the mechanical behavior of nanowires with twin boundaries by atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Xia, E-mail: tianxia@lsec.cc.ac.cn [College of Mechanics and Materials, HoHai University, Nanjing 210098 (China)

    2015-03-10

    Atomistic simulations are used to study the deformation behavior of twinned Cu nanowires with a <111> growth orientation under tension. Due to the existence of the twin boundaries, the strength of the twinned nanowires is higher than that of the twin-free nanowire and the yielding stress of twinned nanowires is inversely proportional to the spacings of the twin boundaries. Moreover, The ductility of the twin-free nanowire is the highest of all and it grows with the increasing spacings of the twin boundaries for twinned nanowires. Besides, we find that the twin boundaries can be served as dislocation sources as well as the free surfaces and grain boundaries.

  12. Atomistic Simulations of Chemical Reactivity of TATB Under Thermal and Shock Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Manaa, M R; Reed, E J; Fried, L E

    2009-09-23

    The study of chemical transformations that occur at the reactive shock front of energetic materials provides important information for the development of predictive models at the grain-and continuum scales. A major shortcoming of current high explosives models is the lack of chemical kinetics data of the reacting explosive in the high pressure and temperature regimes. In the absence of experimental data, long-time scale atomistic molecular dynamics simulations with reactive chemistry become a viable recourse to provide an insight into the decomposition mechanism of explosives, and to obtain effective reaction rate laws. These rates can then be incorporated into thermo-chemical-hydro codes (such as Cheetah linked to ALE3D) for accurate description of the grain and macro scales dynamics of reacting explosives. In this talk, I will present quantum simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystals under thermal decomposition (high density and temperature) and shock compression conditions. This is the first time that condensed phase quantum methods have been used to study the chemistry of insensitive high explosives. We used the quantum-based, self-consistent charge density functional tight binding method (SCC{_}DFTB) to calculate the interatomic forces for reliable predictions of chemical reactions, and to examine electronic properties at detonation conditions for a relatively long time-scale on the order of several hundreds of picoseconds. For thermal decomposition of TATB, we conducted constant volume-temperature simulations, ranging from 0.35 to 2 nanoseconds, at {rho} = 2.87 g/cm{sup 3} at T = 3500, 3000, 2500, and 1500 K, and {rho} = 2.9 g/cm{sup 3} and 2.72 g/cm{sup 3}, at T = 3000 K. We also simulated crystal TATB's reactivity under steady overdriven shock compression using the multi-scale shock technique. We conducted shock simulations with specified shock speeds of 8, 9, and 10 km/s for up to 0.43 ns duration, enabling us to track the

  13. Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

    NARCIS (Netherlands)

    Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

    2013-01-01

    Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules.

  14. Nanoscale deicing by molecular dynamics simulation

    Science.gov (United States)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice

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

    Science.gov (United States)

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

    2016-08-01

    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.

  16. Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows

    CERN Document Server

    Fyta, Maria; Kaxiras, Efthimios; Succi, Sauro

    2007-01-01

    We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and mesoscopic scales and is capable of describing self-consistent hydrodynamic effects on molecular motion at a computational cost which scales linearly with both solute size and solvent volume. For an application of our multiscale method, we consider the much studied problem of biopolymer translocation through nanopores: we find that the method reproduces with remarkable accuracy the statistical scaling behavior of the translocation process and provides valuable insight into the cooperative aspects of biopolymer and hydrodynamic motion.

  17. 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.

  18. 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.)

  19. Atomistic simulation studies on the dynamics and thermodynamics of nonpolar molecules within the zeolite imidazolate framework-8.

    Science.gov (United States)

    Pantatosaki, Evangelia; Pazzona, Federico G; Megariotis, Gregory; Papadopoulos, George K

    2010-02-25

    Statistical-mechanics-based simulation studies at the atomistic level of argon (Ar), methane (CH(4)), and hydrogen (H(2)) sorbed in the zeolite imidazolate framework-8 (ZIF-8) are reported. ZIF-8 is a product of a special kind of chemical process, recently termed as reticular synthesis, which has generated a class of materials of critical importance as molecular binders. In this work, we explore the mechanisms that govern the sorption thermodynamics and kinetics of nonpolar sorbates possessing different sizes and strength of interactions with the metal-organic framework to understand the outstanding properties of this novel class of sorbents, as revealed by experiments published elsewhere. For this purpose, we have developed an in-house modeling procedure involving calculations of sorption isotherms, partial internal energies, various probability density functions, and molecular dynamics for the simulation of the sorbed phase over a wide range of occupancies and temperatures within a digitally reconstructed unit cell of ZIF-8. The results showed that sorbates perceive a marked energetic inhomogeneity within the atomic framework of the metal-organic material under study, resulting in free energy barriers that give rise to inflections in the sorption isotherms and guide the dynamics of guest molecules.

  20. Nanoscale deicing by molecular dynamics simulation.

    Science.gov (United States)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-08-14

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.

  1. 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 be

  2. Structures, nanomechanics, and disintegration of single-walled GaN nanotubes: atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Jeong Won; Hwang, Ho Jung; Song, Ki Oh; Choi, Won Young; Byun, Ki Ryang [Chung-Ang University, Seoul (Korea, Republic of); Kwon, Oh Keun [Semyung University, Jecheon (Korea, Republic of); Lee, Jun Ha [Sangmyung University, Chonan (Korea, Republic of); Kim, Won Woo [Juseong College, Cheongwon (Korea, Republic of)

    2003-09-15

    We have investigated the structural, mechanical, and thermal properties of single-walled GaN nanotubes by using atomistic simulations and a Tersoff-type potential. The Tersoff potential for GaN effectively describes the properties of GaN nanotubes. The nanomechanics of GaN nanotubes under tensile and compressive loadings have also been investigated, and Young's modulus has been calculated. The caloric curves of single-walled GaN nanotubes can be divided into three regions corresponding to nanotubes, the disintegrating range, and vapor. Since the stability or the stiffness of a tube decreases with increasing curving sheet-to-tube strain energy, the disintegration temperatures of GaN nanotubes are closely related to the curving sheet-to-tube strain energy.

  3. Mapping between atomistic simulations and Eshelby inclusions in the shear deformation of an amorphous silicon model

    Science.gov (United States)

    Albaret, T.; Tanguy, A.; Boioli, F.; Rodney, D.

    2016-05-01

    In this paper we perform quasistatic shear simulations of model amorphous silicon bulk samples with Stillinger-Weber-type potentials. Local plastic rearrangements identified based on local energy variations are fitted through their displacement fields on collections of Eshelby spherical inclusions, allowing determination of their transformation strain tensors. The latter are then used to quantitatively reproduce atomistic stress-strain curves, in terms of both shear and pressure components. We demonstrate that our methodology is able to capture the plastic behavior predicted by different Stillinger-Weber potentials, in particular, their different shear tension coupling. These calculations justify the decomposition of plasticity into shear transformations used so far in mesoscale models and provide atomic-scale parameters that can be used to limit the empiricism needed in such models up to now.

  4. Atomistic simulations of surface coverage effects in anisotropic wet chemical etching of crystalline silicon

    Energy Technology Data Exchange (ETDEWEB)

    Gosalvez, M.A.; Foster, A.S.; Nieminen, R.M

    2002-12-30

    Atomistic simulations of anisotropic wet chemical etching of crystalline silicon have been performed in order to determine the dependence of the etch rates of different crystallographic orientations on surface coverage and clustering of OH radicals. We show that the etch rate is a non-monotonic function of OH coverage and that there always exists a coverage value at which the etch rate reaches a maximum. The dependence of the anisotropy of the etching process on coverage, including the dependence of the fastest-etched plane orientation, is implicitly contained in the model and predictions of convex corner under-etching structures are made. We show that the whole etching process is controlled by only a few surface configurations involving a particular type of next-nearest neighbours. The relative value of the removal probabilities of these confitions determines the balance in the occurrence of step propagation and etch pitting for all surface orientations.

  5. 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.

  6. Lipid exchange mechanism of the cholesteryl ester transfer protein clarified by atomistic and coarse-grained simulations.

    Directory of Open Access Journals (Sweden)

    Artturi Koivuniemi

    2012-01-01

    Full Text Available 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 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 through its charged and tryptophan residues. Upon binding, CETP rapidly (in about 10 ns induced the formation of a small hydrophobic patch to the phospholipid surface of the droplet, opening a route from the core of the lipid droplet to the binding pocket of CETP. This was followed by a conformational change of helix X of CETP to an open state, in which we found the accessibility of cholesteryl esters to the C-terminal tunnel opening of CETP to increase. Furthermore, in the absence of helix X, cholesteryl esters rapidly diffused into CETP through the C-terminal opening. The results provide compelling 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.

  7. Atomistic Origin of Brittle Failure of Boron Carbide from Large-Scale Reactive Dynamics Simulations: Suggestions toward Improved Ductility

    Science.gov (United States)

    An, Qi; Goddard, William A.

    2015-09-01

    Ceramics are strong, but their low fracture toughness prevents extended engineering applications. In particular, boron carbide (B4C ), the third hardest material in nature, has not been incorporated into many commercial applications because it exhibits anomalous failure when subjected to hypervelocity impact. To determine the atomistic origin of this brittle failure, we performed large-scale (˜200 000 atoms /cell ) reactive-molecular-dynamics simulations of shear deformations of B4C , using the quantum-mechanics-derived reactive force field simulation. We examined the (0001 )/⟨10 1 ¯ 0 ⟩ slip system related to deformation twinning and the (01 1 ¯ 1 ¯ )/⟨1 ¯ 101 ⟩ slip system related to amorphous band formation. We find that brittle failure in B4C arises from formation of higher density amorphous bands due to fracture of the icosahedra, a unique feature of these boron based materials. This leads to negative pressure and cavitation resulting in crack opening. Thus, to design ductile materials based on B4C we propose alloying aimed at promoting shear relaxation through intericosahedral slip that avoids icosahedral fracture.

  8. Towards understanding photomigration: Insights from atomistic simulations of azopolymer films explicitly including light-induced isomerization dynamics

    Science.gov (United States)

    Böckmann, Marcus; Doltsinis, Nikos L.

    2016-10-01

    The light-induced surface modification of a thin film of poly-(disperse orange-3-methylmethacrylate) is investigated computationally using atomistic molecular dynamics simulations specifically tailored to include photoisomerization dynamics. For a model surface consisting of a periodic pattern of alternating irradiated and dark spots, it is shown that repeated photoisomerization in the irradiated areas initially leads to a local temperature increase and a raised surface profile accompanied by a migration of molecules away from the bright spots. After switching off the light source and letting the system cool down, this leads to an inversion of the surface profile, i.e., dips in the bright spots and bumps in the dark spots. To separate the effect of photoisomerization from the pure heating effect, a second simulation is performed in which no photoisomerization is allowed to occur in the bright spots, but the equivalent amount of energy is introduced there locally in the form of heat. This also leads to a raised surface in these areas; however, no outward migration of molecules is observed and the surface pattern practically vanishes when the system is subsequently cooled back to room temperature.

  9. Atomistic MD simulations reveal the protective role of cholesterol in dimeric beta-amyloid induced disruptions in neuronal membrane mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Cheng, Sara; Chou, George; Vaughn, Mark; Cheng, K.

    2011-10-01

    Interactions of oligomeric beta-amyloid peptides with neuronal membranes have been linked to the pathogenesis of Alzheimer's disease (AD). The molecular details of the interactions of different lipid components, particularly cholesterol (CHOL), of the membranes with the peptides are not clear. Using an atomistic MD simulations approach, the water permeability barrier, structural geometry and order parameters of binary phosphatidylcholine (PC) and PC/CHOL lipid bilayers were examined from various 200 ns-simulation replicates. Our results suggest that the longer length dimer (2 x 42 residues) perturbs the membrane more than the shorter one (2 x 40 residues). In addition, we discovered a significant protective role of cholesterol in protein-induced disruptions of the membranes. The use of a new Monte-Carlo method in characterizing the structures of the conformal annular lipids in close proximity with the proteins will be introduced. We propose that the neurotoxicity of beta-amyloid peptide may be associated with the nanodomain or raft-like structures of the neuronal membranes in-vivo in the development of AD.

  10. Atomistic Origin of Brittle Failure of Boron Carbide from Large-Scale Reactive Dynamics Simulations: Suggestions toward Improved Ductility.

    Science.gov (United States)

    An, Qi; Goddard, William A

    2015-09-01

    Ceramics are strong, but their low fracture toughness prevents extended engineering applications. In particular, boron carbide (B(4)C), the third hardest material in nature, has not been incorporated into many commercial applications because it exhibits anomalous failure when subjected to hypervelocity impact. To determine the atomistic origin of this brittle failure, we performed large-scale (∼200,000  atoms/cell) reactive-molecular-dynamics simulations of shear deformations of B(4)C, using the quantum-mechanics-derived reactive force field simulation. We examined the (0001)/⟨101̅0⟩ slip system related to deformation twinning and the (011̅1̅)/⟨1̅101⟩ slip system related to amorphous band formation. We find that brittle failure in B(4)C arises from formation of higher density amorphous bands due to fracture of the icosahedra, a unique feature of these boron based materials. This leads to negative pressure and cavitation resulting in crack opening. Thus, to design ductile materials based on B(4)C we propose alloying aimed at promoting shear relaxation through intericosahedral slip that avoids icosahedral fracture.

  11. 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.

  12. Molecular dynamics simulations

    OpenAIRE

    Tarmyshov, Konstantin B.

    2007-01-01

    Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...

  13. 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

  14. Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized System Dynamics

    Science.gov (United States)

    Ho, Phay; Knight, Christopher; Bostedt, Christoph; Young, Linda; Tegze, Miklos; Faigel, Gyula

    2016-05-01

    We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  15. Atomistic simulations of CO2 and N2 within cage-type silica zeolites.

    Science.gov (United States)

    Madison, Lindsey; Heitzer, Henry; Russell, Colin; Kohen, Daniela

    2011-03-01

    The behavior of CO(2) and N(2), both as single components and as binary mixtures, in two cage-type silica zeolites was studied using atomistic simulations. The zeolites considered, ITQ-3 and paradigm cage-type zeolite ZK4 (the all-silica analog of LTA), were chosen so that the principles illustrated can be generalized to other adsorbent/adsorbate systems with similar topology and types of interactions. N(2) was chosen both because of the potential uses of N(2)/CO(2) separations and because it differs from CO(2) most significantly in the magnitude of its Coulombic interactions with zeolites. Despite similarities between N(2) and CO(2) diffusion in other materials, we show here that the diffusion of CO(2) within cage-type zeolites is dominated by an energy barrier to diffusion located at the entrance to the narrow channels connecting larger cages. This barrier originates in Coulombic interactions between zeolites and CO(2)'s quadrupole and results in well-defined orientations for the diffusing molecules. Furthermore, CO(2)'s favorable electrostatic interactions with the zeolite framework result in preferential binding in the windows between cages. N(2)'s behavior, in contrast, is more consistent with that of molecules previously studied. Our analysis suggests that CO(2)'s behavior might be common for adsorbates with quadrupoles that interact strongly with a material that has narrow windows between cages.

  16. Atomistic-Scale Simulations of Defect Formation in Graphene under Noble Gas Ion Irradiation.

    Science.gov (United States)

    Yoon, Kichul; Rahnamoun, Ali; Swett, Jacob L; Iberi, Vighter; Cullen, David A; Vlassiouk, Ivan V; Belianinov, Alex; Jesse, Stephen; Sang, Xiahan; Ovchinnikova, Olga S; Rondinone, Adam J; Unocic, Raymond R; van Duin, Adri C T

    2016-09-27

    Despite the frequent use of noble gas ion irradiation of graphene, the atomistic-scale details, including the effects of dose, energy, and ion bombardment species on defect formation, and the associated dynamic processes involved in the irradiations and subsequent relaxation have not yet been thoroughly studied. Here, we simulated the irradiation of graphene with noble gas ions and the subsequent effects of annealing. Lattice defects, including nanopores, were generated after the annealing of the irradiated graphene, which was the result of structural relaxation that allowed the vacancy-type defects to coalesce into a larger defect. Larger nanopores were generated by irradiation with a series of heavier noble gas ions, due to a larger collision cross section that led to more detrimental effects in the graphene, and by a higher ion dose that increased the chance of displacing the carbon atoms from graphene. Overall trends in the evolution of defects with respect to a dose, as well as the defect characteristics, were in good agreement with experimental results. Additionally, the statistics in the defect types generated by different irradiating ions suggested that the most frequently observed defect types were Stone-Thrower-Wales (STW) defects for He(+) irradiation and monovacancy (MV) defects for all other ion irradiations.

  17. Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Shea, Joan-Emma; Levine, Zachary A

    2016-01-01

    The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol.

  18. 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.

    2011-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 are candidate materials for applications in extreme environments because of their high melting point, good mechanical properties and reasonable oxidation resistance. Unlike many ceramics, these materials have high thermal conductivity which can be advantageous, for example, to reduce thermal shock. Recently, we developed Tersoff style interatomic 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. Results at room temperature and at elevated temperatures will be reported.

  19. 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.

  20. 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

  1. Atomistic simulations of electrolyte solutions and hydrogels with explicit solvent models

    CERN Document Server

    Walter, Jonathan; Reiser, Steffen; Horsch, Martin; Vrabec, Jadran; Hasse, Hans

    2011-01-01

    Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the development and optimization of molecular force fields and models, a large number of simulation runs have to be evaluated to obtain the sensitivity of the target properties with respect to the model parameters. The present work discusses force field development for electrolytes regarding thermodynamic properties of their aqueous solutions. Furthermore, simulations are conducted for the volume transition of hydrogels in the presence of electrolytes. It is shown that the properties of these complex systems can be captured by molecular simulation.

  2. Molecular and intermolecular effects in collagen fibril mechanics: a multiscale analytical model compared with atomistic and experimental studies.

    Science.gov (United States)

    Marino, Michele

    2016-02-01

    Both atomistic and experimental studies reveal the dependence of collagen fibril mechanics on biochemical and biophysical features such as, for instance, cross-link density, water content and protein sequence. In order to move toward a multiscale structural description of biological tissues, a novel analytical model for collagen fibril mechanics is herein presented. The model is based on a multiscale approach that incorporates and couples: thermal fluctuations in collagen molecules; the uncoiling of collagen triple helix; the stretching of molecular backbone; the straightening of the telopeptide in which covalent cross-links form; slip-pulse mechanisms due to the rupture of intermolecular weak bonds; molecular interstrand delamination due to the rupture of intramolecular weak bonds; the rupture of covalent bonds within molecular strands. The effectiveness of the proposed approach is verified by comparison with available atomistic results and experimental data, highlighting the importance of cross-link density in tuning collagen fibril mechanics. The typical three-region shape and hysteresis behavior of fibril constitutive response, as well as the transition from a yielding-like to a brittle-like behavior, are recovered with a special insight on the underlying nanoscale mechanisms. The model is based on parameters with a clear biophysical and biochemical meaning, resulting in a promising tool for analyzing the effect of pathological or pharmacological-induced histochemical alterations on the functional mechanical response of collagenous tissues.

  3. Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

    2011-09-01

    Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.

  4. Engineering molecular mechanics: an efficient static high temperature molecular simulation technique.

    Science.gov (United States)

    Subramaniyan, Arun K; Sun, C T

    2008-07-16

    Inspired by the need for an efficient molecular simulation technique, we have developed engineering molecular mechanics (EMM) as an alternative molecular simulation technique to model high temperature (T>0 K) phenomena. EMM simulations are significantly more computationally efficient than conventional techniques such as molecular dynamics simulations. The advantage of EMM is achieved by converting the dynamic atomistic system at high temperature (T>0 K) into an equivalent static system. Fundamentals of the EMM methodology are derived using thermal expansion to modify the interatomic potential. Temperature dependent interatomic potentials are developed to account for the temperature effect. The efficiency of EMM simulations is demonstrated by simulating the temperature dependence of elastic constants of copper and nickel and the thermal stress developed in a confined copper system.

  5. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott [Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080 (United States)

    2015-01-28

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  6. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.

    Science.gov (United States)

    Petsev, Nikolai D; Leal, L Gary; Shell, M Scott

    2015-01-28

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  7. Thermodynamic and mechanical properties of copper precipitates in α-iron from atomistic simulations

    Science.gov (United States)

    Erhart, Paul; Marian, Jaime; Sadigh, Babak

    2013-07-01

    Precipitate hardening is commonly used in materials science to control strength by acting on the number density, size distribution, and shape of solute precipitates in the hardened matrix. The Fe-Cu system has attracted much attention over the last several decades due to its technological importance as a model alloy for Cu steels. In spite of these efforts several aspects of its phase diagram remain unexplained. Here we use atomistic simulations to characterize the polymorphic phase diagram of Cu precipitates in body-centered cubic (BCC) Fe and establish a consistent link between their thermodynamic and mechanical properties in terms of thermal stability, shape, and strength. The size at which Cu precipitates transform from BCC to a close-packed 9R structure is found to be strongly temperature dependent, ranging from approximately 4 nm in diameter (˜2700atoms) at 200 K to about 8 nm (˜22800atoms) at 700 K. These numbers are in very good agreement with the interpretation of experimental data given Monzen [Philos. Mag. APMAADG0141-861010.1080/01418610008212077 80, 711 (2000)]. The strong temperature dependence originates from the entropic stabilization of BCC Cu, which is mechanically unstable as a bulk phase. While at high temperatures the transition exhibits first-order characteristics, the hysteresis, and thus the nucleation barrier, vanish at temperatures below approximately 300 K. This behavior is explained in terms of the mutual cancellation of the energy differences between core and shell (wetting layer) regions of BCC and 9R nanoprecipitates, respectively. The proposed mechanism is not specific for the Fe-Cu system but could generally be observed in immiscible systems, whenever the minority component is unstable in the lattice structure of the host matrix. Finally, we also study the interaction of precipitates with screw dislocations as a function of both structure and orientation. The results provide a coherent picture of precipitate strength that unifies

  8. 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.

  9. 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.

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

    Science.gov (United States)

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

    2003-01-01

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

  11. Characterization and quantification of the role of coherence in ultrafast quantum biological experiments using quantum master equations, atomistic simulations, and quantum process tomography

    CERN Document Server

    Rebentrost, Patrick; Yuen-Zhou, Joel; Aspuru-Guzik, Alán

    2010-01-01

    Long-lived electronic coherences in various photosynthetic complexes at cryogenic and room temperature have generated vigorous efforts both in theory and experiment to understand their origins and explore their potential role to biological function. The ultrafast signals resulting from the experiments that show evidence for these coherences result from many contributions to the molecular polarization. Quantum process tomography (QPT) was conceived in the context of quantum information processing to characterize and understand general quantum evolution of controllable quantum systems, for example while carrying out quantum computational tasks. We introduce our QPT method for ultrafast experiments, and as an illustrative example, apply it to a simulation of a two-chromophore subsystem of the Fenna-Matthews-Olson photosynthetic complex, which was recently shown to have long-lived quantum coherences. Our Fenna-Matthews-Olson model is constructed using an atomistic approach to extract relevant parameters for the s...

  12. Atomistic study of crack propagation and dislocation emission in Cu-Ni multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Clinedinst, J.; Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1997-09-01

    The authors present atomistic simulations of the crack tip configuration in multilayered Cu-Ni materials. The simulations were carried out using molecular statics and EAM potentials. The atomistic structure of the interface was studied first for a totally coherent structure. Cracks were simulated near a Griffith condition in different possible configurations of the crack plane and front with respect to the axis of the layers. Results show that interface effects predominantly control the mechanical behavior of the system studied.

  13. Molecular dynamics simulations of liquid crystals at interfaces

    CERN Document Server

    Shield, M

    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 mole...

  14. Atomistic simulation of laser-pulse surface modification: Predictions of models with various length and time scales

    Energy Technology Data Exchange (ETDEWEB)

    Starikov, Sergey V., E-mail: starikov@ihed.ras.ru; Pisarev, Vasily V. [Moscow Institute of Physics and Technology, Dolgoprudny 141700 (Russian Federation); Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412 (Russian Federation)

    2015-04-07

    In this work, the femtosecond laser pulse modification of surface is studied for aluminium (Al) and gold (Au) by use of two-temperature atomistic simulation. The results are obtained for various atomistic models with different scales: from pseudo-one-dimensional to full-scale three-dimensional simulation. The surface modification after laser irradiation can be caused by ablation and melting. For low energy laser pulses, the nanoscale ripples may be induced on a surface by melting without laser ablation. In this case, nanoscale changes of the surface are due to a splash of molten metal under temperature gradient. Laser ablation occurs at a higher pulse energy when a crater is formed on the surface. There are essential differences between Al ablation and Au ablation. In the first step of shock-wave induced ablation, swelling and void formation occur for both metals. However, the simulation of ablation in gold shows an additional athermal type of ablation that is associated with electron pressure relaxation. This type of ablation takes place at the surface layer, at a depth of several nanometers, and does not induce swelling.

  15. 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.

  16. Monoamine transporters: insights from molecular dynamics simulations

    Science.gov (United States)

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  17. Monoamine transporters: Insights from molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Julie eGrouleff

    2015-10-01

    Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.

  18. Atomistic molecular point of view for liquid lead and lithium in Nuclear Fusion technology

    Energy Technology Data Exchange (ETDEWEB)

    Fraile, A. [Instituto de Fusión Nuclear, ETSI Industriales, Universidad Politécnica de Madrid, José Gutierrez Abascal, 2, 28006 Madrid (Spain); Cuesta-López, S., E-mail: scuesta@ubu.es [Universidad de Burgos, Parque Científico I-D-I, Plaza Misael Bañuelos s/n, 09001 Burgos (Spain); Iglesias, R. [Universidad de Oviedo, Departamento de Física, Calvo Sotelo s/n, 33007 Oviedo (Spain); Caro, A. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Perlado, J.M. [Instituto de Fusión Nuclear, ETSI Industriales, Universidad Politécnica de Madrid, José Gutierrez Abascal, 2, 28006 Madrid (Spain)

    2013-09-15

    Understanding the behavior and properties of liquid metals is a crucial milestone in different current Nuclear Technology developments. Extracting both structural and dynamical properties of liquid metals via Molecular Dynamics simulations, represents a strong pillar for multiscale modeling efforts aiming to understand the suitability of these compounds. Here we present first results on the validation of two semi-empirical potentials for Li and Pb in liquid phase. Our results establish a solid base as a previous, but crucial step, to implement a LiPb cross potential. Structural and thermodynamical analyses confirm that the analyzed potentials for Li and Pb are sufficiently accurate to simulate both elements in the liquid phase, and in conditions of interest for Nuclear Technology.

  19. Atomistic Mechanisms of Fatigue in Nanocrystalline Metals

    Science.gov (United States)

    Farkas, D.; Willemann, M.; Hyde, B.

    2005-04-01

    We investigate the mechanisms of fatigue behavior in nanocrystalline metals at the atomic scale using empirical force laws and molecular level simulations. A combination of molecular statics and molecular dynamics was used to deal with the time scale limitations of molecular dynamics. We show that the main atomistic mechanism of fatigue crack propagation in these materials is the formation of nanovoids ahead of the main crack. The results obtained for crack advance as a function of stress intensity amplitude are consistent with experimental studies and a Paris law exponent of about 2.

  20. Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations

    CERN Document Server

    Yu, Jin

    2015-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We keep away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while address only statistical physics modeling approach and all-atom molecular dynamics simulation approach. We organize this review around our own modeling and simulation practices on a single-subunit T7 RNA poly...

  1. 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

    The transport of aqueous solutions in artificial nanopores is of both fundamental and technological interest. Recently, carbon nano-structured materials (fullerenes) have attracted a great deal of attention in nanotechnology. In fact, due to their large specific surface area, high thermal...... 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...

  2. Experimental approach and atomistic simulations to investigate the radiation tolerance of complex oxides: Application to the amorphization of pyrochlores

    Science.gov (United States)

    Sattonnay, G.; Thomé, L.; Sellami, N.; Monnet, I.; Grygiel, C.; Legros, C.; Tetot, R.

    2014-05-01

    Both experimental approach and atomistic simulations are performed in order to investigate the influence of the composition of pyrochlores on their radiation tolerance. Therefore, Gd2Ti2O7 and Gd2Zr2O7 were irradiated with 4 MeV Au and 92 MeV Xe ions in order to study the structural changes induced by low and high-energy irradiations. XRD results show that, for both irradiations, the structural modifications are strongly dependent on the sample composition: Gd2Ti2O7 is readily amorphized, whereas Gd2Zr2O7 is transformed into a radiation-resistant anion-deficient fluorite structure. Using atomistic simulations with new interatomic potentials derived from the SMTB-Q model, the lattice properties and the defect formation energies were calculated in Gd2Ti2O7 and Gd2Zr2O7. Calculations show that titanates have a more covalent character than zirconates. Moreover, in Gd2Ti2O7 the formation of cation antisite defects leads to strong local distortions around Ti-defects and to a decrease of the Ti coordination number, which are not observed in Gd2Zr2O7. Thus, the radiation resistance is related to the defect stability: the accumulation of structural distortions around Ti-defects could drive the Gd2Ti2O7 amorphization induced by irradiation.

  3. Ice Formation on Kaolinite: Insights from Molecular Dynamics Simulations

    CERN Document Server

    Sosso, Gabriele C; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

    2016-01-01

    The formation of ice affects many aspects of our everyday life as well as technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even via state-of-the-art experimental techniques. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long timescales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaol...

  4. Large Scale 3-D Dislocation Dynamics and Atomistic Simulations of Flow and Strain-Hardening Behavior of Metallic Micropillars

    Science.gov (United States)

    Rao, Satish

    2015-03-01

    Experimental studies show strong strengthening effects for micrometer-scale FCC as well as two-phase superalloy crystals, even at high initial dislocation densities. This talk shows results from large-scale 3-D discrete dislocation simulations (DDS) used to explicitly model the deformation behavior of FCC Ni (flow stress and strain-hardening) as well as superalloy microcrystals for diameters ranging from 1 - 20 microns. The work shows that two size-sensitive athermal hardening processes, beyond forest and precipitation hardening, are sufficient to develop the dimensional scaling of the flow stress, stochastic stress variation, flow intermittency and, high initial strain-hardening rates, similar to experimental observations for various materials. In addition, 3D dislocation dynamics simulations are used to investigate strain-hardening characteristics and dislocation microstructure evolution with strain in large 20 micron size Ni microcrystals (bulk-like) under three different loading axes: 111, 001 and 110. Three different multi-slip loading axes, , and , are explored for shear strains of ~0.03 and final dislocation densities of ~1013/m2. The orientation dependence of initial strain hardening rates and dislocation microstructure evolution with strain are discussed. The simulated strain hardening results are compared with experimental data under similar loading conditions from bulk single-crystal Ni. Finally, atomistic simulation results on the operation of single arm sources in Ni bipillars with a large angle grain boundary is discussed. The atomistic simulation results are compared with experimental mechanical behavior data on Cu bipillars with a similar large angle grain boundary. This work was supported by AFOSR (Dr. David Stargel), and by a grant of computer time from the DOD High Performance Computing Modernization Program, at the Aeronautical Systems Center/Major Shared Resource Center.

  5. Accelerating atomistic simulations through self-learning bond-boost hyperdynamics

    Energy Technology Data Exchange (ETDEWEB)

    Perez, Danny [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory

    2008-01-01

    By altering the potential energy landscape on which molecular dynamics are carried out, the hyperdynamics method of Voter enables one to significantly accelerate the simulation state-to-state dynamics of physical systems. While very powerful, successful application of the method entails solving the subtle problem of the parametrization of the so-called bias potential. In this study, we first clarify the constraints that must be obeyed by the bias potential and demonstrate that fast sampling of the biased landscape is key to the obtention of proper kinetics. We then propose an approach by which the bond boost potential of Miron and Fichthorn can be safely parametrized based on data acquired in the course of a molecular dynamics simulation. Finally, we introduce a procedure, the Self-Learning Bond Boost method, in which the parametrization is step efficiently carried out on-the-fly for each new state that is visited during the simulation by safely ramping up the strength of the bias potential up to its optimal value. The stability and accuracy of the method are demonstrated.

  6. 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...... 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...

  7. Octadecahedral and dodecahedral iron nanoparticles: An atomistic simulation on stability and shape evolutions

    Science.gov (United States)

    Wu, Yu-Ning; Huang, Rao; Zeng, Xiang-Ming; Wen, Yu-Hua

    2016-02-01

    Fe nanoparticles have attracted great interest due to their potent magnetic and catalytic properties which strongly depend on the structures and morphologies. In this article, molecular dynamic simulations were employed to investigate structural and thermal stabilities of body-centered cubic Fe nanoparticles with octadecahedral, dodecahedral and spherical shapes. Size-dependent structural stability was firstly examined. Subsequently, computer simulations on the heating process of octadecahedral Fe nanoparticle discovered that {100} facets premelt earlier than {110} ones. As a result, the dodecahedral nanoparticle enclosed by {110} facets exhibited a better thermal stability than the octadecahedral one terminated by both {110} and {100} facets. Nevertheless, it was found that the octadecahedron presented a better shape stability than the dodecahedron by monitoring the shape factor and statistical radius during continuous heating. This study provides a significant insight not only into the experimental preparation of polyhedral Fe nanoparticles but also into their utilization in high-temperature environments.

  8. Radiation tolerance of ceramics—Insights from atomistic simulation of damage accumulation in pyrochlores

    Energy Technology Data Exchange (ETDEWEB)

    Devanathan, Ramaswami; Weber, William J.; Gale, Julian D.

    2010-10-01

    We have used molecular dynamics simulations to examine the effects of radiation damage accumulation in two pyrochlore-structured ceramics, namely Gd2Ti2O7 and Gd2Zr2O7. It is well known from experiment that the titanate is susceptible to radiation-induced amorphization, while the zirconate does not go amorphous under prolonged irradiation. Our simulations show that cation Frenkel pair accumulation eventually leads to amorphization of Gd2Ti2O7. Anion disorder occurs with cation disorder. The amorphization is accompanied by a density decrease of about 12.7% and a decrease of about 50% in the elastic modulus. In Gd2Zr2O7, amorphization does not occur, because the residual damage is not sufficiently energetic to drive the material amorphous. Subtle differences in damage accumulation and annealing between the two pyrochlores lead to drastically different radiation response as the damage accumulates.

  9. Atomistic simulations of the tensile and melting behavior of silicon nanowires

    Institute of Scientific and Technical Information of China (English)

    Jing Yuhang; Meng Qingyuan; Zhao Wei

    2009-01-01

    Molecular dynamics simulations with Stillinger-Weber potential are used to study the tensile and melting behavior of single-crystalline silicon nanowires (SiNWs). The tensile tests show that the tensile behavior of the SiNWs is strongly dependent on the simulation temperature, the strain rate, and the diameter of the nanowires.For a given diameter, the critical load significantly decreases as the temperature increases and also as the strain rate decreases. Additionally, the critical load increases as the diameter increases. Moreover, the melting tests demonstrate that both melting temperature and melting heat of the SiNWs decrease with decreasing diameter and length, due to the increase in surface energy. The melting process of SiNWs with increasing temperature is also investigated.

  10. Atomistic Simulation and Electronic Structure of Lithium Doped Ionic Liquids: Structure, Transport, and Electrochemical Stability

    Science.gov (United States)

    Haskins, Justin B.; Bauschlicher, Charles W.; Lawson, John W.

    2015-01-01

    Zero-temperature density functional theory (DFT), density functional theory molecular dynamics (DFT-MD), and classical molecular dynamics using polarizable force fields (PFF-MD) are employed to evaluate the influence of Lithium ion on the structure, transport, and electrochemical stability of three potential ionic liquid electrolytes: N--methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([pyr14][TFSI]), N--methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide ([pyr13][FSI]), and 1-ethyl-3--methylimidazolium boron tetrafluoride ([EMIM][BF4]). We characterize the Lithium ion solvation shell through zero-temperature DFT simulations of [Li(Anion)sub n](exp n-1) -clusters, DFT-MD simulations of isolated lithium ions in small ionic liquid systems, and PFF-MD simulations with high Li-doping levels in large ionic liquid systems. At low levels of Li-salt doping, highly stable solvation shells having 2-3 anions are seen in both [pyr14][TFSI] and [pyr13][FSI], while solvation shells with 4 anions dominate in [EMIM][BF sub 4]. At higher levels of doping, we find the formation of complex Li-network structures that increase the frequency of 4 anion-coordinated solvation shells. A comparison of computational and experimental Raman spectra for a wide range of [Li(Anion) sub n](exp n -1) - clusters shows that our proposed structures are consistent with experiment. We estimate the ion diffusion coefficients and quantify both size and simulation time effects. We find estimates of lithium ion diffusion are a reasonable order of magnitude and can be corrected for simulation time effects. Simulation size, on the other hand, is also important, with diffusion coefficients from long PFF-MD simulations of small cells having 20-40% error compared to large-cell values. Finally, we compute the electrochemical window using differences in electronic energy levels of both isolated cation/anion pairs and small ionic liquid systems with Li-salt doping. The single pair and liquid

  11. 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...... 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...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water....

  12. Atomistic Simulation of Solubilization of Polycyclic Aromatic Hydrocarbons in a Sodium Dodecyl Sulfate Micelle.

    Science.gov (United States)

    Liang, Xujun; Marchi, Massimo; Guo, Chuling; Dang, Zhi; Abel, Stéphane

    2016-04-19

    Solubilization of two polycyclic aromatic hydrocarbons (PAHs), naphthalene (NAP, 2-benzene-ring PAH) and pyrene (PYR, 4-benzene-ring PAH), into a sodium dodecyl sulfate (SDS) micelle was studied through all-atom molecular dynamics (MD) simulations. We find that NAP as well as PYR could move between the micelle shell and core regions, contributing to their distribution in both regions of the micelle at any PAH concentration. Moreover, both NAP and PYR prefer to stay in the micelle shell region, which may arise from the greater volume of the micelle shell, the formation of hydrogen bonds between NAP and water, and the larger molecular volume of PYR. The PAHs are able to form occasional clusters (from dimer to octamer) inside the micelle during the simulation time depending on the PAH concentration in the solubilization systems. Furthermore, the micelle properties (i.e., size, shape, micelle internal structure, alkyl chain conformation and orientation, and micelle internal dynamics) are found to be nearly unaffected by the solubilized PAHs, which is irrespective of the properties and concentrations of PAHs.

  13. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev

    2014-05-01

    Full Text Available Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1–100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

  14. Atomistic Monte Carlo simulations of the diffusion of P and C near grain boundaries in BCC iron

    Energy Technology Data Exchange (ETDEWEB)

    Binkele, P.; Kizler, P. [MPA, Univ. Stuttgart, Stuttgart (Germany); Schmauder, S. [IMWF, Univ. Stuttgart, Stuttgart (Germany)

    2004-07-01

    It is well known that thermal ageing of steels can be caused by the segregation of phosphorus (P) and carbon (C) to grain boundaries. Atomistic Monte Carlo simulations of the diffusion of P and C to grain boundaries in bcc iron will allow, if validated, predictions of the time-dependent segregation. Simulations of the Fe-P-C system are presented, where the diffusion of Fe and P is realized via a vacancy mechanism and the diffusion of C is realized via an interstitial mechanism. Time-dependent segregations have been simulated for different temperatures and start conditions and are found to follow Johnson-Mehl-Avrami laws. A comparison of the simulation results with available AES (Auger Electron Spectroscopy) data shows close agreement with respect to P segregation. In simulations starting with a pre-filled grain boundary in increase of P and a decrease of C in the grain boundary are found where the decrease of C proceeds significantly faster than the increase of P for any temperature. The temperature-dependent ratios of the different speeds of P- and C-segregation, due to their different diffusion mechanisms, are calculated as a result of the simulations. (orig.)

  15. Atomistic Simulations of Orientation and Shock Velocity Dependences on Pentaerythritol Tetranitrate Detonation

    Science.gov (United States)

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

    2012-02-01

    Predicting the behavior of energetic materials requires a detailed description of how chemical reaction, energy and pressure fronts propagate during initial stages of detonation. In this talk, classical molecular dynamics (MD) simulations are used to examine orientation and shock velocity dependences in single crystal pentaerythritol tetranitrate (PETN). This work utilizes an empirical, variable charge reactive force field (ReaxFF) that is implemented in the LAMMPS package with a time-averaged bond-order method for on-the-fly chemical species identification. The accuracy of ReaxFF is validated by comparisons of activation barriers for dissociation of a single PETN molecule along various dissociation channels with higher-fidelity, but more expensive, density functional theory (DFT) calculations. The response of single-crystal PETN to shock compression is simulated using the multi-scale shock technique (MSST) along the insensitive (100) directions, as well as the sensitive (001) and (110) directions, at steady shock velocities ranging from 6-10 km/s. Hugoniot curves, particle velocities of shocked molecules, and evolution of reaction products with time from MD simulations with ReaxFF will be discussed and compared to that from DFT calculations.

  16. Mechanical Behavior of Carbon Nanotubes Filled With Metal Nanowires By Atomistic Simulations

    Science.gov (United States)

    Danailov, Daniel; Keblinski, Pawel; Pulickel, Ajayan; Nayak, Saroj

    2002-03-01

    Using molecular dynamics simulations we studied mechanical behavior of (10,10) carbon nanotubes filled with a crystalline fcc metal wires. The interatomic interactions were described by a combination of Terfoff’s bond-order potential for carbon, embedded atom method (EAM) potential for metal and pair potential for carbon-metal interactions. The elastic properties, as well as failure mechanism were determined by simulating three point bending test, by pressing the center and the ends of relatively long tube in determined relatively small ring areas. We observed that following elastic response, at larger deformation, the metal wire yields well before the carbon bonding is affected. The behavior of filled tubes was compared with that of hollow tubes. Interesting is thet the hollow carbon (10,10) nanotube is more strong elastically than the same tube filled with Au-metal nanowire. We also simulated indentation of filled tubes residing on a hard flat surface. Similarly as in the bending test, metal wire yields first, is cut in between hard cylinder and hard plane and pushed away from under the indenter. Upon further increase of the indentation force, carbon tube is broken and forms two open ends that are rapidly zipped around the cut metal wire. Remarkably, the shape of the zipped tube ends strong depend of the speed of the punching of the tube. This result imply a possibility of designing tubes with various closed end shapes with applicationusing in the nanoscale manipulation procedures used for production.

  17. Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme

    Indian Academy of Sciences (India)

    Gorle Suresh; U Deva Priyakumar

    2015-10-01

    Bacillus halodurans (ℎ) ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and is a prototypical member of a large family of enzymes that use two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids. Long timescale molecular dynamics simulations have been performed on the ℎRNase H-DNA-RNA hybrid complex and the respective monomers to understand the recognition mechanism, conformational preorganization, active site dynamics and energetics involved in the complex formation. Several structural and energetic analyses were performed and significant structural changes are observed in enzyme and hybrid duplex during complex formation. Hybrid molecule binding to RNase H enzyme leads to conformational changes in the DNA strand. The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and B-type nucleic acids and the characteristic minor groove width-seem to be crucial for efficient binding. Sugar moieties in certain positions interacting with the protein structure undergo notable conformational transitions. The water coordination and arrangement around the metal ions in active site region are quite stable, suggesting their important role in enzymatic catalysis. Details of key interactions found at the interface of enzyme-nucleic acid complex that are responsible for its stability are discussed.

  18. Multiscale atomistic simulation of metal-oxygen surface interactions: Methodological development, theoretical investigation, and correlation with experiment

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Judith C. [Univ. of Pittsburgh, Pittsburgh, PA (United States)

    2015-01-09

    The purpose of this grant is to develop the multi-scale theoretical methods to describe the nanoscale oxidation of metal thin films, as the PI (Yang) extensive previous experience in the experimental elucidation of the initial stages of Cu oxidation by primarily in situ transmission electron microscopy methods. Through the use and development of computational tools at varying length (and time) scales, from atomistic quantum mechanical calculation, force field mesoscale simulations, to large scale Kinetic Monte Carlo (KMC) modeling, the fundamental underpinings of the initial stages of Cu oxidation have been elucidated. The development of computational modeling tools allows for accelerated materials discovery. The theoretical tools developed from this program impact a wide range of technologies that depend on surface reactions, including corrosion, catalysis, and nanomaterials fabrication.

  19. Thermochemistry of organic reactions in microporous oxides by atomistic simulations: benchmarking against periodic B3LYP.

    Science.gov (United States)

    Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole

    2010-07-15

    The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol.

  20. Atomistic simulations of electrochemical metallization cells: mechanisms of ultra-fast resistance switching in nanoscale devices.

    Science.gov (United States)

    Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

    2016-08-01

    We describe a new method that enables reactive molecular dynamics (MD) simulations of electrochemical processes and apply it to study electrochemical metallization cells (ECMs). The model, called EChemDID, extends the charge equilibration method to capture the effect of external electrochemical potential on partial atomic charges and describes its equilibration over connected metallic structures, on-the-fly, during the MD simulation. We use EChemDID to simulate resistance switching in nanoscale ECMs; these devices consist of an electroactive metal separated from an inactive electrode by an insulator and can be reversibly switched to a low-resistance state by the electrochemical formation of a conducting filament between electrodes. Our structures use Cu as the active electrode and SiO2 as the dielectric and have dimensions at the foreseen limit of scalability of the technology, with a dielectric thickness of approximately 1 nm. We explore the effect of device geometry on switching timescales and find that nanowires with an electroactive shell, where ions migrate towards a smaller inactive electrode core, result in faster switching than planar devices. We observe significant device-to-device variability in switching timescales and intermittent switching for these nanoscale devices. To characterize the evolution in the electronic structure of the dielectric as dissolved metallic ions switch the device, we perform density functional theory calculations on structures obtained from an EChemDID MD simulation. These results confirm the appearance of states around the Fermi energy as the metallic filament bridges the electrodes and show that the metallic ions and not defects in the dielectric contribute to the majority of those states.

  1. Atomistic simulations of tungsten surface evolution under low-energy neon implantation

    Science.gov (United States)

    Backman, Marie; Hammond, Karl D.; Sefta, Faiza; Wirth, Brian D.

    2016-04-01

    Tungsten is a candidate material for the divertor of fusion reactors, where it will be subject to a high flux of particles coming from the fusion plasma as well as a significant heat load. Under helium plasma exposure in fusion-reactor-like conditions, a nanostructured morphology is known to form on the tungsten surface in certain temperature and incident energy ranges, although the formation mechanism is not fully established. A recent experimental study (Yajima et al 2013 Plasma Sci. Technol. 15 282-6) using neon or argon exposure did not produce similar nanostructure. This article presents molecular dynamics simulations of neon implantation in tungsten aimed at investigating the surface evolution and elucidating the role of noble gas mass in fuzz formation. In contrast to helium, neon impacts can sputter both tungsten and previously implanted neon atoms. The shorter range of neon ions, along with sputtering, limit the formation of large bubbles and likely prevents nanostructure formation.

  2. Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations

    Science.gov (United States)

    Kreis, K.; Fogarty, A. C.; Kremer, K.; Potestio, R.

    2015-09-01

    In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One of the main advantages of such approaches is the computational efficiency gained in the coarse-grained region. In this respect the best coarse-grained system to employ in the low resolution region would be the ideal gas, making intermolecular force calculations in the coarse-grained subdomain redundant. In this case, however, a smooth coupling is challenging due to the high energetic imbalance between typical liquids and a system of non-interacting particles. In the present work, we investigate this approach, using as a test case the most biologically relevant fluid, water. We demonstrate that a successful coupling of water to the ideal gas can be achieved with current adaptive resolution methods, and discuss the issues that remain to be addressed.

  3. Atomistic simulation of He bubble in Fe as obstacle to dislocation

    Science.gov (United States)

    Hafez Haghighat, S. M.; Lucas, G.; Schäublin, R.

    2009-07-01

    Degradation of mechanical properties due to nanometric irradiation induced defects is one of the challenging issues in designing materials for future fusion reactors. Various types of defects such as voids and He bubbles may be produced due to high dose of neutron irradiation due to fusion reaction. We study the influence of He bubble on the mobility of an edge dislocation in pure bcc-Fe using molecular dynamics simulation as a function of bubble size, He density and temperature. It appears that low contents He bubbles are penetrable defects, which size and temperature rise make them harder and softer, respectively. At high He contents a size dependent loop punching is observed, which at larger bubble sizes leads to a multistep dislocation-defect interaction. It also appears that the bubble surface curvature and temperature are the main parameters in the screw segments annihilation needed for the release of the dislocation from the bubble.

  4. Investigation of the thermal stability of Cu nanowires using atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Granberg, F.; Parviainen, S., E-mail: stefan.parviainen@helsinki.fi; Djurabekova, F.; Nordlund, K. [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, Helsinki, FIN-00014 (Finland)

    2014-06-07

    We present a method for determining the melting point of copper nanowires based on classical molecular dynamics simulations and use it to investigate the dependence of the melting point on wire diameter. The melting point is determined as the temperature at which there is a significant change in the fraction of liquid atoms in the wire, according to atomic bond angle analysis. The results for the wires with diameters in the range 1.5 nm to 20 nm show that the melting point is inversely proportional to the diameter while the cross-sectional shape of the wire does not have a significant impact. Comparison of results obtained using different potentials show that while the absolute values of the melting points may differ substantially, the melting point depression is similar for all potentials. The obtained results are consistent with predictions based on the semi-empirical liquid drop model.

  5. Force-Field Derivation and Atomistic Simulation of HMX/Graphite Interface and Polycrystal Systems

    Institute of Scientific and Technical Information of China (English)

    龙瑶; 刘永刚; 聂福德; 陈军

    2012-01-01

    Interface is the key issue to understand the performance of composite materials. In this work, we study the interface between octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and graphite, try to find out its contribution to mixture explosives. The work starts from the force-field derivation. We get ab initio based pair potentials across the interface, and then use them to study the interface structural and mechanical properties. A series of large scale molecular dynamics simulations are performed. The structure evolution, energy variation and elastic/plastic transformation of interface and polycrystal systems are calculated. The desensitizing mechanism of graphite to HMX is discussed.

  6. Atomistic simulation of fcc-bcc phase transition in single crystal A1 under uniform compression

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

    By molecular dynamics simulations employing an embedded atom model potential,we investigate the fcc-to-bcc phase transition in single crystal Al,caused by uniform compression.Results show that the fec structure is unstable when the pressure is over 250 GPa,in reasonable agreement with the calculated value through the density functional theory.The morphology evolution of the structural transition and the corresponding transition mechanism are analysed in detail.The bec (011) planes are transited from the fcc (11(1)) plane and the (1(1)1) plane.We suggest that the transition mechanism consists mainly of compression,shear,slid and rotation of the lattice.In addition,our radial distribution function analysis explicitly indicates the phase transition of A1 from fcc phase to bcc structure.

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

    Directory of Open Access Journals (Sweden)

    Francesco Gentile

    2015-05-01

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

  8. Lubricant characterization by molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moore, J.D.; Cui, S.T.; Cummings, P.T.; Cochran, H.D. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemical Engineering]|[Oak Ridge National Lab., TN (United States). Chemical Technology Div.

    1997-12-01

    The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this computational approach offers the possibility of predicting the performance of potential lubricants prior to synthesis. Consequently, molecular simulation is poised to become an important tool for future lubricant development.

  9. Molecular dynamics simulations of uniaxial deformation of thermoplastic polyimides.

    Science.gov (United States)

    Nazarychev, V M; Lyulin, A V; Larin, S V; Gurtovenko, A A; Kenny, J M; Lyulin, S V

    2016-05-07

    The results of atomistic molecular-dynamics simulations of mechanical properties of heterocyclic polymer subjected to uniaxial deformation are reported. A new amorphous thermoplastic polyimide R-BAPO with a repeat unit consisting of dianhydride 1,3-bis-(3',4,-dicarboxyphenoxy)diphenyl (dianhydride R) and diamine 4,4'-bis-(4''-aminophenoxy)diphenyloxide (diamine BAPO) was chosen for the simulations. Our primary goal was to establish the impact of various factors (sample preparation method, molecular mass, and cooling and deformation rates) on the elasticity modulus. In particular, we found that the elasticity modulus was only slightly affected by the degree of equilibration, the molecular mass and the size of the simulation box. This is most likely due to the fact that the main contribution to the elasticity modulus is from processes on scales smaller than the entanglement length. Essentially, our simulations reproduce the logarithmic dependence of the elasticity modulus on cooling and deformation rates, which is normally observed in experiments. With the use of the temperature dependence analysis of the elasticity modulus we determined the flow temperature of R-BAPO to be 580 K in line with the experimental data available. Furthermore, we found that the application of high external pressure to the polymer sample during uniaxial deformation can improve the mechanical properties of the polyimide. Overall, the results of our simulations clearly demonstrate that atomistic molecular-dynamics simulations represent a powerful and accurate tool for studying the mechanical properties of heterocyclic polymers and can therefore be useful for the virtual design of new materials, thereby supporting cost-effective synthesis and experimental research.

  10. Structures of the Alzheimer's Wild-Type Aβ1-40 Dimer from Atomistic Simulations.

    Science.gov (United States)

    Tarus, Bogdan; Tran, Thanh T; Nasica-Labouze, Jessica; Sterpone, Fabio; Nguyen, Phuong H; Derreumaux, Philippe

    2015-08-20

    We have studied the dimer of amyloid beta peptide Aβ of 40 residues by means of all-atom replica exchange molecular dynamics. The Aβ-dimers have been found to be the smallest toxic species in Alzheimer's disease, but their inherent flexibilities have precluded structural characterization by experimental methods. Though the 24-μs-scale simulation reveals a mean secondary structure of 18% β-strand and 10% α helix, we find transient configurations with an unstructured N-terminus and multiple β-hairpins spanning residues 17-21 and 30-36, but the antiparallel and perpendicular peptide orientations are preferred over the parallel organization. Short-lived conformational states also consist of all α topologies, and one compact peptide with β-sheet structure stabilized by a rather extended peptide with α-helical content. Overall, this first all-atom study provides insights into the equilibrium structure of the Aβ1-40 dimer in aqueous solution, opening a new avenue for a comprehensive understanding of the impact of pathogenic and protective mutations in early-stage Alzheimer's disease on a molecular level.

  11. Combined atomistic-continuum model for simulation of laser interaction with metals: application in the calculation of melting thresholds in Ni targets of varying thickness

    Science.gov (United States)

    Ivanov, D. S.; Zhigilei, L. V.

    The threshold laser fluence for the onset of surface melting is calculated for Ni films of different thicknesses and for a bulk Ni target using a combined atomistic-continuum computational model. The model combines the classical molecular dynamics (MD) method for simulation of non-equilibrium processes of lattice superheating and fast phase transformations with a continuum description of the laser excitation and subsequent relaxation of the conduction band electrons based on the two-temperature model (TTM). In the hybrid TTM-MD method, MD substitutes the TTM equation for the lattice temperature, and the diffusion equation for the electron temperature is solved simultaneously with MD integration of the equations of motion of atoms. The dependence of the threshold fluence on the film thickness predicted in TTM-MD simulations qualitatively agrees with TTM calculations, while the values of the thresholds for thick films and bulk targets are 10% higher in TTM-MD. The quantitative differences between the predictions of TTM and TTM-MD demonstrate that the kinetics of laser melting as well as the energy partitioning between the thermal energy of atomic vibrations and energy of the collective atomic motion driven by the relaxation of the laser-induced pressure should be taken into account in interpretation of experimental results on surface melting.

  12. Effect of point and grain boundary defects on the mechanical behavior of monolayer MoS{sub 2} under tension via atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Dang, Khanh Q. [Department of Mechanical Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States); Spearot, Douglas E., E-mail: dspearot@uark.edu [Department of Mechanical Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States); Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States)

    2014-07-07

    Atomistic simulation is used to study the structure and energy of defects in monolayer MoS{sub 2} and the role of defects on the mechanical properties of monolayer MoS{sub 2}. First, energy minimization is used to study the structure and energy of monosulfur vacancies positioned within the bottom S layer of the MoS{sub 2} lattice, and 60° symmetric tilt grain boundaries along the zigzag and armchair directions, with comparison to experimental observations and density functional theory calculations. Second, molecular dynamics simulations are used to subject suspended defect-containing MoS{sub 2} membranes to a state of multiaxial tension. A phase transformation is observed in the defect-containing membranes, similar to prior work in the literature. For monolayer MoS{sub 2} membranes with point defects, groups of monosulfur vacancies promote stress-concentration points, allowing failure to initiate away from the center of the membrane. For monolayer MoS{sub 2} membranes with grain boundaries, failure initiates at the grain boundary and it is found that the breaking force for the membrane is independent of grain boundary energy.

  13. 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.

  14. Superlattice of stress domains in nanometer-size semiconductor devices predicted from atomistic simulations

    Science.gov (United States)

    Bachlechner, Martina E.; Ebbsjö, Ingvar; Kalia, Rajiv K.; Kodiyalam, Sanjay; Madhukar, Anupam; Nakano, Aiichiro; Omeltchenko, Andrey; Walsh, Phillip; Vashishta, Priya

    2001-03-01

    Semiconductor industry association estimates pixel sizes in next generation devices to be on the order of 70 nm by the year of 2008. Although recent measurements of local strain distributions2 and strain relaxation in nano wires have reached 100-nm spatial resolution, experimental tools for determining stresses for sub 100 nm, feature sizes are still to be developed4. On the other hand, recent developments in efficient simulation algorithms on state-of-the-art parallel computers5 enable us to gain valuable information on interface structure and atomic level stresses in nanopixels of < 100 nm size. Here, we present results for a 27.5-million atom molecular-dynamics simulations of a 70 nm x 70 nm crystalline silicon nanopixel covered with amorphous silicon nitride and placed on a 140 nm x 140 nm crystalline silicon substrate. The stresses parallel to the silicon/silicon nitride interface exhibit a hexagonal superlattice of stress domains with a lattice constant of 12.8 (±1.8) nm. From our analysis of the 70 nm x 70 nm pixel and on comparing with a smaller 25 nm x 25 nm nanopixel, we conclude that for square pixels the superlattice constant is independent of the pixel size and is entirely determined by the mismatch between silicon and silicon nitride. Such stress inhomogeneity with values of up to ±2 GPa will have a significant impact on the performance of semiconductor devices with sub 100 nm features.

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

    Science.gov (United States)

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

    2016-05-01

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

  16. Atomistic simulation of point defects and diffusion in B2 NiAl

    Energy Technology Data Exchange (ETDEWEB)

    Mishin, Y.; Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1998-08-04

    NiAl is a strongly ordered compound with a large atomic size difference between the components. Due to these features it demonstrates the so-called triple-defect mechanism of compositional disorder with Ni anti-structural atoms in Ni-rich compositions and Ni vacancies in Al-rich compositions. Diffusion mechanisms in triple-defect compounds are more involved than in antisite disorder compounds. Because every Ni atom in the B2 structure is surrounded by Al atoms and vise versa, every nearest-neighbor (NN) jump of a vacancy induces local disorder, which is very unfavorable. The authors therefore have to consider diffusion of Ni and Al along their own sublattices by next-nearest-neighbor (NNN) vacancy jumps. Alternatively, one can think of cycled mechanisms in which the crystal order is destroyed only locally and temporarily, but is totally restored when the diffusion cycle is complete. In this study the authors apply molecular statics simulations to evaluate the energetics of the point defect formation and migration in NiAl by different mechanisms. The goal of their simulations is to predict the mechanisms that are the easiest, thus dominating, at different alloy compositions.

  17. Micron-scale Reactive Atomistic Simulation of Void Collapse and Hotspot Growth in PETN

    Science.gov (United States)

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

    2015-06-01

    Material defects and other heterogeneities such as dislocations, micro-porosity, and grain boundaries play key roles in the shock-induced initiation of detonation in energetic materials. We performed non-equilibrium molecular dynamics simulations to explore the effect of nanoscale voids on hotspot growth and initiation in micron-scale pentaerythritol tetranitrate (PETN) crystals under weak shock loading (Up = 1.25 km/s; Us = 4.5 km/s). We used the ReaxFF potential implemented in LAMMPS. We built a pseudo-2D PETN crystal with dimensions 0.3 μm × 0.22 μm × 1.3 nm containing a 20 nm cylindrical void. Once the initial shockwave traversed the entire sample, the shock-front absorbing boundary condition was applied, allowing the simulation to continue beyond 1 nanosecond. Results show an exponentially increasing hotspot growth rate. The hotspot morphology is initially symmetric about the void axis, but strong asymmetry develops at later times, due to strong coupling between exothermic chemistry, temperature, and divergent secondary shockwaves emanating from the collapsing void. 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.

  18. Atomistic simulations of calcium uranyl(VI) carbonate adsorption on calcite and stepped-calcite surfaces.

    Science.gov (United States)

    Doudou, Slimane; Vaughan, David J; Livens, Francis R; Burton, Neil A

    2012-07-17

    Adsorption of actinyl ions onto mineral surfaces is one of the main mechanisms that control the migration of these ions in environmental systems. Here, we present computational classical molecular dynamics (MD) simulations to investigate the behavior of U(VI) in contact with different calcite surfaces. The calcium-uranyl-carbonate [Ca(2)UO(2)(CO(3))(3)] species is shown to display both inner- and outer-sphere adsorption to the flat {101̅4} and the stepped {314̅8} and {31̅2̅16} planes of calcite. Free energy calculations, using the umbrella sampling method, are employed to simulate adsorption paths of the same uranyl species on the different calcite surfaces under aqueous condition. Outer-sphere adsorption is found to dominate over inner-sphere adsorption because of the high free energy barrier of removing a uranyl-carbonate interaction and replacing it with a new uranyl-surface interaction. An important binding mode is proposed involving a single vicinal water monolayer between the surface and the sorbed complex. From the free energy profiles of the different calcite surfaces, the uranyl complex was also found to adsorb preferentially on the acute-stepped {314̅8} face of calcite, in agreement with experiment.

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

    Science.gov (United States)

    Thompson, Aidan

    2013-06-01

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

  20. Crystallography from Hauy to Laue : controversies on the molecular and atomistic nature of solids

    NARCIS (Netherlands)

    Kubbinga, Henk

    2012-01-01

    The history of crystallography has been assessed in the context of the emergence and spread of the molecular theory. The present paper focuses on the 19th century, which saw the emancipation of crystallography as a science sui generis. Around 1800, Laplace's molecularism called the tune in the vario

  1. Atomistic simulations, mesoscopic modeling, and theoretical analysis of thermal conductivity of bundles composed of carbon nanotubes

    Science.gov (United States)

    Volkov, Alexey N.; Salaway, Richard N.; Zhigilei, Leonid V.

    2013-09-01

    The propensity of carbon nanotubes (CNTs) to self-organize into continuous networks of bundles has direct implications for thermal transport properties of CNT network materials and defines the importance of clear understanding of the mechanisms and scaling laws governing the heat transfer within the primary building blocks of the network structures—close-packed bundles of CNTs. A comprehensive study of the thermal conductivity of CNT bundles is performed with a combination of non-equilibrium molecular dynamics (MD) simulations of heat transfer between adjacent CNTs and the intrinsic conductivity of CNTs in a bundle with a theoretical analysis that reveals the connections between the structure and thermal transport properties of CNT bundles. The results of MD simulations of heat transfer in CNT bundles consisting of up to 7 CNTs suggest that, contrary to the widespread notion of strongly reduced conductivity of CNTs in bundles, van der Waals interactions between defect-free well-aligned CNTs in a bundle have negligible effect on the intrinsic conductivity of the CNTs. The simulations of inter-tube heat conduction performed for partially overlapping parallel CNTs indicate that the conductance through the overlap region is proportional to the length of the overlap for CNTs and CNT-CNT overlaps longer than several tens of nm. Based on the predictions of the MD simulations, a mesoscopic-level model is developed and applied for theoretical analysis and numerical modeling of heat transfer in bundles consisting of CNTs with infinitely large and finite intrinsic thermal conductivities. The general scaling laws predicting the quadratic dependence of the bundle conductivity on the length of individual CNTs in the case when the thermal transport is controlled by the inter-tube conductance and the independence of the CNT length in another limiting case when the intrinsic conductivity of CNTs plays the dominant role are derived. An application of the scaling laws to bundles of

  2. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

    Science.gov (United States)

    Kirmizialtin, Serdal; Hennelly, Scott P.; Schug, Alexander; Onuchic, Jose N.; Sanbonmatsu, Karissa Y.

    2016-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remains a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2’-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the forcefield according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  3. Atomistic simulations of displacement cascades in Y{sub 2}O{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Dholakia, Manan, E-mail: manan@igcar.gov.in [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu (India); Chandra, Sharat [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu (India); Valsakumar, M.C. [School of Engineering Sciences and Technology, University of Hyderabad, Hyderabad 500 046 (India); Mathi Jaya, S. [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu (India)

    2014-11-15

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

  4. 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.

  5. Atomistic simulation of martensite-austenite phase transition in nanoscale nickel-titanium crystals

    Science.gov (United States)

    Kexel, Christian; Schramm, Stefan; Solov'yov, Andrey V.

    2015-09-01

    Shape-memory (SM) alloys can, after initial inelastic deformation, reconstruct their pristine lattice structure upon heating. The underlying phenomenon is the structural solid-solid phase transition from low-temperature lower-symmetry martensite to the high-temperature higher-symmetry austenite. Conventional nickel-titanium (NiTi) with near-equiatomic concentration already possesses an eminent importance for many applications, whereas the nanostructured equivalent can exhibit yet enhanced thermomechanical properties. However, no plausible microscopic theory of the SM effect in NiTi exists, especially for nanoscale systems. We investigate the thermally induced martensite-austenite phase transition in free equiatomic nanocrystals, comprising up to approximately 40 000 atoms, by means of molecular-dynamics simulations (MD) using a classical Gupta-type many-body scheme. Thereby we complement and extend a previously published study [D. Mutter, P. Nielaba, Eur. Phys. J. B 84, 109 (2011)]. The structural transition, revealing features of a first-order phase transition, is demonstrated. It is contrasted with the melting phase transition, a quantum solid model and bulk experimental findings. Moreover, a nucleation-growth process is observed as well as the irreversibility of the transition upon cooling.

  6. Atomistic simulation of the point defects in TaW ordered alloy

    Indian Academy of Sciences (India)

    Zhong-Liang Lin; Jian-Min Zhang; Yan Zhang; Vincent Ji

    2011-01-01

    Combining molecular dynamics (MD) simulation with modified analytic embeddedatom method (MAEAM), the formation, migration and activation energies of the point defects for six-kind migration mechanisms in B2-type TaW alloy have been investigated. The results showed that the anti-site defects TaW and WTa were easier to form than Ta and W vacancies owing to their lower formation energies. Comparing the migration and activation energies needed for six-kind migration mechanisms of a Ta (or W) vacancy, we found that one nearest-neighbour jump (1NNJ) was the most favourable because of its lowest migration and activation energies, but it would lead to a disorder in the alloy. One next-nearest-neighbour jump (1NNNJ) and one third-nearest-neighbour jump (1TNNJ) could maintain the ordered property of the alloy but required higher migration and activation energies. So the 1NNNJ and 1TNNJ should be replaced by straight [100] six nearestneighbor cyclic jumps (S[100]6NNCJ) (especially) or bent [100] six nearest-neighbour cyclic jumps (B[100]6NNCJ) and [110] six nearest-neighbor cyclic jumps ([110]6NNCJ), respectively.

  7. Orientation dependence of structural transition in fcc Al driven under uniaxial compression by atomistic simulations

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

    By molecular dynamics simulations employing an embedded atom method potential, we have investigated structural transformations in single crystal Al caused by uniaxial strain loading along the[001],[011]and[111]directions.We find that the structural transition is strongly dependent on the crystal orientations. The entire structure phase transition only occurs when loading along the[001]direction, and the increased amplitude of temperature for[001]loading is evidently lower than that for other orientations. The morphology evolutions of the structural transition for [011]and[111]loadings are analysed in detail. The results indicate that only 20% of atoms transit to the hcp phase for[011]and[111]loadings, and the appearance of the hcp phase is due to the partial dislocation moving forward on {111}fcc family. For[011]loading, the hcp phase grows to form laminar morphology in four planes, which belong to the{111}fcc family;while for[111]loading, the hcp phase grows into a laminar structure in three planes, which belong to the {111}fcc family except for the(111)plane. In addition, the phase transition is evaluated by using the radial distribution functions.

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

    Science.gov (United States)

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

    2014-11-07

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

  9. Molecular Dynamics Simulation of Miscibility in Several Polymer Blends

    CERN Document Server

    Ahmadi, Amirhossein

    2009-01-01

    The miscibility in several polymer blend mixtures (polymethylmethacrylate/polystyrene, (1,4-cis) polyisoprene/polystyrene, and polymethylmethacrylate/polyoxyethylene) has been investigated using Molecular Dynamics simulations for atomistic representations of the polymer chains. The trajectories obtained from simulation boxes representing the mixtures have been analyzed in terms of the collective scattering structure function. The Flory-Huggins parameter is determined from fits of the simulation results for this function to the random phase approximation expression. The numerical values of this parameter and its variation with temperature obtained with this procedure show a general qualitative and quantitative agreement with existing experimental data for the different systems. These results together with those previously obtained for the polyvylmethylether/polystyrene blends with the same method are compared with data yielded by other computational simpler approaches.

  10. Molecular dynamics simulation: A tool for exploration and discovery

    Science.gov (United States)

    Rapaport, Dennis C.

    2009-03-01

    The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).

  11. Revealing structural and dynamical properties of high density lipoproteins through molecular simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vattulainen, I.

    2012-01-01

    The structure and function of high density lipoprotein (HDL) particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of HDL. Further......, because of the complex composition of HDL, understanding the impact of its structure and dynamics on the function of HDL in reverse cholesterol transport has also been a major issue. Recent progress in molecular simulation methodology and computing power has made a difference, as it has enabled...... essentially atomistic considerations of HDL particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of HDL particles as revealed by atomistic and coarse-grained molecular...

  12. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing.

    Science.gov (United States)

    Zagrovic, Bojan; Snow, Christopher D; Shirts, Michael R; Pande, Vijay S

    2002-11-08

    By employing thousands of PCs and new worldwide-distributed computing techniques, we have simulated in atomistic detail the folding of a fast-folding 36-residue alpha-helical protein from the villin headpiece. The total simulated time exceeds 300 micros, orders of magnitude more than previous simulations of a molecule of this size. Starting from an extended state, we obtained an ensemble of folded structures, which is on average 1.7A and 1.9A away from the native state in C(alpha) distance-based root-mean-square deviation (dRMS) and C(beta) dRMS sense, respectively. The folding mechanism of villin is most consistent with the hydrophobic collapse view of folding: the molecule collapses non-specifically very quickly ( approximately 20ns), which greatly reduces the size of the conformational space that needs to be explored in search of the native state. The conformational search in the collapsed state appears to be rate-limited by the formation of the aromatic core: in a significant fraction of our simulations, the C-terminal phenylalanine residue packs improperly with the rest of the hydrophobic core. We suggest that the breaking of this interaction may be the rate-determining step in the course of folding. On the basis of our simulations we estimate the folding rate of villin to be approximately 5micros. By analyzing the average features of the folded ensemble obtained by simulation, we see that the mean folded structure is more similar to the native fold than any individual folded structure. This finding highlights the need for simulating ensembles of molecules and averaging the results in an experiment-like fashion if meaningful comparison between simulation and experiment is to be attempted. Moreover, our results demonstrate that (1) the computational methodology exists to simulate the multi-microsecond regime using distributed computing and (2) that potential sets used to describe interatomic interactions may be sufficiently accurate to reach the folded state

  13. Quantum molecular dynamics simulations of hydrogen production and solar cells

    Science.gov (United States)

    Mou, Weiwei

    The global energy crisis presents two major challenges for scientists around the world: Producing cleaner energy which is sustainable for the environment; And improving the efficiency of energy production as well as consumption. It is crucial and yet elusive to understand the atomistic mechanisms and electronic properties, which are needed in order to tackle those challenges. Quantum molecular dynamics simulations and nonadiabatic quantum molecular dynamics are two of the dominant methods used to address the atomistic and electronic properties in various energy studies. This dissertation is an ensemble of three studies in energy research: (1) Hydrogen production from the reaction of aluminum clusters with water to provide a renewable energy cycle; (2) The photo-excited charge transfer and recombination at a quaterthiophene/zinc oxide interface to improve the power conversion efficiency of hybrid poly(3-hexylthiophene) (P3HT) /ZnO solar cells; and (3) the charge transfer at a rubrene/C60 interface to understand why phenyl groups in rubrene improve the performance of rubrene/C60 solar cells.

  14. Does Fe(2+) in olivine-based interstellar grains play any role in the formation of H2? Atomistic insights from DFT periodic simulations.

    Science.gov (United States)

    Navarro-Ruiz, J; Ugliengo, P; Sodupe, M; Rimola, A

    2016-05-25

    Using periodic DFT-D2 methods, atomistic simulations of interstellar H adsorption and H2 formation on a (010) Fe-containing olivine surface are presented. At variance with the (010) Mg2SiO4 surface and key to these processes are the large Fe/H interaction energies, suggesting that olivine surfaces are good reservoirs of H atoms for subsequent recombination to form H2.

  15. Symmetry Breaking and Fine Structure Splitting in Zincblende Quantum Dots: Atomistic Simulations of Long-Range Strain and Piezoelectric Field

    Science.gov (United States)

    Ahmed, Shaikh; Usman, Muhammad; Heitzinger, Clemens; Rahman, Rajib; Schliwa, Andrei; Klimeck, Gerhard

    2007-04-01

    Electrons and holes captured in self-assembled quantum dots (QDs) are subject to symmetry breaking that cannot be represented in with continuum material representations. Atomistic calculations reveal symmetry lowering due to effects of strain and piezo-electric fields. These effects are fundamentally based on the crystal topology in the quantum dots. This work studies these two competing effects and demonstrates the fine structure splitting that has been demonstrated experimentally can be attributed to the underlying atomistic structure of the quantum dots.

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

    Science.gov (United States)

    Nagata, Yuki; Lennartz, Christian

    2008-07-21

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

  17. Meaningful timescales from Monte Carlo simulations of molecular systems

    CERN Document Server

    Costa, Liborio I

    2016-01-01

    A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems with atomistic detail is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is associated with minima in the energy landscape, in the proposed method, the state of the system is associated with the set of paths traveled by the atoms and the transition probabilities for an atom to be displaced are proportional to the corresponding velocities. In this way, the number of possible state-to-state transitions is reduced to a discrete set, and a direct link between the Monte Carlo time step and true physical time is naturally established. The resulting rejection-free algorithm is validated against event-driven molecular dynamics: the equilibrium and non-equilibrium dynamics of hard disks converge to the exact results with decreasing displacement size.

  18. 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.

  19. Fluid Simulations with Atomistic Resolution: Multiscale Model with Account of Nonlocal Momentum Transfer

    NARCIS (Netherlands)

    Svitenkov, A.I.; Chivilikhin, S.A.; Hoekstra, A.G.; Boukhanovsky, A.V.

    2015-01-01

    Nano- and microscale flow phenomena turn out to be highly non-trivial for simulation and require the use of heterogeneous modeling approaches. While the continuum Navier-Stokes equations and related boundary conditions quickly break down at those scales, various direct simulation methods and hybrid

  20. 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%.

  1. Molecular dynamics simulations of a single stranded (ss) DNA

    CERN Document Server

    Chatterjee, Subhasish; Thakur, Siddarth; Burin, Alexander

    2012-01-01

    The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) of the nucleic acid backbone of the ssDNA were studied using molecular dynamics (MD) simulations. The AMBER program was used for building the structural model of the ssDNA, and atomistic MD simulations in three different ensembles were carried out using the NAMD program. The microcanonical (NVE), conical (NVT) and isobaric-isothermal (NPT) ensembles were employed to compare the equilibrium characteristics of ssDNA in aqueous solutions. Our results indicate that the conformational stability of the ssDNA is dependent on the thermodynamic conditions.

  2. Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures

    NARCIS (Netherlands)

    Rzepiela, Andrzej J.; Schafer, Lars V.; Goga, Nicolae; Risselada, H. Jelger; De Vries, Alex H.; Marrink, Siewert J.

    2010-01-01

    We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which

  3. Molecular dynamics simulation of diffusivity

    Institute of Scientific and Technical Information of China (English)

    Juanfang LIU; Danling ZENG; Qin LI; Hong GAO

    2008-01-01

    Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.

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

    Science.gov (United States)

    Karim, Eaman T.; Shugaev, Maxim; Wu, Chengping; Lin, Zhibin; Hainsey, Robert F.; Zhigilei, Leonid V.

    2014-05-01

    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.

  5. Molecular dynamics simulation on the buckling behavior of GaN nanowires under uniaxial compression

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhiguo; Zu, Xiaotao; Yang, Li; Gao, Fei; Weber, William J

    2008-01-01

    Molecular dynamics simulation is one of the most promising methods for investigating the mechanical behavior of nanostructures, such as nanowires and nanotubes. Atomistic simulations are performed to investigate the buckling properties of [001], [11¯0] and [110] oriented GaN nanowires under uniaxial compression, these three types of nanowires correspond to experimentally synthesized nanowires. The effects of simulation temperature, and wire length on the buckling behavior are investigated. The simulation results show that critical stress decreases with the increase of wire length, which is in agreement with the Euler theory. Buckling occurs as a result of dynamic processes, buckling strain (and corresponding stress) decreases as temperature is increased.

  6. 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.

  7. Atomistic simulation of dislocation core structures in ordered TiAl

    Energy Technology Data Exchange (ETDEWEB)

    Panova, J.; Farkas, D. [Virginia Polytechnic Inst., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1995-12-31

    Interatomic potentials of the Embedded Atom type were used in the simulation of the dislocation core structures in TiAl. Different orientations of the dislocation line were simulated for the most commonly observed TiAl slip systems. Low-temperature dislocation behavior is interpreted in terms of ordinary dislocation motion. The effect of applied stress on the shape of the dislocation core and its mobility is examined as well. For the superdislocations several possible types of dissociations were studied.

  8. Atomistic deformation mechanisms in twinned copper nanospheres.

    Science.gov (United States)

    Bian, Jianjun; Niu, Xinrui; Zhang, Hao; Wang, Gangfeng

    2014-01-01

    In the present study, we perform molecular dynamic simulations to investigate the compression response and atomistic deformation mechanisms of twinned nanospheres. The relationship between load and compression depth is calculated for various twin spacing and loading directions. Then, the overall elastic properties and the underlying plastic deformation mechanisms are illuminated. Twin boundaries (TBs) act as obstacles to dislocation motion and lead to strengthening. As the loading direction varies, the plastic deformation transfers from dislocations intersecting with TBs, slipping parallel to TBs, and then to being restrained by TBs. The strengthening of TBs depends strongly on the twin spacing.

  9. Atomistic simulation of the motion of dislocations in metals under phonon drag conditions

    NARCIS (Netherlands)

    Kuksin, A. Yu; Yanilkin, A. V.

    2013-01-01

    The mobility of dislocations in the over-barrier motion in different metals (Al, Cu, Fe, Mo) has been investigated using the molecular dynamics method. The phonon drag coefficients have been calculated as a function of the pressure and temperature. The results obtained are in good agreement with the

  10. 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...

  11. Nonuniqueness of local stress of three-body potentials in molecular simulations

    Science.gov (United States)

    Nakagawa, Koh M.; Noguchi, Hiroshi

    2016-11-01

    Microscopic stress fields are widely used in molecular simulations to understand mechanical behavior. Recently, decomposition methods of multibody forces to central force pairs between the interacting particles have been proposed. Here, we introduce a force center of a three-body potential and propose different force decompositions that also satisfy the conservation of translational and angular momentum. We compare the force decompositions by stress-distribution magnitude and discuss their difference in the stress profile of a bilayer membrane by using coarse-grained and atomistic molecular dynamics simulations.

  12. 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.

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

  14. Molecular dynamics simulation of pyridine

    Science.gov (United States)

    Trumpakaj, Zygmunt; Linde, Bogumił

    2015-04-01

    Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.

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

    Directory of Open Access Journals (Sweden)

    Vijayan ManickamAchari

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

  16. Atomistic simulations of pristine and defective hexagonal BN and SiC sheets under uniaxial tension

    Energy Technology Data Exchange (ETDEWEB)

    Le, Minh-Quy, E-mail: quy.leminh@hust.edu.vn [Department of Mechanics of Materials and Structures, School of Mechanical Engineering, Hanoi University of Science and Technology, No. 1, Dai Co Viet Road, Hanoi (Viet Nam); International Institute for Computational Science and Engineering, Hanoi University of Science and Technology, No. 1, Dai Co Viet Road, Hanoi (Viet Nam); Nguyen, Danh-Truong [Department of Mechanics of Materials and Structures, School of Mechanical Engineering, Hanoi University of Science and Technology, No. 1, Dai Co Viet Road, Hanoi (Viet Nam)

    2014-10-06

    The uniaxial tensile mechanical properties of pristine and defective hexagonal boron nitride (BN) and silicon carbide (SiC) sheets are investigated through a molecular dynamics finite element method with Tersoff and Tersoff-like potentials. 2-Atom vacancy and 2 types of Stone–Wales defects are considered. It is found that uniaxial tensile stress–strain curves of defective and pristine sheets are almost identical up to fracture points. A centered single defect reduces significantly fracture stress and fracture strain from those of the corresponding pristine sheet. In contrast, Young's modulus is nearly unchanged by a single defect. One 2-atom vacancy in the sheet's center reduces 15–18% and 16–25% in fracture stress, and 32–34% and 32–48% in fracture strain of BN and SiC sheets, respectively. Reduction in fracture properties depends on the tensile direction as well as the orientation of Stone–Wales defects.

  17. Industrial Applications of Molecular Simulations

    CERN Document Server

    Meunier, Marc

    2011-01-01

    The field of quantum and molecular simulations has experienced strong growth since the time of the early software packages. A recent study, showed a large increase in the number of people publishing papers based on ab initio methods from about 3,000 in 1991 to roughly 20,000 in 2009, with particularly strong growth in East Asia. Looking to the future, the question remains as to how these methods can be further integrated into the R&D value chain, bridging the gap from engineering to manufacturing. Using successful case studies as a framework, Industrial Applications of Molecular Simulations de

  18. Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

    Science.gov (United States)

    Ji, Pengfei; Zhang, Yuwen

    2016-03-01

    On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.

  19. Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provide a general way that is accessible to other metals in laser heating.

  20. Accelerated path integral methods for atomistic simulations at ultra-low temperatures

    Science.gov (United States)

    Uhl, Felix; Marx, Dominik; Ceriotti, Michele

    2016-08-01

    Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated path integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH5+. We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH4 to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.

  1. Simulating surface-enhanced Raman optical activity using atomistic electrodynamics-quantum mechanical models.

    Science.gov (United States)

    Chulhai, Dhabih V; Jensen, Lasse

    2014-10-01

    Raman optical activity has proven to be a powerful tool for probing the geometry of small organic and biomolecules. It has therefore been expected that the same mechanisms responsible for surface-enhanced Raman scattering may allow for similar enhancements in surface-enhanced Raman optical activity (SEROA). However, SEROA has proved to be an experimental challenge and mirror-image SEROA spectra of enantiomers have so far not been measured. There exists a handful of theories to simulate SEROA, all of which treat the perturbed molecule as a point-dipole object. To go beyond these approximations, we present two new methods to simulate SEROA: the first is a dressed-tensors model that treats the molecule as a point-dipole and point-quadrupole object; the second method is the discrete interaction model/quantum mechanical (DIM/QM) model, which considers the entire charge density of the molecule. We show that although the first method is acceptable for small molecules, it fails for a medium-sized one such as 2-bromohexahelicene. We also show that the SEROA mode intensities and signs are highly sensitive to the nature of the local electric field and gradient, the orientation of the molecule, and the surface plasmon frequency width. Our findings give some insight into why experimental SEROA, and in particular observing mirror-image SEROA for enantiomers, has been difficult.

  2. Accelerated path integral methods for atomistic simulations at ultra-low temperatures.

    Science.gov (United States)

    Uhl, Felix; Marx, Dominik; Ceriotti, Michele

    2016-08-07

    Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated path integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH5 (+). We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH4 to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.

  3. Early and transient stages of Cu oxidation: Atomistic insights from theoretical simulations and in situ experiments

    Science.gov (United States)

    Zhu, Qing; Zou, Lianfeng; Zhou, Guangwen; Saidi, Wissam A.; Yang, Judith C.

    2016-10-01

    Understanding of metal oxidation is critical to corrosion control, catalysis synthesis, and advanced materials engineering. Although, metal oxidation process is rather complicated, different processes, many of them coupled, are involved from the onset of reaction. Since first introduced, there has been great success in applying heteroepitaxial theory to the oxide growth on a metal surface as demonstrated in the Cu oxidation experiments. In this paper, we review the recent progress in experimental findings on Cu oxidation as well as the advances in the theoretical simulations of the Cu oxidation process. We focus on the effects of defects such as step edges, present on realistic metal surfaces, on the oxide growth dynamics. We show that the surface steps can change the mass transport of both Cu and O atoms during oxide growth, and ultimately lead to the formation of different oxide morphology. We also review the oxidation of Cu alloys and explore the effect of a secondary element to the oxide growth on a Cu surface. From the review of the work on Cu oxidation, we demonstrate the correlation of theoretical simulations at multiple scales with various experimental techniques.

  4. Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

    Science.gov (United States)

    2014-10-01

    of these networks, the specific volume and the coefficient of volumetric thermal expansion (CVTE), are shown in Fig. 4. Specific volume is...CVTE values are somewhat lower than expected from experimental measurements of the coefficient of linear thermal expansion ,27 which can be...coefficient of volumetric thermal expansion db equilibrium bond length DCPD dicyclopentadiene GAFF general AMBER force field ID identification K

  5. Accelerating a hybrid continuum-atomistic fluidic model with on-the-fly machine learning

    CERN Document Server

    Stephenson, David; Lockerby, Duncan A

    2016-01-01

    We present a hybrid continuum-atomistic scheme which combines molecular dynamics (MD) simulations with on-the-fly machine learning techniques for the accurate and efficient prediction of multiscale fluidic systems. By using a Gaussian process as a surrogate model for the computationally expensive MD simulations, we use Bayesian inference to predict the system behaviour at the atomistic scale, purely by consideration of the macroscopic inputs and outputs. Whenever the uncertainty of this prediction is greater than a predetermined acceptable threshold, a new MD simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial enhancement to the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging-diverging channel, and make comparisons between the new s...

  6. Atomistic simulations of thiol-terminated modifiers for hybrid photovoltaic interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Malloci, G. [Istituto Officina dei Materiali (CNR-IOM), Unità di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Italy); Petrozza, A. [Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, I-20133 Milano (Italy); Mattoni, A., E-mail: mattoni@iom.cnr.it [Istituto Officina dei Materiali (CNR-IOM), Unità di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Italy)

    2014-06-02

    Small aromatic molecules such as benzene or pyridine derivatives are often used as interface modifiers (IMs) at polymer/metal oxide hybrid interfaces. We performed a theoretical investigation on prototypical thiol-terminated IMs aimed at improving the photovoltaic performances of poly(3-hexylthiophene)/TiO{sub 2} devices. By means of first-principles calculations in the framework of the density functional theory we investigate 3-furanthiol (3FT), 4-mercaptobenzoicacid (4MB), and 6-isoquinolinethiol (6QT) molecules. We discuss the role of these molecules as modifiers alternative to 4-mercaptopyridine (4MP) which has recently shown to induce a large improvement in the overall power conversion efficiency of mesoporous films of TiO{sub 2} infiltrated by poly(3-hexylthiophene). The IMs investigated are expected to keep the beneficial features of 4MP giving at the same time the possibility to further tune the interlayer properties (e.g., its thickness, stability, and density). Dense interlayers of 6QT turn out to be slightly unstable since the titania substrate induces a compressive strain in the molecular film. On the contrary, we predict very stable films for both 3FT and 4MB molecules, which makes them interesting candidates for future experimental investigations. - Highlights: • We performed a theoretical investigation on thiol-terminated interface modifiers. • We investigate 3-furanthiol (3FT), 4-mercaptobenzoicacid (4MB), and 6-isoquinolinethiol molecules. • We discuss the role of these molecules as modifiers alternative to 4-mercaptopyridine. • Dense interlayers of 6-isoquinolinethiol turn out to be slightly unstable. • We predict very stable self-assembled thin-films for both 3FT and 4MB molecules.

  7. Efficiency of various lattices from hard ball to soft ball: theoretical study of thermodynamic properties of dendrimer liquid crystal from atomistic simulation.

    Science.gov (United States)

    Li, Youyong; Lin, Shiang-Tai; Goddard, William A

    2004-02-18

    Self-assembled supramolecular organic liquid crystal structures at nanoscale have potential applications in molecular electronics, photonics, and porous nanomaterials. Most of these structures are formed by aggregation of soft spherical supramolecules, which have soft coronas and overlap each other in the packing process. Our main focus here is to study the possible packing mechanisms via molecular dynamics simulations at the atomistic level. We consider the relative stability of various lattices packed by the soft dendrimer balls, first synthesized and characterized by Percec et al. (J. Am. Chem. Soc. 1997, 119, 1539) with different packing methods. The dendrons, which form the soft dendrimer balls, have the character of a hard aromatic region from the point of the cone to the edge with C(12) alkane "hair". After the dendrons pack into a sphere, the core of the sphere has the hard aromatic groups, while the surface is covered with the C(12) alkane "hair". In our studies, we propose three ways to organize the hair on the balls, Smooth/Valentino balls, Sticky/Einstein balls, and Asymmetric/Punk balls, which lead to three different packing mechanisms, Slippery, Sticky, and Anisotropic, respectively. We carry out a series of molecular dynamics (MD) studies on three plausible crystal structures (A15, FCC, and BCC) as a function of density and analyze the MD based on the vibrational density of state (DoS) method to extract the enthalpy, entropy, and free energies of these systems. We find that anisotropic packed A15 is favored over FCC, BCC lattices. Our predicted X-ray intensities of the best structures are in excellent agreement with experiment. "Anisotropic ball packing" proposed here plays an intermediate role between the enthalpy-favored "disk packing" and entropy-favored "isotropic ball packing", which explains the phase transitions at different temperatures. Free energies of various lattices at different densities are essentially the same, indicating that the

  8. Atomistic Simulations of Helium Clustering and Grain Boundary Reconstruction in Alpha-Iron

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Li; Gao, Fei; Kurtz, Richard J.; Zu, Xiaotao

    2015-01-01

    The accumulation and clustering of He atoms at Σ3 <110> {112} and Σ73b<110>{661} grain boundaries (GBs) in bcc Fe, as well as their effects on GB reconstruction, have been investigated using atomic-level computer simulations. The accumulation of He atoms and the evolution of the GB structure all depend on local He concentration, temperature and the original GB structure. At a local He concentration of 1%, small He clusters are formed in the Σ3 GB, accompanied by the emission of single self-interstitial Fe atoms (SIAs). At a He concentration of 5%, a large number of SIAs are emitted from He clusters in the Σ3 GB and collect at the periphery of these clusters. The SIAs eventually form <100> dislocation loops between two He clusters. It is likely that impurities may promote the formation of <100> loops and enhance their stabilities in α-Fe. At a He concentration of 10%, the large number of emitted SIAs are able to rearrange themselves, forming a new GB plane within the Σ3 GB, which results in self-healing of the GB and leads to GB migration. In contrast to the Σ3 GB, He clusters are mainly formed along the GB dislocation lines in the Σ73b, and the emitted SIAs accumulate at the cores of the GB dislocations, leading to the climb of the dislocations within the GB plane. As compared to bulk Fe, a higher number density of clusters form at GBs, but the average cluster size is smaller. The product of cluster density and average cluster size is roughly constant at a given He level, and is about the same in bulk and GB regions and varies linearly with the He concentration.

  9. Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.

    Science.gov (United States)

    Tavernelli, Ivano

    2015-03-17

    Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-15

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

  11. Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.

    Energy Technology Data Exchange (ETDEWEB)

    Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

    2010-09-01

    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

  12. 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

  13. Grand canonical Molecular Dynamics Simulations

    CERN Document Server

    Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K

    2011-01-01

    For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.

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

    Science.gov (United States)

    Pousaneh, Faezeh; Edholm, Olle; Maciołek, Anna

    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.

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

    Directory of Open Access Journals (Sweden)

    Vashishta P.

    2011-05-01

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

  16. Atomistic aspects of crack propagation along high angle grain boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1997-12-31

    The author presents atomistic simulations of the crack tip configuration near a high angle {Sigma} = 5 [001](210) symmetrical tilt grain boundary in NiAl. The simulations were carried out using molecular statics and embedded atom (EAM) potentials. The cracks are stabilized near a Griffith condition involving the cohesive energy of the grain boundary. The atomistic configurations of the tip region are different in the presence of the high angle grain boundary than in the bulk. Three different configurations of the grain boundary were studied corresponding to different local compositions. It was found that in ordered NiAl, cracks along symmetrical tilt boundaries show a more brittle behavior for Al rich boundaries than for Ni-rich boundaries. Lattice trapping effects in grain boundary fracture were found to be more significant than in the bulk.

  17. Trypsinogen activation as observed in accelerated molecular dynamics simulations.

    Science.gov (United States)

    Boechi, Leonardo; Pierce, Levi; Komives, Elizabeth A; McCammon, J Andrew

    2014-11-01

    Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus's group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme.

  18. Application of bi-Helmholtz nonlocal elasticity and molecular simulations to the dynamical response of carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Koutsoumaris, C. Chr.; Tsamasphyros, G. J. [School of Applied Mathematical and Physical Sciences National Technical University of Athens (NTUA) 5 Iroon Polytechniou Str., Zografou, Zografou Campus, Athens, GR-157 73 (Greece); Vogiatzis, G. G.; Theodorou, D. N. [School of Chemical Engineering National Technical University of Athens (NTUA) 5 Iroon Polytechniou Str., Zografou, Zografou Campus, Athens, GR-157 73 (Greece)

    2015-12-31

    The nonlocal theory of elasticity is employed for the study of the free vibrations of carbon nanotubes (CNT). For the first time, a bi-Helmholtz operator has been used instead of the standard Helmholtz operator in a nonlocal beam model. Alongside the continuum formulation and its numerical solution, atomistic Molecular Dynamics (MD) simulations have been conducted in order to directly evaluate the eigenfrequencies of vibrating CNTs with a minimum of adjustable parameters. Our results show that the bi-Helmholtz operator is the most appropriate one to fit MD simulation results. However, the estimation of vibration eigenfrequencies from molecular simulations still remains an open (albeit well-posed) problem.

  19. Ice formation on kaolinite: Insights from molecular dynamics simulations

    Science.gov (United States)

    Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

    2016-12-01

    The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.

  20. Enhanced molecular dynamics for simulating porous interphase layers in batteries.

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)

    2009-10-01

    Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from 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 propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.

  1. Insights from molecular dynamics simulations for computational protein design.

    Science.gov (United States)

    Childers, Matthew Carter; Daggett, Valerie

    2017-02-01

    A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

  2. Possibilités actuelles du calcul des constantes élastiques de polymères par des méthodes de simulation atomistique Current Possibilities of the Computation of Elastic Constants of Polymers Using Atomistic Simulations

    Directory of Open Access Journals (Sweden)

    Dal Maso F.

    2006-12-01

    Full Text Available Les propriétés élastiques des phases amorphe et cristalline pures de polymères semi-cristallins ne sont en général pas mesurables directement avec les moyens physiques habituels. Il est donc nécessaire de recourir à des méthodes de calcul numérique. Cet article décrit certaines de ces méthodes, fondées sur des modélisations atomistiques, ainsi qu'une évaluation des implémentations actuelles. Il est montré que la méthode proposée par Zehnder et al. (1996 fournit les meilleurs résultats, au prix d'un temps long de calcul, dû à la dynamique moléculaire. Néanmoins, aucune de ces méthodes n'est vraiment utilisable simplement au jour le jour, car elles requièrent des moyens importants de calcul. Elastic properties of pure crystalline and amorphous phases of a semicrystalline polymer are usually not directly measurable by usual physical means. It therefore is necessary to resort to numerical computing methods. This paper describes some of these methods, based on atomistic simulations, as well as an assessment of current implementations. It is shown that the method proposed by Zehnder et al. (1996 gives the best results, at the expense of long computing time, due to molecular dynamic simulation. Nevertheless none of these methods are really usable on a daily basis, since there are demanding important computing capabilities.

  3. Accelerating molecular simulations of proteins using Bayesian inference on weak information

    Science.gov (United States)

    Perez, Alberto; MacCallum, Justin L.; Dill, Ken A.

    2015-01-01

    Atomistic molecular dynamics (MD) simulations of protein molecules are too computationally expensive to predict most native structures from amino acid sequences. Here, we integrate “weak” external knowledge into folding simulations to predict protein structures, given their sequence. For example, we instruct the computer “to form a hydrophobic core,” “to form good secondary structures,” or “to seek a compact state.” This kind of information has been too combinatoric, nonspecific, and vague to help guide MD simulations before. Within atomistic replica-exchange molecular dynamics (REMD), we develop a statistical mechanical framework, modeling using limited data with coarse physical insight(s) (MELD + CPI), for harnessing weak information. As a test, we apply MELD + CPI to predict the native structures of 20 small proteins. MELD + CPI samples to within less than 3.2 Å from native for all 20 and correctly chooses the native structures (<4 Å) for 15 of them, including ubiquitin, a millisecond folder. MELD + CPI is up to five orders of magnitude faster than brute-force MD, satisfies detailed balance, and should scale well to larger proteins. MELD + CPI may be useful where physics-based simulations are needed to study protein mechanisms and populations and where we have some heuristic or coarse physical knowledge about states of interest. PMID:26351667

  4. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations

    Science.gov (United States)

    Levine, Zachary Alan

    Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant

  5. 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

  6. Exploring the structure-solubility relationship of asphaltene models in toluene, heptane, and amphiphiles using a molecular dynamic atomistic methodology.

    Science.gov (United States)

    Aray, Yosslen; Hernández-Bravo, Raiza; Parra, José G; Rodríguez, Jesús; Coll, David S

    2011-10-27

    The solubility parameters, δ, of several asphaltene models were calculated by mean of an atomistic NPT ensemble. Continental and archipelago models were explored. A relationship between the solubility parameter and the molecule structure was determined. In general, increase of the fused-rings number forming the aromatic core and the numbers of heteroatoms such as oxygen, nitrogen, and sulfur produces an increase of the solubility parameter, while increases of the numbers and length of the aliphatic chains yield a systematic decrease of this parameter. Molecules with large total carbon atom number at the tails, n(c), and small aromatic ring number, n(r), exhibit the biggest values of δ, while molecules with small n(c) and large n(r) show the smallest δ values. A good polynomial correlation δ = 5.967(n(r)/n(c)) - 3.062(n(r)/n(c))(2) + 0.507(n(r)/n(c))(3) + 16.593 with R(2) = 0.965 was found. The solubilities of the asphaltene models in toluene, heptane, and amphiphiles were studied using the Scatchard-Hildebrand and the Hansen sphere methodologies. Generally, there is a large affinity between the archipelago model and amphiphiles containing large aliphatic tails and no aromatic rings, while continental models show high affinity for amphiphiles containing an aromatic ring and small aliphatic chains.

  7. Molecular Simulation of Reverse Micelles

    Science.gov (United States)

    Chowdhary, Janamejaya; Ladanyi, Branka

    2009-03-01

    Reverse micelles (RM) are surfactant assemblies containing a nanosized water pool dissolved in a hydrophobic solvent. Understanding their properties is crucial for insight into the effect of confinement on aqueous structure, dynamics as well as physical processes associated with solutes in confinement. We perform molecular dynamics simulations for the RM formed by the surfactant Aerosol-OT (AOT) in isooctane (2,2,4-trimethyl pentane) in order to study the effect of reverse micelle size on the aqueous phase. The structure of the RM is quantified in terms of the radial and pair density distributions. Dynamics are studied in terms of the mean squared displacements and various orientational time correlation functions in different parts of the RM so as to understand the effect of proximity to the interface on aqueous dynamics. Shape fluctuations of the RM are also analyzed.

  8. Systematic Structural Change in Selected Rare Earth Oxide Pyrochlores as Determined by Wide-Angle CBED and a Comparison with the Results of Atomistic Computer Simulation

    Science.gov (United States)

    Tabira, Yasunori; Withers, Ray L.; Minervini, Licia; Grimes, Robin W.

    2000-08-01

    An unknown oxygen atom fractional co-ordinate characteristic of the pyrochlore structure type has been determined for selected rare earth zirconate and titanate pyrochlores via a systematic row wide-angle CBED technique and shown to vary systematically with rare earth ion size. In the case of the titanate pyrochlore Gd2Ti2O7, the obtained results contrast with previously published X-ray results. Atomistic computer simulation is used to predict the value of the same parameter for a wide range of oxide pyrochlores. Comparison of calculated values with experimentally determined values shows that the general trends are correctly predicted although there appears to be systematic underestimation of both the observed values (by approximately 0.007) as well as their rate of change with rare earth ion size. Cation anti-site disorder is proposed as the origin of these discrepancies.

  9. Comparison of the Solid Solution Properties of Mg-RE (Gd, Dy, Y Alloys with Atomistic Simulation

    Directory of Open Access Journals (Sweden)

    Yurong Wu

    2008-01-01

    Full Text Available Molecular dynamic simulations have been performed to study the solid solution mechanism of Mg100-xREx (RE=Gd,Dy,Y, x=0.5,1,2,3,4  at.%. The obtained results reveal that the additions of Gd, Dy and Y increase the lattice constants of Mg-RE alloys. Also the axis ratio c/a remains unchanged with increase in temperature, restraining the occurrence of nonbasal slip and twinning. Furthermore, it is confirmed that bulk modulus of Mg alloys can be increased remarkably by adding the Gd, Dy, Y, especially Gd, because the solid solubility of Gd in Mg decrease sharply with temperature in comparison with Dy and Y. Consequently, the addition of the RE can enhance the strength of Mg-based alloys, which is in agreement with the experimental results.

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

    Science.gov (United States)

    Chen, Zhe; Kecskes, Laszlo J.; Zhu, Kaigui; Wei, Qiuming

    2016-12-01

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

  11. Investigation of the role of polysaccharide in the dolomite growth at low temperature by using atomistic simulations

    CERN Document Server

    Shen, Zhizhang; Szlufarska, Izabela; Xu, Huifang

    2016-01-01

    Dehydration of water from surface Mg2+ is most likely the rate-limiting step in the dolomite growth at low temperature. Here, we investigate the role of polysaccharide in this step using classical molecular dynamics (MD) calculations. Free energy (potential of mean force, PMF) calculations have been performed for water molecules leaving the first two hydration layers above the dolomite (104) surface under the following three conditions: without catalyst, with monosaccharide (mannose) and with oligosaccharide (three units of mannose). MD simulations reveal that there is no obvious effect of monosaccharide in lowering the dehydration barrier for surface Mg2+. However, we found that there are metastable configurations of oligosaccharide, which can decrease the dehydration barrier of surface Mg2+ by about 0.7-1.1 kcal/mol. In these configurations, the molecule lies relatively flat on the surface and forms a bridge shape. The hydrophobic space near the surface created by the non-polar -CH groups of the oligosaccha...

  12. Striped gold nanoparticles: New insights from molecular dynamics simulations

    Science.gov (United States)

    Velachi, Vasumathi; Bhandary, Debdip; Singh, Jayant K.; Cordeiro, M. Natália D. S.

    2016-06-01

    Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199-3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols' arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper, we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl's chain length, the length difference between the thiol mixtures, and solvent properties.

  13. Atomistic insight into the minimum wear depth of Cu(111) surface

    OpenAIRE

    2013-01-01

    In the present work, we investigate the minimum wear depth of single crystalline Cu(111) under single asperity friction by means of molecular dynamics simulations. The atomistic mechanisms governing the incipient plasticity are elucidated by characterizing specific defect structures and are correlated to the observed mechanical and frictional responses of the material. Furthermore, the effect of probe radius on the friction process is studied. Our simulations indicate that the formation of we...

  14. Molecular dynamics simulations of highly cross-linked polymer networks: prediction of thermal and mechanical properties

    Science.gov (United States)

    Shenogina, Natalia; Tsige, Mesfin; Mukhopadhyay, Sharmila; Patnaik, Soumya

    2012-02-01

    We use all-atom molecular dynamics (MD) simulations to predict the mechanical and thermal properties of thermosetting polymers. Atomistic simulation is a promising tool which can provide detailed structure-property relationships of densely cross-linked polymer networks. In this work we study the thermo-mechanical properties of thermosetting polymers based on amine curing agents and epoxy resins and have focused on the DGEBA/DETDA epoxy system. At first we describe the modeling approach to construction of realistic all-atom models of densely cross-linked polymer matrices. Subsequently, a series of atomistic simulations was carried out to examine the simulation cell size effect as well as the role of cross-linking density and chain length of the resin strands on thermo-mechanical properties at different temperatures. Two different methods were used to deform the polymer networks. Both static and dynamic approaches to calculating the mechanical properties were considered and the thermo-mechanical properties obtained from our simulations were found in reasonable agreement with experimental values.

  15. Experimental and atomistic simulation studies of corrosion inhibition of copper by a new benzotriazole derivative in acid medium

    Energy Technology Data Exchange (ETDEWEB)

    Khaled, K.F. [Electrochemistry Research Laboratory, Chemistry Department, Ain Shams University, Roxy, Cairo 11711 (Egypt)], E-mail: khaledrice2003@yahoo.com

    2009-07-15

    The efficiency of N-(2-thiazolyl)-1H-benzotriazole-1-carbothioamide (TBC) as a non-toxic corrosion inhibitor for copper in 0.5 M HCl has been tested by weight loss and electrochemical techniques. Electrochemical techniques show that TBC is a mixed-type inhibitor and its inhibition mechanism on copper surface is adsorption assisted by H-bond formation. Impedance measurements show a wide peak presumably given by more than one time constant in the presence of TBC. Also, impedance results show that the values of CPEs (constant phase elements) tend to decrease and both polarization resistance and inhibition efficiency tend to increase with increasing of TBC concentration due to an increase in the electric double layer. Monte Carlo simulations incorporating molecular mechanics and molecular dynamics show that the TBC adsorb on the copper surface firmly through the thiazolyl and carbothioamide groups, the adsorption energy as well as hydrogen bond length have been calculated for both TBC and benzotriazole (BTA) for comparison. Quantum chemical calculations reveal that TBC has higher HOMO, lower LUMO, lower energy gap and lower dipole moment ({mu}) than BTA, which proves that TBC is better copper corrosion inhibitor compared with BTA in 0.5 M HCl.

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

    Directory of Open Access Journals (Sweden)

    Rozanska Xavier

    2015-03-01

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

  17. Molecular Simulations of Porphyrins and Heme Proteins

    Energy Technology Data Exchange (ETDEWEB)

    SHELNUTT,JOHN A.

    2000-01-18

    An overview of the use of classical mechanical molecular simulations of porphyrins, hydroporphyrins, and heme proteins is given. The topics cover molecular mechanics calculations of structures and conformer energies of porphyrins, energies of barriers for interconversion between stable conformers, molecular dynamics of porphyrins and heme proteins, and normal-coordinate structural analysis of experimental and calculated porphyrin structures. Molecular mechanics and dynamics are currently a fertile area of research on porphyrins. In the future, other computational methods such as Monte Carlo simulations, which have yet to be applied to porphyrins, will come into use and open new avenues of research into molecular simulations of porphyrins.

  18. Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids

    Science.gov (United States)

    Morrow, Brian H.; Koenig, Peter H.; Shen, Jana K.

    2012-11-01

    Detailed knowledge of the self-assembly and phase behavior of pH-sensitive surfactants has implications in areas such as targeted drug delivery. Here we present a study of the formation of micelle and bilayer from lauric acids using a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with conformational sampling in explicit solvent and the pH-based replica-exchange protocol. We find that at high pH conditions a spherical micelle is formed, while at low pH conditions a bilayer is formed with a considerable degree of interdigitation. The mid-point of the phase transition is in good agreement with experiment. Preliminary investigation also reveals that the effect of counterions and salt screening shifts the transition mid-point and does not change the structure of the surfactant assembly. Based on these data we suggest that CpHMD simulations may be applied to computational design of surfactant-based nano devices in the future.

  19. The alloying processes in solid–solid and liquid–solid Li–Pb interfaces with atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gan, Xianglai [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Deng, Huiqiu; Xiao, Shifang; Li, Xiaofan [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Hu, Wangyu, E-mail: wyuhu@hnu.edu.cn [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China)

    2015-05-25

    Highlights: • B2-LiPb forms in these three kinds of Li–Pb interfaces. • The nucleation of the B2-LiPb at the solid–solid Li–Pb interface is the earliest. • The B2-LiPb acts as a diffusion barrier. • The block Li in the critical interface sample collapses from distortion. • The interface width growth rate of the liquid–solid interface is the largest. - Abstract: The alloying processes of solid–solid (at 400 K) and liquid–solid (at 500 K) Li–Pb interfaces are investigated by molecular dynamics simulations with embedded-atom method (EAM) potentials. As a comparison, a critical Li–Pb interface at 450 K near the melting point of Li is also studied. Three-stage feature, including the interface disordering, nucleation and growth of an intermetallic phase (B2-LiPb), has been clearly observed in these three cases. It is found that the alloying products are the same, however, the nucleation of the intermetallic phase at the solid–solid Li–Pb interface is earlier than that in the other two cases. The block Li in the solid–solid interface sample keeps the body-centered cubic structure during the course of simulation, while in the critical Li–Pb interface sample, it collapses from the excessive lattice distortion. As simulation time increasing, the interface widths increase gradually with decreasing growth rates, and the growth rate is the largest for the liquid–solid interface and the smallest for the solid–solid interface. The interface width of the solid–solid Li–Pb interface saturates at about 0.3 ns for the diffusion barrier—B2-LiPb almost traversed across the entire interface plane at that time.

  20. Atomistic simulation study of the effect of martensitic transformation volume change on crack-tip material evolution and fracture toughness

    Energy Technology Data Exchange (ETDEWEB)

    Grujicic, M. [Clemson Univ., SC (United States). Dept. of Mechanical Engineering; Lai, S.G. [Clemson Univ., SC (United States). Dept. of Mechanical Engineering; Gumbsch, P. [Max Planck-Institut fur Metallforshung Institut fuer Werstoffwissenshaft, Seestrasse 92, D-7000 Stuttgart I (Germany)

    1997-07-15

    The effect of the sign of the F.C.C.{yields}B.C.C. martensitic transformation volume change in Fe-20Ni on material evolution in a region surrounding the crack tip and the accompanying change in the fracture resistance of the material have been investigated using molecular dynamics simulations. The interaction between atoms has been modeled using the embedded atom method (EAM) interatomic potentials. To obtain both the positive and the negative values of the transformation volume change, small adjustments had to be made in the EAM functions. These changes did not significantly affect of the key materials properties, such as the relative thermodynamic stability of the F.C.C. and B.C.C. structures, elastic constants, (11 anti 2){sub bcc} twin boundary energy, (10 anti 1){sub fcc}/(1 anti 21){sub bcc} interfacial energy, etc. The simulation results show that the sign of the transformation volume change has a profound effect on the material evolution and the path of the advancing crack. When the volume change is negative, the region ahead of the crack tip undergoes the transformation only after the other regions around the crack tip have already transformed. The crack tip undergoes a significant blunting and tends to stay on the original crack plane. In sharp contrast, when the volume change is positive, the region ahead of the crack tip transforms first and significant decohesion along the F.C.C./B.C.C. interfaces takes place. Consequently the crack tends to branch out. The effect of material evolution at the crack tip on the ability of the material to withstand further fracture has been quantified by calculating the Eshelby`s F{sub 1} conservation integral. The sign of the transformation volume change is found to have a major effect on the change of the F{sub 1} integral with the simulation time. (orig.)

  1. Hybrid particle-field molecular dynamics simulations for dense polymer systems.

    Science.gov (United States)

    Milano, Giuseppe; Kawakatsu, Toshihiro

    2009-06-07

    We propose a theoretical scheme for a hybrid simulation technique where self-consistent field theory and molecular dynamics simulation are combined (MD-SCF). We describe the detail of the main implementation issues on the evaluation of a smooth three-dimensional spatial density distribution and its special gradient based on the positions of particles. The treatments of our multiscale model system on an atomic scale or on a specific coarse-grained scale are carefully discussed. We perform a series of test simulations on this hybrid model system and compare the structural correlations on the atomic scale with those of classical MD simulations. The results are very encouraging and open a way to an efficient strategy that possess the main advantages common to the SCF and the atomistic approaches, while avoiding the disadvantages of each of the treatments.

  2. Temperature dependence of creep compliance of highly cross-linked epoxy: A molecular simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Khabaz, Fardin, E-mail: rajesh.khare@ttu.edu; Khare, Ketan S., E-mail: rajesh.khare@ttu.edu; Khare, Rajesh, E-mail: rajesh.khare@ttu.edu [Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409 (United States)

    2014-05-15

    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.

  3. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  4. Atomistic simulations of P(NDI2OD-T2) morphologies: from single chain to condensed phases.

    Science.gov (United States)

    Caddeo, Claudia; Fazzi, Daniele; Caironi, Mario; Mattoni, Alessandro

    2014-10-30

    We investigate theoretically the structure, crystallinity, and solubility of a high-mobility n-type semiconducting copolymer, P(NDI2OD-T2), and we propose a set of new force field parameters. The force field is reparametrized against density functional theory (DFT) calculations, with the aim to reproduce the correct torsional angles that govern the polymer chain flexibility and morphology. We simulate P(NDI2OD-T2) oligomers in different environments, namely, in vacuo, in the bulk phase, and in liquid toluene and chloronaphthalene solution. The choice of these solvents is motivated by the fact that they induce different kinds of molecular preaggregates during the casting procedures, resulting in variable device performances. Our results are in good agreement with the available experimental data; the polymer bulk structure, in which the chains are quite planar, is correcly reproduced, yet the isolated chains are flexible enough to fold in vacuo. We also calculate the solubility of P(NDI2OD-T2) in toluene and chloronaphthalene, predicting a much better solubility of the polymer in the latter, also in accordance to experimental observations. Different morphologies and dynamics of the oligomers in the two solvents have been observed. The proposed parameters make it possible to obtain the description of P(NDI2OD-T2) in different environments and can serve as a basis for extensive studies of this polymer semiconductor, such as, for example, the dynamics of aggregation in solvent.

  5. A numerical study of ultraprecision machining of monocrystalline silicon with laser nano-structured diamond tools by atomistic simulation

    Science.gov (United States)

    Dai, Houfu; Chen, Genyu; Zhou, Cong; Fang, Qihong; Fei, Xinjiang

    2017-01-01

    Three-dimension molecular dynamics (MD) simulations is employed to investigate the ultraprecision machining of single crystal silicon with structured nanoscale diamond tool fabricated by laser. The advantages and disadvantages of diamond machining using structured tools are discussed in comparison with those of using non-structured tools. The von Mises stress distribution, hydrostatic stress distribution, atomic displacement, stress, the radial distribution function, cutting forces, frictional coefficient, subsurface temperature and potential energy during the nanometric machining process are studied. A theoretical analysis model is also established to investigate the subsurface damage mechanism by analyzing the distribution of residual stress during the nanoscale machining process. The results show that a structured nanoscale tool in machining brittle material silicon causes a smaller hydrostatic stress, a less compressive normal stress σxx and σyy , a lower temperature and a smaller cutting force. However, the structured nanoscale tool machining results in smaller chip volume and more beta-silicon phase. Besides, the friction coefficient for tool with V-shape groove is smaller than those for non-structured tools and other structured nanoscale tools. This means that the tool with V-shape groove can reduce the resistance to cutting during the nanoscale machining process. In addition, the results also point out that the potential energy of subsurface atoms and the number of other atoms for pyramid-structured tool are much smaller than those of using non-structured tools and other structured nanoscale tools.

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

    Science.gov (United States)

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

    2017-03-01

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

  7. Boundary-dependent mechanical properties of graphene annular under in-plane circular shearing via atomistic simulations

    Science.gov (United States)

    Li, Yinfeng; Lin, Qianling; Cui, Daxiang

    2017-02-01

    Graphene annulus possesses special wrinkling phenomenon with wide range of potential applications. Using molecular dynamics simulation, this study concerns the effect of boundary on the mechanical properties of circular and elliptical graphene annuli under circular shearing at inner edge. Both the wrinkle characteristic and torque capacity of annular graphene can be effectively tuned by outer boundary radius and aspect ratio. For circular annulus with fixed inner radius, the critical angle of rotation can be increased by several times without sacrificing its torque capacity by increasing outer boundary radius. The wrinkle characteristic of graphene annulus with elliptical outer boundary differs markedly with that of circular annulus. Torque capacity anomalously decreases with the increase of aspect ratio, and a coupled effect of the boundary aspect ratio and the ratio of minor axis to inner radius on wrinkling are revealed. By studying the stress distribution and wrinkle characteristics, we find the decay of torque capacity is the result of circular stress concentration around the minor axis, while the nonuniform stress distribution is anomalously caused by the change of wrinkle profiles near the major axis. The specific mechanism of out-of-plane deformation on in-plane strength provides a straightforward means to develop novel graphene-based devices.

  8. Investigation of the Role of Polysaccharide in the Dolomite Growth at Low Temperature by Using Atomistic Simulations.

    Science.gov (United States)

    Shen, Zhizhang; Szlufarska, Izabela; Brown, Philip E; Xu, Huifang

    2015-09-29

    Dehydration of water from surface Mg(2+) is most likely the rate-limiting step in the dolomite growth at low temperature. Here, we investigate the role of polysaccharide in this step using classical molecular dynamics (MD) calculations. Free energy (potential of mean force, PMF) calculations have been performed for water molecules leaving the first two hydration layers above the dolomite (104) surface under the following three conditions: without catalyst, with monosaccharide (mannose), and with oligosaccharide (three units of mannose). MD simulations reveal that there is no obvious effect of monosaccharide in lowering the dehydration barrier for surface Mg(2+). However, we found that there are metastable configurations of oligosaccharide, which can decrease the dehydration barrier of surface Mg(2+) by about 0.7-1.1 kcal/mol. In these configurations, the molecule lies relatively flat on the surface and forms a bridge shape. The hydrophobic space near the surface created by the nonpolar -CH groups of the oligosaccharide in the bridge conformation is the reason for the observed reduction of dehydration barrier.

  9. Boundary-dependent mechanical properties of graphene annular under in-plane circular shearing via atomistic simulations

    Science.gov (United States)

    Li, Yinfeng; Lin, Qianling; Cui, Daxiang

    2017-01-01

    Graphene annulus possesses special wrinkling phenomenon with wide range of potential applications. Using molecular dynamics simulation, this study concerns the effect of boundary on the mechanical properties of circular and elliptical graphene annuli under circular shearing at inner edge. Both the wrinkle characteristic and torque capacity of annular graphene can be effectively tuned by outer boundary radius and aspect ratio. For circular annulus with fixed inner radius, the critical angle of rotation can be increased by several times without sacrificing its torque capacity by increasing outer boundary radius. The wrinkle characteristic of graphene annulus with elliptical outer boundary differs markedly with that of circular annulus. Torque capacity anomalously decreases with the increase of aspect ratio, and a coupled effect of the boundary aspect ratio and the ratio of minor axis to inner radius on wrinkling are revealed. By studying the stress distribution and wrinkle characteristics, we find the decay of torque capacity is the result of circular stress concentration around the minor axis, while the nonuniform stress distribution is anomalously caused by the change of wrinkle profiles near the major axis. The specific mechanism of out-of-plane deformation on in-plane strength provides a straightforward means to develop novel graphene-based devices. PMID:28198805

  10. Direct dynamics simulations of the product channels and atomistic mechanisms for the OH(-) + CH3I reaction. Comparison with experiment.

    Science.gov (United States)

    Xie, Jing; Sun, Rui; Siebert, Matthew R; Otto, Rico; Wester, Roland; Hase, William L

    2013-08-15

    Electronic structure and direct dynamics calculations were used to study the potential energy surface and atomic-level dynamics for the OH(-) + CH3I reactions. The results are compared with crossed molecular beam, ion imaging experiments. The DFT/B97-1/ECP/d level of theory gives reaction energetics in good agreement with experiment and higher level calculations, and it was used for the direct dynamics simulations that were performed for reactant collision energies of 2.0, 1.0, 0.5, and 0.05 eV. Five different pathways are observed in the simulations, forming CH3OH + I(-), CH2I(-) + H2O, CH2 + I(-) + H2O, IOH(-) + CH3, and [CH3--I--OH](-). The SN2 first pathway and the proton-transfer second pathway dominate the reaction dynamics. Though the reaction energetics favor the SN2 pathway, the proton-transfer pathway is more important except for the lowest collision energy. The relative ion yield determined from the simulations is in overall good agreement with experiment. Both the SN2 and proton-transfer pathways occur via direct rebound, direct stripping, and indirect mechanisms. Except for the highest collision energy, 70-90% of the indirect reaction for the SN2 pathway occurs via formation of the hydrogen-bonded OH(-)---HCH2I prereaction complex. For the proton-transfer pathway the indirect reaction is more complex with the roundabout mechanism and formation of the OH(-)---HCH2I and CH2I(-)---HOH complexes contributing to the reaction. The majority of the SN2 reaction is direct at 2.0, 1.0, and 0.5 eV, dominated by stripping. At 0.05 eV the two direct mechanisms and the indirect mechanisms have nearly equal contributions. The majority of the proton-transfer pathway is direct stripping at 2.0, 1.0, and 0.5 eV, but the majority of the reaction is indirect at 0.05 eV. The product relative translational energy distributions are in good agreement with experiment for both the SN2 and proton-transfer pathways. For both, direct reaction preferentially transfers the product

  11. 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

  12. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations.

    Science.gov (United States)

    Lemmin, Thomas; Soto, Cinque S; Clinthorne, Graham; DeGrado, William F; Dal Peraro, Matteo

    2013-01-01

    The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM) domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices.

  13. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations.

    Directory of Open Access Journals (Sweden)

    Thomas Lemmin

    Full Text Available The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices.

  14. Effects of Zr doping on the surface energy and surface structure of UO{sub 2}: Atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Hongxing, E-mail: xiaohongxing2003@163.com [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China); Long, Chongsheng; Chen, Hongsheng [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China); Tian, Xiaofeng [The College of Nuclear Technology and Automation Engineering, Chengdu University of Technology, Chengdu (China); Wei, Tianguo; Zhao, Yi; Gao, Wen [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China)

    2015-10-01

    A shell-core model is applied to investigate the effects of Zr doping on the surface energies and surface structures of the three low Miller index surfaces in UO{sub 2} using the molecular dynamics (MD) technique. The surface energies and atomic structures of the Zr-doped and undoped UO{sub 2} (1 0 0), (1 1 0) and (1 1 1) surfaces are compared. Simulation results indicate that (i) the surface energy of (U{sub 1−y}Zr{sub y})O{sub 2} depend on the crystallographic orientation, as well as of undoped UO{sub 2}. The (1 0 0) surface exhibits the highest surface energy, followed by the (1 1 0) surface, and the (1 1 1) surface; (ii) Zr doping will significantly increase the surface energy of UO{sub 2} by approximately 20% on (1 0 0) surface, 10% on (1 1 0) surface and 15% on (1 1 1) surface with the ZrO{sub 2} contents ranging from 0 to 12.5 mol%, respectively; (iii) the surface energies of the three low Miller index surfaces decrease with increasing temperature both in undoped UO{sub 2} and in (U{sub 1−y}Zr{sub y})O{sub 2}; (iv) the addition of Zr induces a severe distortion of the (U{sub 1−y}Zr{sub y})O{sub 2} surface structure, and the outermost top layer exhibits the strongest rumpling; (v) the considerable reconstructions can be observed in the two top layers of Zr-doped and undoped UO{sub 2} surfaces when the temperature is elevated to 900–1500 K.

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

    Science.gov (United States)

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

    2012-03-01

    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 PbTiO3 and tetragonal Pb(Zr,Ti)O3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed.

  16. Continuum simulations of water flow past fullerene molecules

    Science.gov (United States)

    Popadić, A.; Praprotnik, M.; Koumoutsakos, P.; Walther, J. H.

    2015-09-01

    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 solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.

  17. Nanoscale finite element models for vibrations of single-walled carbon nanotubes:atomistic versus continuum

    Institute of Scientific and Technical Information of China (English)

    R ANSARI; S ROUHI; M ARYAYI

    2013-01-01

    By the atomistic and continuum finite element models, the free vibration behavior of single-walled carbon nanotubes (SWCNTs) is studied. In the atomistic finite element model, the bonds and atoms are modeled by the beam and point mass elements, respectively. The molecular mechanics is linked to structural mechanics to determine the elastic properties of the mentioned beam elements. In the continuum finite element approach, by neglecting the discrete nature of the atomic structure of the nanotubes, they are modeled with shell elements. By both models, the natural frequencies of SWCNTs are computed, and the effects of the geometrical parameters, the atomic structure, and the boundary conditions are investigated. The accuracy of the utilized methods is verified in comparison with molecular dynamic simulations. The molecular structural model leads to more reliable results, especially for lower aspect ratios. The present analysis provides valuable information about application of continuum models in the investigation of the mechanical behaviors of nanotubes.

  18. Atomistic Failure Mechanism of Single Wall Carbon Nanotubes with Small Diameters

    Institute of Scientific and Technical Information of China (English)

    JI Dong; GAO Xiang; KONG Xiang-Yang; LI Jia-Ming

    2007-01-01

    @@ Single wall carbon nanotubes with small diameters (< 5.0 (A)) subjected to bending deformation are simulated by orthogonal tight-binding molecular dynamics approach. Based on the calculations of C-C bond stretching and breaking in the bending nanotubes, we elucidate the atomistic failure mechanisms of nanotube with small diameters. In the folding zone of bending nanotube, a large elongation of C-C bonds occurs, accounting for the superelastic behaviour.

  19. Fluctuation Solution Theory Properties from Molecular Simulation

    DEFF Research Database (Denmark)

    Abildskov, Jens; Wedberg, R.; O’Connell, John P.

    2013-01-01

    The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...... thermodynamic properties of solutions...

  20. Atomistic Hydrodynamics and the Dynamical Hydrophobic Effect in Porous Graphene.

    Science.gov (United States)

    Strong, Steven E; Eaves, Joel D

    2016-05-19

    Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For numerical simulation to play a predictive and descriptive role, one must have theoretically sound methods that span orders of magnitude in physical scales, from the atomistic motions of particles inside the channels to the large-scale hydrodynamic gradients that drive transport. Here, we use constraint dynamics to derive a nonequilibrium molecular dynamics method for simulating steady-state mass flow of a fluid moving through the nanoscopic spaces of a porous solid. After validating our method on a model system, we use it to study the hydrophobic effect of water moving through pores of electrically doped single-layer graphene. The trend in permeability that we calculate does not follow the hydrophobicity of the membrane but is instead governed by a crossover between two competing molecular transport mechanisms.

  1. Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics.

    Science.gov (United States)

    Weber, Adrian C J; Pizzirusso, Antonio; Muccioli, Luca; Zannoni, Claudio; Meerts, W Leo; de Lange, Cornelis A; Burnell, E Elliott

    2012-05-07

    The NMR spectra of n-pentane as solute in the liquid crystal 5CB are measured at several temperatures in the nematic phase. Atomistic molecular dynamics simulations of this system are carried out to predict the dipolar couplings of the orientationally ordered pentane, and the spectra predicted from these simulations are compared with the NMR experimental ones. The simulation predictions provide an excellent starting point for analysis of the experimental NMR spectra using the covariance matrix adaptation evolutionary strategy. This shows both the power of atomistic simulations for aiding spectral analysis and the success of atomistic molecular dynamics in modeling these anisotropic systems.

  2. Is the microscopic stress computed from molecular simulations in mechanical equilibrium?

    Science.gov (United States)

    Torres-Sánchez, Alejandro; Vanegas, Juan M.; Arroyo, Marino

    The microscopic stress field connects atomistic simulations with the mechanics of materials at the nano-scale through statistical mechanics. However, its definition remains ambiguous. In a recent work we showed that this is not only a theoretical problem, but rather that it greatly affects local stress calculations from molecular simulations. We find that popular definitions of the local stress, which are continuously being employed to understand the mechanics of various systems at the nanoscale, violate the continuum statements of mechanical equilibrium. We exemplify these facts in local stress calculations of defective graphene, lipid bilayers, and fibrous proteins. Furthermore, we propose a new physical and sound definition of the microscopic stress that satisfies the continuum equations of balance, irrespective of the many-body nature of the inter-atomic potential. Thus, our proposal provides an unambiguous link between discrete-particle models and continuum mechanics at the nanoscale.

  3. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  4. Molecular Dynamic Simulation of Thin Film Growth Stress Evolution

    Science.gov (United States)

    Zheng, Haifeng

    2011-12-01

    With the increasing demand for thin films across a wide range of technology, especially in electronic and magnetic applications, controlling the stresses in deposited thin films has become one of the more important challenges in modern engineering. It is well known that large intrinsic stress---in the magnitude of several gigapascals---can result during the thin film preparation. The magnitude of stress depends on the deposition technique, film thickness, types and structures of materials used as films and substrates, as well as other factors. Such large intrinsic stress may lead to film cracking and peeling in case of tensile stress, and delamination and blistering in case of compression. However it may also have beneficial effects on optoelectronics and its applications. For example, intrinsic stresses can be used to change the electronic band gap of semiconducting materials. The far-reaching fields of microelectronics and optoelectronics depend critically on the properties, behavior, and reliable performance of deposited thin films. Thus, understanding and controlling the origins and behavior of such intrinsic stresses in deposited thin films is a highly active field of research. In this study, on-going tensile stress evolution during Volmer-Weber growth mode was analyzed through numerical methods. A realistic model with semi-cylinder shape free surfaces was used and molecular dynamics simulations were conducted. Simulations were at room temperature (300 K), and 10 nanometer diameter of islands were used. A deposition rate that every 3 picoseconds deposit one atom was chosen for simulations. The deposition energy was and lattice orientation is [0 0 1]. Five different random seeds were used to ensure average behaviors. In the first part of this study, initial coalescence stress was first calculated by comparing two similar models, which only differed in the distance between two neighboring islands. Three different substrate thickness systems were analyzed to

  5. Combined Atomistic Molecular Calculations and Experimental Investigations for the Architecture, Screening, Optimization, and Characterization of Pyrazinamide Containing Oral Film Formulations for Tuberculosis Management.

    Science.gov (United States)

    Adeleke, Oluwatoyin A; Monama, Nkwe O; Tsai, Pei-Chin; Sithole, Happy M; Michniak-Kohn, Bozena B

    2016-02-01

    semicrystalline in nature and displayed a dual phased ex vivo mucosal permeation pattern. In silico and in vitro physicomechanical quantities revealed OF 2's flexibility, robustness, and compressibility. OF 2 was most stable under controlled environmental humidity, pressure, and temperature conditions in silico and in vitro. OF 2 was potentially non-cytotoxic and biocompatible. Succinctly, this work demonstrated the applicability of a combination of atomistic molecular mechanics and dynamics calculations as well as experimental analyses to the fabrication, screening, optimization, and characterization of drug formulations. Lastly, the fabricated OF 2 formulation can function as a potential alternative for the effective loading and delivery of PYZ.

  6. Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

    Science.gov (United States)

    Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

    2017-01-01

    This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...

  8. Bridging Atomistic/Continuum Scales in Solids with Moving Dislocations

    Institute of Scientific and Technical Information of China (English)

    TANG Shao-Qiang; LIU Wing K.; KARPOV Eduard G.; HOU Thomas Y.

    2007-01-01

    @@ We propose a multiscale method for simulating solids with moving dislocations. Away from atomistic subdomains where the atomistic dynamics are fully resolved, a dislocation is represented by a localized jump profile, superposed on a defect-free field. We assign a thin relay zone around an atomistic subdomain to detect the dislocation profile and its propagation speed at a selected relay time. The detection technique utilizes a lattice time history integral treatment. After the relay, an atomistic computation is performed only for the defect-free field. The method allows one to effectively absorb the fine scale fluctuations and the dynamic dislocations at the interface between the atomistic and continuum domains. In the surrounding region, a coarse grid computation is adequate.

  9. Atomistic comparative study of VUV photodeposited silicon nitride on InP(100) by simulation and atomic force microscopy

    Science.gov (United States)

    Flicstein, J.; Guillonneau, E.; Marquez, J.; How Kee Chun, L. S.; Maisonneuve, D.; David, C.; Wang, Zh.; Palmier, J. F.; Courant, J. L.

    2000-02-01

    We report on an accurate validation of a new Monte Carlo three-dimensional model. Simulations up to 1200 Å layer thickness have been carried out for amorphous thin film layers of SiN:H deposited at low temperature (400-650 K) on (100) InP, by vacuum ultraviolet (VUV, ˜185 nm)-induced chemical vapor deposition (CVD). The computer simulations in the mesoscopic-submicronic range are compared with atomic force microscopy and index of refraction measurements. The reconstituted surface roughness and the voids discrete representations of the bulk are found to be in good agreement with these measurements. Simultaneously at around 450 K (at ˜175°C), thermal characteristic evolution of the both surface roughness and bulk porosity showed a transition from rough to smooth deposition and from low to high density.

  10. The Ca(2+ influence on calmodulin unfolding pathway: a steered molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Yong Zhang

    Full Text Available The force-induced unfolding of calmodulin (CaM was investigated at atomistic details with steered molecular dynamics. The two isolated CaM domains as well as the full-length CaM were simulated in N-C-terminal pulling scheme, and the isolated N-lobe of CaM was studied specially in two other pulling schemes to test the effect of pulling direction and compare with relevant experiments. Both Ca(2+-loaded CaM and Ca(2+-free CaM were considered in order to define the Ca(2+ influence to the CaM unfolding. The results reveal that the Ca(2+ significantly affects the stability and unfolding behaviors of both the isolated CaM domains and the full-length CaM. In Ca(2+-loaded CaM, N-terminal domain unfolds in priori to the C-terminal domain. But in Ca(2+-free CaM, the unfolding order changes, and C-terminal domain unfolds first. The force-extension curves of CaM unfolding indicate that the major unfolding barrier comes from conquering the interaction of two EF-hand motifs in both N- and C- terminal domains. Our results provide the atomistic-level insights in the force-induced CaM unfolding and explain the observation in recent AFM experiments.

  11. 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.

  12. Molecular Simulations using Spherical Harmonics

    Institute of Scientific and Technical Information of China (English)

    CAI, Wen-Sheng; XU, Jia-Wei; SHAO, Xue-Guang; MAIGRET, Bernard

    2003-01-01

    Computer-aided drug design is to develop a chemical that binds to a target macromolecule known to play a key role in a disease state. In recognition of ligands by their protein receptors,molecular surfaces are often used because they represent the interacting part of molecules and they should reflex the complementarity between ligand and receptor. However, assessing the surface complementarity by searching all relative position of two surfaces is often computationally expensive. The complementarity of lobe-hole is very important in protein-ligand interactions. Spherical harmonic models based on expansions of spherical harmonic functions were used as a fingerprint to approximate the binding cavity and the ligand, respectively. This defines a new way to identify the complementarity between lobes and holes. The advantage of this method is that two spherical harmonic surfaces to be compared can be defined separately. This method can be used as a filter to eliminate candidates among a large number of conformations, and it will speed up the docking procedure. Therefore, it is possible to select complementary ligands or complementary conformations of a ligand and the macromoleeules, by comparing their fingerprints previously stored in a database.

  13. Thermodynamics of supersaturated steam: Molecular simulation results

    Science.gov (United States)

    Moučka, Filip; Nezbeda, Ivo

    2016-12-01

    Supersaturated steam modeled by the Gaussian charge polarizable model [P. Paricaud, M. Předota, and A. A. Chialvo, J. Chem. Phys. 122, 244511 (2005)] and BK3 model [P. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)] has been simulated at conditions occurring in steam turbines using the multiple-particle-move Monte Carlo for both the homogeneous phase and also implemented for the Gibbs ensemble Monte Carlo molecular simulation methods. Because of these thermodynamic conditions, a specific simulation algorithm has been developed to bypass common simulation problems resulting from very low densities of steam and cluster formation therein. In addition to pressure-temperature-density and orthobaric data, the distribution of clusters has also been evaluated. The obtained extensive data of high precision should serve as a basis for development of reliable molecular-based equations for properties of metastable steam.

  14. Atomistic properties of γ uranium.

    Science.gov (United States)

    Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

    2012-02-22

    The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

  15. Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes

    Science.gov (United States)

    Chugunov, Anton O.; Volynsky, Pavel E.; Krylov, Nikolay A.; Boldyrev, Ivan A.; Efremov, Roman G.

    2014-12-01

    Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0-100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and ``branched'' hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.

  16. Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations

    Science.gov (United States)

    Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru

    Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.

  17. Atomistic simulation of charge effects: From tunable thin film growth to isolation of surface states with spin-orbit coupling

    Science.gov (United States)

    Ming, Wenmei

    This dissertation revitalizes the importance of surface charge effects in semiconductor nanostructures, in particular in the context of thin film growth and exotic electronic structures under delicate spin-orbit coupling. A combination of simulation techniques, including density functional theory calculation, kinetic Monte Carlo method, nonequilibrium Green's function method, and tight binding method, were employed to reveal the underlying physical mechanisms of four topics: (1) Effects of Li doping on H-diffusion in MgH 2 for hydrogen storage. It addresses both the effect of Fermi level tuning by charged dopant and the effect of dopant-defect interaction, and the latter was largely neglected in previous works; (2) Tuning nucleation density of the metal island with charge doping of the graphene substrate. It is the first time that the surface charge doping effect is proposed and studied as an effective approach to tune the kinetics of island nucleation at the early stage of thin film growth; (3) Complete isolation of Rashba surface states on the saturated semiconductor surface. It shows that the naturally saturated semiconductor surface of InSe(0001) with Au single layer film provides a mechanism for the formation of Rashba states with large spin splitting; it opens up an innovative route to obtaining ideal Rashba states without the overwhelming bulk spin-degenerate carriers in spin-dependent transport; (4) Formation of large band gap quantum spin Hall state on Si surface. This study reveals the importance of atomic orbital composition in the formation of a topological insulator, and shows promisingly the possible integration of topological insulator technology into Si-based modern electronic devices.

  18. Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

    Science.gov (United States)

    Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

    2016-11-08

    Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively (13)C-labeled choline with (29)Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like (1)H-(13)C CP-REDOR (rotational-echo double resonance), (1)H-(13)C HETCOR (heteronuclear correlation), and (1)H-(29)Si-(1)H double CP are employed to determine spatial parameters. The measurement of (29)Si-(13)C internuclear distances for selectively (13)C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

  19. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Science.gov (United States)

    Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  20. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    Full Text Available The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  1. Surface complexation of heavy metal cations on clay edges: insights from first principles molecular dynamics simulation of Ni(II)

    Science.gov (United States)

    Zhang, Chi; Liu, Xiandong; Lu, Xiancai; He, Mengjia; Jan Meijer, Evert; Wang, Rucheng

    2017-04-01

    Aiming at an atomistic mechanism of heavy metal cation complexing on clay surfaces, we carried out systematic first principles molecular dynamics (FPMD) simulations to investigate the structures, free energies and acidity constants of Ni(II) complexes formed on edge surfaces of 2:1 phyllosilicates. Three representative complexes were studied, including monodentate complex on the tbnd SiO site, bidentate complex on the tbnd Al(OH)2 site, and tetradentate complex on the octahedral vacancy where Ni(II) fits well into the lattice. The complexes structures were characterized in detail. Computed free energy values indicate that the tetradentate complex is significantly more stable than the other two. The calculated acidity constants indicate that the tetradentate complex can get deprotonated (pKa = 8.4) at the ambient conditions whereas the other two hardly deprotonate due to extremely high pKa values. By comparing with the 2 Site Protolysis Non Electrostatic Surface Complexation and Cation Exchange (2SPNE SC/CE) model, the vacant site has been assigned to the strong site and the other two to the weak site, respectively. Thus a link has been built between atomistic simulations and macroscopic experiments and it is deduced that this should also apply to other heavy metal cations based on additional simulations of Co(II) and Cu(II) and previous simulations of Fe(II) and Cd(II)). This study forms a physical basis for understanding the transport and fixation of heavy metal elements in many geologic environments.

  2. Accelerated molecular dynamics simulations of protein folding.

    Science.gov (United States)

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.

  3. 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

    2014-09-01

    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.

  4. Atomistic Modelling of Si Nanoparticles Synthesis

    Directory of Open Access Journals (Sweden)

    Giovanni Barcaro

    2017-02-01

    Full Text Available Silicon remains the most important material for electronic technology. Presently, some efforts are focused on the use of Si nanoparticles—not only for saving material, but also for improving the efficiency of optical and electronic devices, for instance, in the case of solar cells coated with a film of Si nanoparticles. The synthesis by a bottom-up approach based on condensation from low temperature plasma is a promising technique for the massive production of such nanoparticles, but the knowledge of the basic processes occurring at the atomistic level is still very limited. In this perspective, numerical simulations can provide fundamental information of the nucleation and growth mechanisms ruling the bottom-up formation of Si nanoclusters. We propose to model the low temperature plasma by classical molecular dynamics by using the reactive force field (ReaxFF proposed by van Duin, which can properly describe bond forming and breaking. In our approach, first-principles quantum calculations are used on a set of small Si clusters in order to collect all the necessary energetic and structural information to optimize the parameters of the reactive force-field for the present application. We describe in detail the procedure used for the determination of the force field and the following molecular dynamics simulations of model systems of Si gas at temperatures in the range 2000–3000 K. The results of the dynamics provide valuable information on nucleation rate, nanoparticle size distribution, and growth rate that are the basic quantities for developing a following mesoscale model.

  5. Atomistic stimulation of defective oxides

    CERN Document Server

    Minervini, L

    2000-01-01

    defect processes. The predominant intrinsic disorder reaction and the mechanism by which excess oxygen is accommodated are established. Furthermore, the most favourable migration mechanism and pathway for oxygen ions is predicted. Chapters 7 and 8 investigate pyrochlore oxides. These materials are candidates for solid oxide fuel cell components and as actinide host phases. Such applications require a detailed understanding of the defect processes. The defect energies, displayed as contour maps, are able to account for structure stability and, given an appropriate partial charge potential model, to accurately determine the oxygen positional parameter. In particular, the dependence of the positional parameter on intrinsic disorder is predicted. It is demonstrated, by radiation damage experiments, that these results are able to predict the radiation performance of pyrochlore oxides. Atomistic simulation calculations based on energy minimization techniques and classical pair potentials are used to study several i...

  6. Hamiltonian adaptive resolution simulation for molecular liquids.

    Science.gov (United States)

    Potestio, Raffaello; Fritsch, Sebastian; Español, Pep; Delgado-Buscalioni, Rafael; Kremer, Kurt; Everaers, Ralf; Donadio, Davide

    2013-03-08

    Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well-defined statistical ensembles can be generated making use of all standard molecular dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.

  7. 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.

  8. Cold melting of beryllium: Atomistic view on Z-machine experiments

    Science.gov (United States)

    Dremov, V. V.; Rykounov, A. A.; Sapozhnikov, F. A.; Karavaev, A. V.; Yakovlev, S. V.; Ionov, G. V.; Ryzhkov, M. V.

    2015-07-01

    Analysis of phase diagram of beryllium at high pressures and temperatures obtained as a result of ab initio calculations and large scale classical molecular dynamics simulations of beryllium shock loading have shown that the so called cold melting takes place when shock wave propagates through polycrystalline samples. Comparison of ab initio calculation results on sound speed along the Hugoniot with experimental data obtained on Z-machine also evidences for possible manifestation of the cold melting. The last may explain the discrepancy between atomistic simulations and experimental data on the onset of the melting on the Hugoniot.

  9. Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

    Science.gov (United States)

    Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.

    2007-01-01

    The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

  10. Computer simulation of molecular sorption in zeolites

    CERN Document Server

    Calmiano, M D

    2001-01-01

    The work presented in this thesis encompasses the computer simulation of molecular sorption. In Chapter 1 we outline the aims and objectives of this work. Chapter 2 follows in which an introduction to sorption in zeolites is presented, with discussion of structure and properties of the main zeolites studied. Chapter 2 concludes with a description of the principles and theories of adsorption. In Chapter 3 we describe the methodology behind the work carried out in this thesis. In Chapter 4 we present our first computational study, that of the sorption of krypton in silicalite. We describe work carried out to investigate low energy sorption sites of krypton in silicalite where we observe krypton to preferentially sorb into straight and sinusoidal channels over channel intersections. We simulate single step type I adsorption isotherms and use molecular dynamics to study the diffusion of krypton and obtain division coefficients and the activation energy. We compare our results to previous experimental and computat...

  11. Trapped ion simulation of molecular spectrum

    Science.gov (United States)

    Shen, Yangchao; Lu, Yao; Zhang, Kuan; Zhang, Shuaining; Huh, Joonsuk; Kim, Kihwan

    2016-05-01

    Boson sampling had been suggested as a classically intractable and quantum mechanically manageable problem via computational complexity theory arguments. Recently, Huh and co-workers proposed theoretically a modified version of boson sampling, which is designed to simulate a molecular problem, as a practical application. Here, we report the experimental implementation of the theoretical proposal with a trapped ion system. As a first demonstration, we perform the quantum simulation of molecular vibronic profile of SO2, which incorporates squeezing, rotation and coherent displacements operations, and the collective projection measurement on phonon modes. This work was supported by the National Basic Research Program of China 11CBA00300, 2011CBA00301, National Natural Science Foundation of China 11374178, 11574002. Basic Science Research Program of Korea NRF-2015R1A6A3A04059773.

  12. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations—Existence of infinite overlapping networks in a fragile ionic liquid

    Energy Technology Data Exchange (ETDEWEB)

    Habasaki, Junko, E-mail: habasaki.j.aa@m.titech.ac.jp [Department of Innovative and Engineered Materials, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8502 (Japan); Ngai, K. L. [CNR-IPCF Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa (Italy)

    2015-04-28

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO{sub 3}), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, T{sub B} (or T{sub c}) and the glass transition temperature T{sub g}, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, N{sub B}, within the first minimum of the pair correlation function, g(r){sub min}, increases. On crossing T{sub B} (>T{sub g}), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at T{sub g}. The glass transition temperature, T{sub g}, is characterized by the saturation of the total number of “bonds,” N{sub B} and the corresponding decrease in degree of freedom, F = [(3N − 6) − N{sub B}], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at T{sub g}, the number of bonds shows a remarkable change at around T{sub B}. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, f{sub g}, of each coordination polyhedron, which can be defined by f{sub g} = [(3N{sub V} − 6) − N{sub b}]. Here, 3N{sub v} is the degree of freedom of N{sub V} vertices of the polyhedron, and N{sub b} is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion

  13. Multiscale Simulations of Carbon Nanotubes and Liquids

    Science.gov (United States)

    Koumoutsakos, Petros

    2005-11-01

    We present molecular dynamics and hybrid continuum/atomistic simulations of carbon nanotubes in liquid environments with an emphasis on aqueous solutions. We emphasize computational issues such as interaction potentials and coupling techniques and their influence on the simulated physics. We present results from simulations of water flows inside and outside doped and pure carbon nanotubes and discuss their implications for experimental studies.

  14. Nanodrop contact angles from molecular dynamics simulations

    Science.gov (United States)

    Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim

    2016-11-01

    The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.

  15. Quantum Entanglement Molecular Absorption Spectrum Simulator

    Science.gov (United States)

    Nguyen, Quang-Viet; Kojima, Jun

    2006-01-01

    Quantum Entanglement Molecular Absorption Spectrum Simulator (QE-MASS) is a computer program for simulating two photon molecular-absorption spectroscopy using quantum-entangled photons. More specifically, QE-MASS simulates the molecular absorption of two quantum-entangled photons generated by the spontaneous parametric down-conversion (SPDC) of a fixed-frequency photon from a laser. The two-photon absorption process is modeled via a combination of rovibrational and electronic single-photon transitions, using a wave-function formalism. A two-photon absorption cross section as a function of the entanglement delay time between the two photons is computed, then subjected to a fast Fourier transform to produce an energy spectrum. The program then detects peaks in the Fourier spectrum and displays the energy levels of very short-lived intermediate quantum states (or virtual states) of the molecule. Such virtual states were only previously accessible using ultra-fast (femtosecond) laser systems. However, with the use of a single-frequency continuous wave laser to produce SPDC photons, and QEMASS program, these short-lived molecular states can now be studied using much simpler laser systems. QE-MASS can also show the dependence of the Fourier spectrum on the tuning range of the entanglement time of any externally introduced optical-path delay time. QE-MASS can be extended to any molecule for which an appropriate spectroscopic database is available. It is a means of performing an a priori parametric analysis of entangled photon spectroscopy for development and implementation of emerging quantum-spectroscopic sensing techniques. QE-MASS is currently implemented using the Mathcad software package.

  16. Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

    Science.gov (United States)

    Lee, Cheng-Kuang; Pao, Chun-Wei

    2016-08-17

    Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies.

  17. Molecular simulation of nitrogen adsorption in nanoporous silica.

    Science.gov (United States)

    Coasne, B; Galarneau, A; Di Renzo, F; Pellenq, R J M

    2010-07-06

    This article reports on a molecular simulation study of nitrogen adsorption and condensation at 77 K in atomistic silica cylindrical nanopores (MCM-41). Two models are considered for the nitrogen molecule and its interaction with the silica substrate. In the "pea" model, the nitrogen molecule is described as a single Lennard-Jones sphere and only Lennard-Jones interactions between the nitrogen molecule and the oxygens atoms of the silica substrate are taken into account. In the "bean" model (TraPPE force field), the nitrogen molecule is composed of two Lennard-Jones sites and a linear array of three charges on the atomic positions and at the center of the nitrogen-nitrogen bond. In the bean model, the interactions between the sites on the nitrogen molecule and the Si, O, and H atoms of the substrate are the sum of the Coulombic and dispersion interactions with a repulsive short-range contribution. The data obtained with the pea and bean models in silica nanopores conform to the typical behavior observed in the experiments for adsorption/condensation in cylindrical MCM-41 nanopores; the adsorbed amount increases continuously in the multilayer adsorption regime until an irreversible jump occurs because of capillary condensation and evaporation of the fluid within the pore. Our results suggest that the pea model can be used for characterization purposes where one is interested in capturing the global experimental behavior upon adsorption and desorption in silica nanopores. However, the bean model is more suitable to investigating the details of the interaction with the surface because this model, which accounts for the partial charges located on the nitrogen atoms of the molecule (quadrupole), allows a description of the specific interactions between this adsorbate and silica surfaces (silanol groups and siloxane bridges) or grafted silica surfaces. In particular, the bean model provides a more realistic picture of nitrogen adsorption in the vicinity of silica

  18. Structural characterization of interfacial n-octanol and 3-octanol using molecular dynamic simulations.

    Science.gov (United States)

    Napoleon, Raeanne L; Moore, Preston B

    2006-03-01

    Structurally isomeric octanol interfacial systems, water/vapor, 3-octanol/vapor, n-octanol/vapor, 3-octanol/water, and n-octanol/water are investigated at 298 K using molecular dynamics simulation techniques. The present study is intended to investigate strongly associated liquid/liquid interfaces and probe the atomistic structure of these interfaces. The octanol and water molecules were initially placed randomly into a box and were equilibrated using constant pressure techniques to minimize bias within the initial conditions as well as to fully sample the structural conformations of the interface. An interface formed via phase separation during equilibration and resulted in a slab geometry with a molecularly sharp interface. However, some water molecules remained within the octanol phase with a mole fraction of 0.12 after equilibration. The resulting "wet" octanol interfaces were analyzed using density profiles and orientational order parameters. Our results support the hypothesis of an ordered interface only 1 or 2 molecular layers deep before bulk properties are reached for both the 3-octanol and water systems. However, in contrast to most other interfacial systems studied by molecular dynamics simulations, the n-octanol interface extends for several molecular layers. The octanol hydroxyl groups form a hydrogen-bonding network with water which orders the surface molecules toward a preferred direction and produces a hydrophilic/hydrophobic layering. The ordered n-octanol produces an oscillating low-high density of oxygen atoms out of phase with a high-low density of carbon atoms, consistent with an oscillating dielectric. In contrast, the isomeric 3-octanol has only a single carbon-rich layer directly proximal to the interface, which is a result of the different molecular topology. Both 3-octanol and n-octanol roughen the water interface with respect to the water/vapor interface. The "wet" octanol phases, in the octanol/water systems reach bulk properties in a

  19. Molecular Dynamics Simulations of Shocks Including Electronic Heat Conduction and Electron-Phonon Coupling

    Science.gov (United States)

    Ivanov, Dmitriy S.; Zhigilei, Leonid V.; Bringa, Eduardo M.; De Koning, Maurice; Remington, Bruce A.; Caturla, Maria Jose; Pollaine, Stephen M.

    2004-07-01

    Shocks are often simulated using the classical molecular dynamics (MD) method in which the electrons are not included explicitly and the interatomic interaction is described by an effective potential. As a result, the fast electronic heat conduction in metals and the coupling between the lattice vibrations and the electronic degrees of freedom can not be represented. Under conditions of steep temperature gradients that can form near the shock front, however, the electronic heat conduction can play an important part in redistribution of the thermal energy in the shocked target. We present the first atomistic simulation of a shock propagation including the electronic heat conduction and electron-phonon coupling. The computational model is based on the two-temperature model (TTM) that describes the time evolution of the lattice and electron temperatures by two coupled non-linear differential equations. In the combined TTM-MD method, MD substitutes the TTM equation for the lattice temperature. Simulations are performed with both MD and TTM-MD models for an EAM Al target shocked at 300 kbar. The target includes a tilt grain boundary, which provides a region where shock heating is more pronounced and, therefore, the effect of the electronic heat conduction is expected to be more important. We find that the differences between the predictions of the MD and TTM-MD simulations are significantly smaller as compared to the hydrodynamics calculations performed at similar conditions with and without electronic heat conduction.

  20. Molecular Simulation of Nonequilibrium Hypersonic Flows

    Science.gov (United States)

    Schwartzentruber, T. E.; Valentini, P.; Tump, P.

    2011-08-01

    Large-scale conventional time-driven molecular dynam- ics (MD) simulations of normal shock waves are performed for monatomic argon and argon-helium mixtures. For pure argon, near perfect agreement between MD and direct simulation Monte Carlo (DSMC) results using the variable-hard-sphere model are found for density and temperature profiles as well as for velocity distribution functions throughout the shock. MD simulation results for argon are also in excellent agreement with experimental shock thickness data. Preliminary MD simulation results for argon-helium mixtures are in qualitative agreement with experimental density and temperature profile data, where separation between argon and helium density profiles due to disparate atomic mass is observed. Since conventional time-driven MD simulation of di- lute gases is computationally inefficient, a combined Event-Driven/Time-Driven MD algorithm is presented. The ED/TD-MD algorithm computes impending collisions and advances molecules directly to their next collision while evaluating the collision using conventional time-driven MD with an arbitrary interatomic potential. The method timestep thus approaches the mean-collision- time in the gas, while also detecting and simulating multi- body collisions with a small approximation. Extension of the method to diatomic and small polyatomic molecules is detailed, where center-of-mass velocities and extended cutoff radii are used to advance molecules to impending collisions. Only atomic positions are integrated during collisions and molecule sorting algorithms are employed to determine if atoms are bound in a molecule after a collision event. Rotational relaxation to equilibrium for a low density diatomic gas is validated by comparison with large-scale conventional time-driven MD simulation, where the final rotational distribution function is verified to be the correct Boltzmann rotational energy distribution.

  1. Molecular dynamics simulations of classical stopping power.

    Science.gov (United States)

    Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S

    2013-11-22

    Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results.

  2. Simulated Quantum Computation of Molecular Energies

    CERN Document Server

    Aspuru-Guzik, A; Love, P J; Head-Gordon, M; Aspuru-Guzik, Al\\'an; Dutoi, Anthony D.; Love, Peter J.; Head-Gordon, Martin

    2005-01-01

    The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical interest using modest numbers of quantum bits. Calculations of the water and lithium hydride molecular ground-state energies have been carried out on a quantum computer simulator using a recursive phase-estimation algorithm. The recursive algorithm reduces the number of quantum bits required for the readout register from about 20 to 4. Mappings of the molecular wave function to the quantum bits are described. An adiabatic method for the preparation of a good approximate ground-state wave function is described and demonstrated for a stretched hydrogen molecule. The number of quantum bits required scales linearly with the number of basis functions, and the number of gates required grows polynomially with the number of quantum bits.

  3. SPILADY: A parallel CPU and GPU code for spin-lattice magnetic molecular dynamics simulations

    Science.gov (United States)

    Ma, Pui-Wai; Dudarev, S. L.; Woo, C. H.

    2016-10-01

    Spin-lattice dynamics generalizes molecular dynamics to magnetic materials, where dynamic variables describing an evolving atomic system include not only coordinates and velocities of atoms but also directions and magnitudes of atomic magnetic moments (spins). Spin-lattice dynamics simulates the collective time evolution of spins and atoms, taking into account the effect of non-collinear magnetism on interatomic forces. Applications of the method include atomistic models for defects, dislocations and surfaces in magnetic materials, thermally activated diffusion of defects, magnetic phase transitions, and various magnetic and lattice relaxation phenomena. Spin-lattice dynamics retains all the capabilities of molecular dynamics, adding to them the treatment of non-collinear magnetic degrees of freedom. The spin-lattice dynamics time integration algorithm uses symplectic Suzuki-Trotter decomposition of atomic coordinate, velocity and spin evolution operators, and delivers highly accurate numerical solutions of dynamic evolution equations over extended intervals of time. The code is parallelized in coordinate and spin spaces, and is written in OpenMP C/C++ for CPU and in CUDA C/C++ for Nvidia GPU implementations. Temperatures of atoms and spins are controlled by Langevin thermostats. Conduction electrons are treated by coupling the discrete spin-lattice dynamics equations for atoms and spins to the heat transfer equation for the electrons. Worked examples include simulations of thermalization of ferromagnetic bcc iron, the dynamics of laser pulse demagnetization, and collision cascades.

  4. Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface.

    Science.gov (United States)

    Raffaini, Giuseppina; Ganazzoli, Fabio

    2004-04-13

    We report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison with our previous results for two albumin fragments.

  5. Molecular dynamics simulation of non-covalent single-walled carbon nanotube functionalization with surfactant peptides.

    Science.gov (United States)

    Barzegar, Abolfazl; Mansouri, Alireza; Azamat, Jafar

    2016-03-01

    Non-covalent functionalized single-walled carbon nanotubes (SWCNTs) with improved solubility and biocompatibility can successfully transfer drugs, DNA, RNA, and proteins into the target cells. Theoretical studies such as molecular docking and molecular dynamics simulations in fully atomistic scale were used to investigate the hydrophobic and aromatic π-π-stacking interaction of designing four novel surfactant peptides for non-covalent functionalization of SWCNTs. The results indicated that the designed peptides have binding affinity towards SWCNT with constant interactions during MD simulation times, and it can even be improved by increasing the number of tryptophan residues. The aromatic content of the peptides plays a significant role in their adsorption in SWCNT wall. The data suggest that π-π stacking interaction between the aromatic rings of tryptophan and π electrons of SWCNTs is more important than hydrophobic effects for dispersing carbon nanotubes; nevertheless SWCNTs are strongly hydrophobic in front of smooth surfaces. The usage of aromatic content of peptides for forming SWCNT/peptide complex was proved successfully, providing new insight into peptide design strategies for future nano-biomedical applications.

  6. Nano-tribology through molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    WANG; Hui(

    2001-01-01

    [1]Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.[2]Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.[3]Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.[4]Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.[5]Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.[6]Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.[7]Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.[8]Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.[9]Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.[10]Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.[11]Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.[12]Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.[13]Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.

  7. 大规模并行原子模拟在钛合金界面行为研究中的应用%Implementing Large-Scale Parallel Atomistic Simulations in the Investigation of Interfacial Behaviors in Titanium Alloys

    Institute of Scientific and Technical Information of China (English)

    王皞; 徐东生; 杨锐

    2013-01-01

    界面对钛合金的力学性能有至关重要的影响。界面行为的原子模拟涉及的原子数目庞大,必须借助大规模并行计算。本研究组开发了大规模并行分子动力学程序,并将其应用于钛合金中不同种类界面行为的模拟研究。本文以钛铝金属间化合物中的孪晶界和α钛中的特殊大角晶界为例,介绍研究组在钛合金晶界行为的计算模拟方面的近期研究成果。所模拟的体系尺寸达到微米级,所需 CPU 核数几十至几百不等。研究发现,钛铝模拟晶胞沿伪孪晶方向剪切变形时,等静压力下可产生 L11结构的伪孪晶形核长大,而等静张力下剪切可产生真孪晶的形核长大,提出钛铝中一种新的孪晶长大机制。在α钛中,特定取向的两个晶粒所形成的晶界与位错发生相互作用,裂纹形核依赖于加载外力的取向而发生在晶界处或硬取向晶粒内,从而可能导致疲劳断裂行为与加载取向相关。这些结果有助于理解钛合金的塑性变形行为,并为更高尺度的模拟研究提供了原子尺度细节。%The mechanical behavior of titanium alloys is often inlfuenced signiifcantly by interfaces. The atomistic investigation of interfaces corresponds with large numbers of atoms, hence requiring large-scale parallel simulations. A molecular dynamics code for such simulations is developed in our group, and used in the investigations of interfacial behaviors in titanium alloys. The present paper introduces our recent works on the simulations of interfacial behaviors in titanium alloys, with the coherent twin boundary in TiAl and a special large-angle grain boundary inα-titanium as two examples. The size of the simulated cells is around micrometers, using tens to hundreds of CPU cores. It is found that, in TiAl under shear along the pseudo-twin direction, pseudo-twin and true twin nucleates and grows under hydrostatic compression and tension respectively

  8. Molecular Dynamics Simulations of Interface Failure

    Science.gov (United States)

    Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.

    2007-03-01

    The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.

  9. [Oligoglycine surface structures: molecular dynamics simulation].

    Science.gov (United States)

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  10. Molecular Dynamics Simulations of Hypervelocity Impacts

    Science.gov (United States)

    Owens, Eli T.; Bachlechner, Martina E.

    2007-03-01

    Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.

  11. Molecular dynamics simulations of magnetized dusty plasmas

    Science.gov (United States)

    Piel, Alexander; Reichstein, Torben; Wilms, Jochen

    2012-10-01

    The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)

  12. Molecular Dynamics Simulations for Predicting Surface Wetting

    Directory of Open Access Journals (Sweden)

    Jing Chen

    2014-06-01

    Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.

  13. Nano-tribology through molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    王慧; 胡元中; 邹鲲; 冷永胜

    2001-01-01

    The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.

  14. 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.

  15. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands.

    Science.gov (United States)

    Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A; Bernardi, Anna; Colombo, Giorgio

    2016-04-01

    Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone's active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.

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

    Science.gov (United States)

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

    2016-07-01

    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 peptide conformations. These findings are consistent with experimental results, and give a molecular level interpretation for the reduced cytotoxicity of Vpr13-33 to some extent upon graphene exposure. Meanwhile, this study provides some significant insights into the detailed mechanism of graphene-induced protein conformation transition.

  17. Reactive molecular dynamics simulation and chemical kinetic modeling of pyrolysis and combustion of n-dodecane

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Quan-De [College of Chemistry, Sichuan University, Chengdu (China); Wang, Jing-Bo; Li, Juan-Qin; Tan, Ning-Xin; Li, Xiang-Yuan [College of Chemical Engineering, Sichuan University, Chengdu (China)

    2011-02-15

    The initiation mechanisms and kinetics of pyrolysis and combustion of n-dodecane are investigated by using the reactive molecular dynamics (ReaxFF MD) simulation and chemical kinetic modeling. From ReaxFF MD simulations, we find the initiation mechanisms of pyrolysis of n-dodecane are mainly through two pathways, (1) the cleavage of C-C bond to form smaller hydrocarbon radicals, and (2) the dehydrogenation reaction to form an H radical and the corresponding n-C{sub 12}H{sub 25} radical. Another pathway is the H-abstraction reactions by small radicals including H, CH{sub 3}, and C{sub 2}H{sub 5}, which are the products after the initiation reaction of n-dodecane pyrolysis. ReaxFF MD simulations lead to reasonable Arrhenius parameters compared with experimental results based on first-order kinetic analysis of n-dodecane pyrolysis. The density/pressure effects on the pyrolysis of n-dodecane are also analyzed. By appropriate mapping of the length and time from macroscopic kinetic modeling to ReaxFF MD, a simple comparison of the conversion of n-dodecane from ReaxFF MD simulations and that from kinetic modeling is performed. In addition, the oxidation of n-dodecane is studied by ReaxFF MD simulations. We find that formaldehyde molecule is an important intermediate in the oxidation of n-dodecane, which has been confirmed by kinetic modeling, and ReaxFF leads to reasonable reaction pathways for the oxidation of n-dodecane. These results indicate that ReaxFF MD simulations can give an atomistic description of the initiation mechanism and product distributions of pyrolysis and combustion for hydrocarbon fuels, and can be further used to provide molecular based robust kinetic reaction mechanism for chemical kinetic modeling of hydrocarbon fuels. (author)

  18. 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.

  19. Strengthening effects of various grain boundaries with nano-spacing as barriers of dislocation motion from molecular dynamics simulations

    Science.gov (United States)

    Yuan, FuPing

    2017-03-01

    Strengthening in metals is traditionally achieved through the controlled creation of various grain boundaries (GBs), such as low-angle GBs, high-angle GBs, and twin boundaries (TBs). In the present study, a series of large-scale molecular dynamics simulations with spherical nanoindentation and carefully designed model were conducted to investigate and compare the strengthening effects of various GBs with nano-spacing as barriers of dislocation motion. Simulation results showed that high-angle twist GBs and TBs are similar barriers and low-angle twist GBs are less effective in obstructing dislocation motion. Corresponding atomistic mechanisms were also given. At a certain indentation depth, dislocation transmission and dislocation nucleation from the other side of boundaries were observed for low-angle twist GBs, whereas dislocations were completely blocked by high-angle twist GBs and TBs at the same indentation depth. The current findings should provide insights for comprehensive understanding of the strengthening effects of various GBs at nanoscale.

  20. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    CERN Document Server

    Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver

    2015-01-01

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...

  1. 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.

  2. 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.

  3. Atomistic Properties of Solids

    CERN Document Server

    Sirdeshmukh, Dinker B; Subhadra, K G

    2011-01-01

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

  4. Molecular Modeling of Thermosetting Polymers: Effects of Degree of Curing and Chain Length on Thermo-Mechanical Properties

    Science.gov (United States)

    2012-08-01

    the mechanical properties of one particular thermosetting polymer, DGEBA /DETDA epoxy system using atomistic molecular dynamics simulations. A series...response of the DGEBA /DETDA epoxy system, the atomistic simulation part described below will only consider a DGEBA monomer as the resin...on the reaction of the DGEBA (diglycidyl ether of bisphenol A) monomers with curing agent EPI-Cure-W (diethylenetoluenediamine, DETDA) (Figure 2

  5. The injection of a screw dislocation into a crystal: Atomistics vs. continuum elastodynamics

    Science.gov (United States)

    Verschueren, J.; Gurrutxaga-Lerma, B.; Balint, D. S.; Dini, D.; Sutton, A. P.

    2017-01-01

    The injection (creation) process of a straight screw dislocation is compared atomistically with elastodynamic continuum theory. A method for injecting quiescent screw dislocations into a crystal of tungsten is simulated using non-equilibrium molecular dynamics. The resulting stress fields are compared to the those of elastodynamic solutions for the injection of a quiescent screw dislocation. A number of differences are found: a plane wave emission is observed to emanate from the whole surface of the cut used to create the dislocation, affecting the displacement field along the dislocation line (z), and introducing displacement field components perpendicular to the line (along x and y). It is argued that, in part, this emission is the result of the finite time required to inject the dislocation, whereby the atoms in the cut surface must temporarily be displaced to unstable positions in order to produce the required slip. By modelling this process in the continuum it is shown that the displacements components normal to the dislocation line arise from transient displacements of atoms in the cut surface parallel to x and y. It is shown that once these displacements are included in the elastodynamic continuum formulation the plane wave emission in uz is correctly captured. A detailed comparison between the atomistic and continuum models is then offered, showing that the main atomistic features can also be captured in the continuum.

  6. The dynamical complexity of work-hardening: a large-scale molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Markus J. Buehler; Alexander Hartmaier; Mark A. Duchaineau; Farid F. Abraham; Huajian Gao

    2005-01-01

    We analyze a large-scale molecular dynamics simulation of work hardening in a model system of a ductile solid.With tensile loading, we observe emission of thousands of dislocations from two sharp cracks. The dislocations interact in a complex way, revealing three fundamental mechanisms of work-hardening in this ductile material. These are (1) dislocation cutting processes, jog formation and generation of trails of point defects; (2) activation of secondary slip systems by Frank-Read and cross-slip mechanisms; and (3) formation of sessile dislocations such as Lomer-Cottrell locks.We report the discovery of a new class of point defects referred to as trail of partial point defects, which could play an important role in situations when partial dislocations dominate plasticity. Another important result of the present work is the rediscovery of the Fleischer-mechanism of cross-slip of partial dislocations that was theoretically proposed more than 50 years ago, and is now, for the first time, confirmed by atomistic simulation. On the typical time scale of molecular dynamics simulations, the dislocations self-organize into a complex sessile defect topology. Our analysis illustrates numerous mechanisms formerly only conjectured in textbooks and observed indirectly in experiments. It is the first time that such a rich set of fundamental phenomena have been revealed in a single computer simulation, and its dynamical evolution has been studied. The present study exemplifies the simulation and analysis of the complex nonlinear dynamics of a many-particle system during failure using ultra-large scale computing.

  7. Atomistic simulations of a solid/liquid interface: a combined force field and first principles approach to the structure and dynamics of acetonitrile near an anatase surface

    Energy Technology Data Exchange (ETDEWEB)

    Schiffmann, Florian; Hutter, Juerg; VandeVondele, Joost [Physical Chemistry Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich (Switzerland)

    2008-02-13

    The acetonitrile/anatase(101) interface can be considered a prototypical interface between an oxide and a polar aprotic liquid, and is common in dye sensitized solar cells. Using first principles molecular dynamics simulations of a slab of TiO{sub 2} in contact with neat acetonitrile (MeCN), the liquid structure near this interface has been characterized. Furthermore, in order to investigate properties that require extensive sampling, a classical force field to describe the MeCN/TiO{sub 2} interaction has been optimized, and we show that this force field accurately describes the structure near the interface. We find a surprisingly strong interaction of MeCN with TiO{sub 2}, which leads to an ordered first MeCN layer displaying a significantly enhanced molecular dipole. The strong dipolar interactions between solvent molecules lead to pronounced layering further away from the interface, each successive layer having an alternate orientation of the molecular dipoles. At least seven distinct solvent layers (approximately 12 A) can be discerned in the orientational distribution function. The observed structure also strongly suppresses diffusion parallel to the interface in the first nanometer of the liquid. These results show that the properties of the liquid near the interface differ from those in the bulk, which suggests that solvation near the interface will be distinctly different from solvation in the bulk.

  8. Quantum molecular dynamics simulations of dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  9. 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.

  10. Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations.

    Science.gov (United States)

    Dobrev, Plamen; Donnini, Serena; Groenhof, Gerrit; Grubmüller, Helmut

    2017-01-10

    Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a "water" molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing "water" molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH.

  11. Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics

    Energy Technology Data Exchange (ETDEWEB)

    Amani, Ehsan, E-mail: eamani@aut.ac.ir; Movahed, Saeid, E-mail: smovahed@aut.ac.ir

    2016-06-07

    In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. - Highlights: • A hybrid continuum-atomistic model is proposed for electrokinetics in nanochannels. • The model is validated by molecular dynamics. • This is a promising approach to model more complicated geometries and physics.

  12. Molecular simulations of lipid systems: Edge stability and structure in pure and mixed bilayers

    Science.gov (United States)

    Jiang, Yong

    2007-12-01

    Understanding the structural, mechanical and dynamical properties of lipid self-assembled systems is fundamental to understand the behavior of the cell membrane. This thesis has investigated the equilibrium properties of lipid systems with edge defects through various molecular simulation techniques. The overall goal of this study is to understand the free energy terms of the edges and to develop efficient methods to sample equilibrium distributions of mixed-lipid systems. In the first main part of my thesis, an atomistic molecular model is used to study lipid ribbon which has two edges on both sides. Details of the edge structures, such as area per lipid and tail torsional statistics are presented. Line tension, calculated from pressure tensor in MD simulation has good agreement with result from other sources. To further investigate edge properties on a longer timescale and larger length scale, we have applied a coarse-grained forcefield on mixed lipid systems and try to interpret the edge fluctuations in terms of free energy parameters such as line tension and bending modulus. We have identified two regimes with quite different edge behavior: a high line tension regime and a low line tension regime. The last part of this thesis focuses on a hybrid Molecular dynamics and Configurational-bias Monte Carlo (MCMD) simulation method in which molecules can change their type by growing and shrinking the terminal acyl united carbon atoms. A two-step extension of the MCMD method has been developed to allow for a larger difference in the components' tail lengths. Results agreed well with previous one-step mutation results for a mixture with a length difference of four carbons. The current method can efficiently sample mixtures with a length difference of eight carbons, with a small portion of lipids of intermediate tail length. Preliminary results are obtained for "bicelle"-type (DMPC/DHPC) ribbons.

  13. 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).

  14. Scalable Quantum Simulation of Molecular Energies

    CERN Document Server

    O'Malley, P J J; Kivlichan, I D; Romero, J; McClean, J R; Barends, R; Kelly, J; Roushan, P; Tranter, A; Ding, N; Campbell, B; Chen, Y; Chen, Z; Chiaro, B; Dunsworth, A; Fowler, A G; Jeffrey, E; Megrant, A; Mutus, J Y; Neill, C; Quintana, C; Sank, D; Vainsencher, A; Wenner, J; White, T C; Coveney, P V; Love, P J; Neven, H; Aspuru-Guzik, A; Martinis, J M

    2015-01-01

    We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. We use a programmable array of superconducting qubits to compute the energy surface of molecular hydrogen using two distinct quantum algorithms. First, we experimentally execute the unitary coupled cluster method using the variational quantum eigensolver. Our efficient implementation predicts the correct dissociation energy to within chemical accuracy of the numerically exact result. Next, we experimentally demonstrate the canonical quantum algorithm for chemistry, which consists of Trotterization and quantum phase estimation. We compare the experimental performance of these approaches to show clear evidence that the variational quantum eigensolver is robust to certain errors, inspiring hope that quantum simulation of classically intractable molecules may be viable in the near future.

  15. Going Backward : A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

    NARCIS (Netherlands)

    Wassenaar, Tsjerk A.; Pluhackova, Kristyna; Böckmann, Rainer A.; Marrink, Siewert J.; Tieleman, D. Peter

    2014-01-01

    The conversion of coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations. For this process, called backmapping or reverse transformation, several tools are available, but these commonly require libraries of molecul

  16. Insights into the structural stability of Bax from molecular dynamics simulations at high temperatures

    Science.gov (United States)

    Rosas-Trigueros, Jorge Luis; Correa-Basurto, José; Guadalupe Benítez-Cardoza, Claudia; Zamorano-Carrillo, Absalom

    2011-01-01

    Bax is a member of the Bcl-2 protein family that participates in mitochondrion-mediated apoptosis. In the early stages of the apoptotic pathway, this protein migrates from the cytosol to the outer mitochondrial membrane, where it is inserted and usually oligomerizes, making cytochrome c-compatible pores. Although several cellular and structural studies have been reported, a description of the stability of Bax at the molecular level remains elusive. This article reports molecular dynamics simulations of monomeric Bax at 300, 400, and 500 K, focusing on the most relevant structural changes and relating them to biological experimental results. Bax gradually loses its α-helices when it is submitted to high temperatures, yet it maintains its globular conformation. The resistance of Bax to adopt an extended conformation could be due to several interactions that were found to be responsible for maintaining the structural stability of this protein. Among these interactions, we found salt bridges, hydrophobic interactions, and hydrogen bonds. Remarkably, salt bridges were the most relevant to prevent the elongation of the structure. In addition, the analysis of our results suggests which conformational movements are implicated in the activation/oligomerization of Bax. This atomistic description might have important implications for understanding the functionality and stability of Bax in vitro as well as within the cellular environment. PMID:21936009

  17. Coarse-grained protein molecular dynamics simulations

    Science.gov (United States)

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-01

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  18. Detailed atomistic simulation of the nano-sorption and nano-diffusivity of water, tyrosol, vanillic acid, and p-coumaric acid in single wall carbon nanotubes.

    Science.gov (United States)

    Anastassiou, Alexandros; Karahaliou, Elena K; Alexiadis, Orestis; Mavrantzas, Vlasis G

    2013-10-28

    We report results from a detailed computer simulation study for the nano-sorption and mobility of four different small molecules (water, tyrosol, vanillic acid, and p-coumaric acid) inside smooth single-wall carbon nanotubes (SWCNTs). Most of the results have been obtained with the molecular dynamics (MD) method, but especially for the most narrow of the CNTs considered, the results for one of the molecules addressed here (water) were further confirmed through an additional Grand Canonical (μVT) Monte Carlo (GCMC) simulation using a value for the water chemical potential μ pre-computed with the particle deletion method. Issues addressed include molecular packing and ordering inside the nanotube for the four molecules, average number of sorbed molecules per unit length of the tube, and mean residence time and effective axial diffusivities, all as a function of tube diameter and tube length. In all cases, a strong dependence of the results on tube diameter was observed, especially in the way the different molecules are packed and organized inside the CNT. For water for which predictions of properties such as local structure and packing were computed with both methods (MD and GCMC), the two sets of results were found to be fully self-consistent for all types of SWCNTs considered. Water diffusivity inside the CNT (although, strongly dependent on the CNT diameter) was computed with two different methods, both of which gave identical results. For large enough CNT diameters (larger than about 13 Å), this was found to be higher than the corresponding experimental value in the bulk by about 55%. Surprisingly enough, for the rest of the molecules simulated (phenolic), the simulations revealed no signs of mobility inside nanotubes with a diameter smaller than the (20, 20) tube. This is attributed to strong phenyl-phenyl attractive interactions, also to favorable interactions of these molecules with the CNT walls, which cause them to form highly ordered, very stable

  19. Detailed atomistic simulation of the nano-sorption and nano-diffusivity of water, tyrosol, vanillic acid, and p-coumaric acid in single wall carbon nanotubes

    Science.gov (United States)

    Anastassiou, Alexandros; Karahaliou, Elena K.; Alexiadis, Orestis; Mavrantzas, Vlasis G.

    2013-10-01

    We report results from a detailed computer simulation study for the nano-sorption and mobility of four different small molecules (water, tyrosol, vanillic acid, and p-coumaric acid) inside smooth single-wall carbon nanotubes (SWCNTs). Most of the results have been obtained with the molecular dynamics (MD) method, but especially for the most narrow of the CNTs considered, the results for one of the molecules addressed here (water) were further confirmed through an additional Grand Canonical (μVT) Monte Carlo (GCMC) simulation using a value for the water chemical potential μ pre-computed with the particle deletion method. Issues addressed include molecular packing and ordering inside the nanotube for the four molecules, average number of sorbed molecules per unit length of the tube, and mean residence time and effective axial diffusivities, all as a function of tube diameter and tube length. In all cases, a strong dependence of the results on tube diameter was observed, especially in the way the different molecules are packed and organized inside the CNT. For water for which predictions of properties such as local structure and packing were computed with both methods (MD and GCMC), the two sets of results were found to be fully self-consistent for all types of SWCNTs considered. Water diffusivity inside the CNT (although, strongly dependent on the CNT diameter) was computed with two different methods, both of which gave identical results. For large enough CNT diameters (larger than about 13 Å), this was found to be higher than the corresponding experimental value in the bulk by about 55%. Surprisingly enough, for the rest of the molecules simulated (phenolic), the simulations revealed no signs of mobility inside nanotubes with a diameter smaller than the (20, 20) tube. This is attributed to strong phenyl-phenyl attractive interactions, also to favorable interactions of these molecules with the CNT walls, which cause them to form highly ordered, very stable

  20. Molecular Dynamics Simulations and XAFS (MD-XAFS)

    Energy Technology Data Exchange (ETDEWEB)

    Schenter, Gregory K.; Fulton, John L.

    2017-01-20

    MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.

  1. Journal of Molecular Structure: THEOCHEM

    OpenAIRE

    Mundim, K.C.; Malbouisson, L.A.C.; Dorfman, S.; Fuks, D.; Van Humbeeck, J.; Liubich, V.

    2001-01-01

    Texto completo: acesso restrito. p. 191–197 The results of atomistic simulations of migration and formation energies of mono- and di-vacancies in bulk tungsten are presented in our paper. The interatomic potential for tungsten was extracted with the recursive procedure from ab initio calculations of the cohesive energy. A stochastic molecular dynamics using a generalized simulated annealing procedure was employed in the simulations. Calculated values of mono- and di-vacancies energy parame...

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

    Science.gov (United States)

    Wang, D.; Gao, N.; Wang, Z. G.; Gao, X.; He, W. H.; Cui, M. H.; Pang, L. L.; Zhu, Y. B.

    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 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 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.

  3. 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.

  4. MOLOCH computer code for molecular-dynamics simulation of processes in condensed matter

    Directory of Open Access Journals (Sweden)

    Derbenev I.V.

    2011-01-01

    Full Text Available Theoretical and experimental investigation into properties of condensed matter is one of the mainstreams in RFNC-VNIITF scientific activity. The method of molecular dynamics (MD is an innovative method of theoretical materials science. Modern supercomputers allow the direct simulation of collective effects in multibillion atom sample, making it possible to model physical processes on the atomistic level, including material response to dynamic load, radiation damage, influence of defects and alloying additions upon material mechanical properties, or aging of actinides. During past ten years, the computer code MOLOCH has been developed at RFNC-VNIITF. It is a parallel code suitable for massive parallel computing. Modern programming techniques were used to make the code almost 100% efficient. Practically all instruments required for modelling were implemented in the code: a potential builder for different materials, simulation of physical processes in arbitrary 3D geometry, and calculated data processing. A set of tests was developed to analyse algorithms efficiency. It can be used to compare codes with different MD implementation between each other.

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

    Science.gov (United States)

    Fokin, Vladimir B.; Povarnitsyn, Mikhail E.; Levashov, Pavel R.

    2017-02-01

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

  6. Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation.

    Science.gov (United States)

    Huang, Nan-Lan; Lin, Jung-Hsin

    2015-08-18

    Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.

  7. Theinfluence of a hierarchical porous carbon network on the coherent dynamics of a nanoconfined room temperature ionic liquid: A neutron spin echo and atomistic simulation investigation

    Energy Technology Data Exchange (ETDEWEB)

    Banuelos, Jose Leo [ORNL; Feng, Guang [ORNL; Fulvio, Pasquale F [ORNL; Li, Song [Vanderbilt University, Nashville; Rother, Gernot [ORNL; Arend, Nikolas [ORNL; Faraone, Antonio [National Institute of Standards and Technology (NIST); Dai, Sheng [ORNL; Cummings, Peter T [ORNL; Wesolowski, David J [ORNL

    2014-01-01

    The molecular-scale dynamic properties of the room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, or [C4mim+ ][Tf2N ], confined in hierarchical microporous mesoporous carbon, were investigated using neutron spin echo (NSE) and molecular dynamics (MD) simulations. Both NSE and MD reveal pronounced slowing of the overall collective dynamics, including the presence of an immobilized fraction of RTIL at the pore wall, on the time scales of these approaches. A fraction of the dynamics, corresponding to RTIL inside 0.75 nm micropores located along the mesopore surfaces, are faster than those of RTIL in direct contact with the walls of 5.8 nm and 7.8 nm cylindrical mesopores. This behavior is ascribed to the near-surface confined-ion density fluctuations resulting from the ion ion and ion wall interactions between the micropores and mesopores as well as their confinement geometries. Strong micropore RTIL interactions result in less-coordinated RTIL within the micropores than in the bulk fluid. Increasing temperature from 296 K to 353 K reduces the immobilized RTIL fraction and results in nearly an order of magnitude increase in the RTIL dynamics. The observed interfacial phenomena underscore the importance of tailoring the surface properties of porous carbons to achieve desirable electrolyte dynamic behavior, since this impacts the performance in applications such as electrical energy storage devices.

  8. Molecular Dynamics Simulations of Polyelectrolyte Solutions

    Science.gov (United States)

    Dobrynin, Andrey

    2014-03-01

    Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) β . The exponent β = -1/2 for chain persistence length lp , β = 1/4 for solution correlation length, β = -1/5 and β = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings

  9. Multiresolution molecular mechanics: Implementation and efficiency

    Science.gov (United States)

    Biyikli, Emre; To, Albert C.

    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.

  10. Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

    CERN Document Server

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

    2015-01-01

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using t...

  11. Molecular insight into amyloid oligomer destabilizing mechanism of flavonoid derivative 2-(4' benzyloxyphenyl)-3-hydroxy-chromen-4-one through docking and molecular dynamics simulations.

    Science.gov (United States)

    Kumar, Akhil; Srivastava, Swati; Tripathi, Shubhandra; Singh, Sandeep Kumar; Srikrishna, Saripella; Sharma, Ashok

    2016-06-01

    Aggregation of amyloid peptide (Aβ) has been shown to be directly related to progression of Alzheimer's disease (AD). Aβ is neurotoxic and its deposition and aggregation ultimately lead to cell death. In our previous work, we reported flavonoid derivative (compound 1) showing promising result in transgenic AD model of Drosophila. Compound 1 showed prevention of Aβ-induced neurotoxicity and neuroprotective efficacy in Drosophila system. However, mechanism of action of compound 1 and its effect on the amyloid is not known. We therefore performed molecular docking and atomistic, explicit-solvent molecular dynamics simulations to investigate the process of Aβ interaction, inhibition, and destabilizing mechanism. Results showed different preferred binding sites of compound 1 and good affinity toward the target. Through the course of 35 ns molecular dynamics simulation, conformations_5 of compound 1 intercalates into the hydrophobic core near the salt bridge and showed major structural changes as compared to other conformations. Compound 1 showed interference with the salt bridge and thus reducing the inter strand hydrogen bound network. This minimizes the side chain interaction between the chains A-B leading to disorder in oligomer. Contact map analysis of amino acid residues between chains A and B also showed lesser interaction with adjacent amino acids in the presence of compound 1 (conformations_5). The study provides an insight into how compound 1 interferes and disorders the Aβ peptide. These findings will further help to design better inhibitors for aggregation of the amyloid oligomer.

  12. Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Bond, Stephen D.

    2014-01-01

    The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods whos cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

  13. pysimm: A python package for simulation of molecular systems

    Science.gov (United States)

    Fortunato, Michael E.; Colina, Coray M.

    In this work, we present pysimm, a python package designed to facilitate structure generation, simulation, and modification of molecular systems. pysimm provides a collection of simulation tools and smooth integration with highly optimized third party software. Abstraction layers enable a standardized methodology to assign various force field models to molecular systems and perform simple simulations. These features have allowed pysimm to aid the rapid development of new applications specifically in the area of amorphous polymer simulations.

  14. Inactivation of TEM-1 by avibactam (NXL-104): insights from quantum mechanics/molecular mechanics metadynamics simulations.

    Science.gov (United States)

    Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco; Colombo, Giorgio

    2014-08-12

    The fast and constant development of drug-resistant bacteria represents a serious medical emergence. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this context, avibactam represents a promising, innovative inhibitor of beta-lactamases with a novel molecular structure compared to previously developed inhibitors, showing a promising inhibitory activity toward a significant number of beta-lactamase enzymes. In this work, we studied, at the atomistic level, the mechanisms of formation of the covalent complex between avibactam and TEM-1, an experimentally well-characterized class A beta-lactamase, using classical and quantum mechanics/molecular mechanics (QM/MM) simulations combined with metadynamics. Our simulations provide a detailed structural and energetic picture of the molecular steps leading to the formation of the avibactam/TEM-1 covalent adduct. In particular, they support a mechanism in which the rate-determining step is the water-assisted Glu166 deprotonation by Ser70. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements. Additionally, our simulations highlight the important role of Lys73 in assisting the Ser70 and Ser130 deprotonations. While based on the specific case of the avibactam/TEM-1, the simple protocol we present here can be immediately extended and applied to the study of covalent complex formation in different enzyme-inhibitor pairs.

  15. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  16. Simulating chemical systems : MPI and GPU parallelization of novel SD algorithms

    NARCIS (Netherlands)

    Goga, N.

    2013-01-01

    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 th

  17. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    Science.gov (United States)

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; Stocks, G. Malcolm; Landau, David P.

    2017-01-01

    Using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. By calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. Comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnons leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.

  18. Molecular dynamics simulations of vibrated granular gases.

    Science.gov (United States)

    Barrat, Alain; Trizac, Emmanuel

    2002-11-01

    We present molecular dynamics simulations of monodisperse or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met experimentally, density and temperature fields display heterogeneous profiles in the direction perpendicular to the walls. A general equation of state for an arbitrary mixture of fluidized inelastic hard spheres is derived and successfully tested against numerical data. Single-particle velocity distribution functions with non-Gaussian features are also obtained, and the influence of various parameters (inelasticity coefficients, density, etc.) are analyzed. The validity of a recently proposed random restitution coefficient model is assessed through the study of projected collisions onto the direction perpendicular to that of energy injection. For the binary mixture, the nonequipartition of translational kinetic energy is studied and compared both to experimental data and to the case of homogeneous energy injection ("stochastic thermostat"). The rescaled velocity distribution functions are found to be very similar for both species.

  19. MOLECULAR DYNAMIC SIMULATION OF PEPTIDE POLYELECTROLYTES

    Directory of Open Access Journals (Sweden)

    I. M. Neelov

    2014-07-01

    Full Text Available The paper deals with investigation of the conformational properties of some charged homopolypeptides in dilute aqueous solutions by computer simulation. A method of molecular dynamics for the full-atomic models of polyaspartic acid and polylysine with explicit account of water and counter-ions is used for this purpose. For systems containing these polypeptides we calculated time trajectories and the size, shape, distribution functions and time correlation functions of inertia radius and the distances between the ends of peptide chains. We have also calculated the solvatation characteristics of considered polyelectrolytes. We have found out that polyaspartic acid in dilute aqueous solution has more compact structure and more spherical shape than polylysine. We have shown that these differences are due to different interaction between the polypeptides and water molecules (in particular, the quality and quantity of hydrogen bonds formed by these peptides with water, and the difference in an amount of ion pairs formed by the charged groups of the peptides and counter-ions. The obtained results should be taken into account for elaboration of new products based on the investigated peptides and their usage in various industrial and biomedical applications.

  20. New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

    Science.gov (United States)

    Saether, E.; Yamakov, V.; Glaessgen, E.

    2008-01-01

    A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

  1. Diffusion in Liquids: Equilibrium Molecular Simulations and Predictive Engineering Models

    NARCIS (Netherlands)

    Liu, X.

    2013-01-01

    The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations.

  2. Thermodynamic integration based on classical atomistic simulations to determine the Gibbs energy of condensed phases: Calculation of the aluminum-zirconium system

    Science.gov (United States)

    Harvey, J.-P.; Gheribi, A. E.; Chartrand, P.

    2012-12-01

    In this work, an in silico procedure to generate a fully coherent set of thermodynamic properties obtained from classical molecular dynamics (MD) and Monte Carlo (MC) simulations is proposed. The procedure is applied to the Al-Zr system because of its importance in the development of high strength Al-Li alloys and of bulk metallic glasses. Cohesive energies of the studied condensed phases of the Al-Zr system (the liquid phase, the fcc solid solution, and various orthorhombic stoichiometric compounds) are calculated using the modified embedded atom model (MEAM) in the second-nearest-neighbor formalism (2NN). The Al-Zr MEAM-2NN potential is parameterized in this work using ab initio and experimental data found in the literature for the AlZr3-L12 structure, while its predictive ability is confirmed for several other solid structures and for the liquid phase. The thermodynamic integration (TI) method is implemented in a general MC algorithm in order to evaluate the absolute Gibbs energy of the liquid and the fcc solutions. The entropy of mixing calculated from the TI method, combined to the enthalpy of mixing and the heat capacity data generated from MD/MC simulations performed in the isobaric-isothermal/canonical (NPT/NVT) ensembles are used to parameterize the Gibbs energy function of all the condensed phases in the Al-rich side of the Al-Zr system in a CALculation of PHAse Diagrams (CALPHAD) approach. The modified quasichemical model in the pair approximation (MQMPA) and the cluster variation method (CVM) in the tetrahedron approximation are used to define the Gibbs energy of the liquid and the fcc solid solution respectively for their entire range of composition. Thermodynamic and structural data generated from our MD/MC simulations are used as input data to parameterize these thermodynamic models. A detailed analysis of the validity and transferability of the Al-Zr MEAM-2NN potential is presented throughout our work by comparing the predicted properties obtained

  3. 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.

  4. Atomistic Determination of Cross-Slip Pathway and Energetics

    DEFF Research Database (Denmark)

    Rasmussen, Torben; Jacobsen, Karsten Wedel; Leffers, Torben;

    1997-01-01

    The mechanism for cross slip of a screw dislocation in Cu is determined by atomistic simulations that only presume the initial and final states of the process. The dissociated dislocation constricts in the primary plane and redissociates into the cross-slip plane while still partly in the primary...

  5. Atomistic modeling of dropwise condensation

    Science.gov (United States)

    Sikarwar, B. S.; Singh, P. L.; Muralidhar, K.; Khandekar, S.

    2016-05-01

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

  6. 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.

  7. Solubility of cellulose in supercritical water studied by molecular dynamics simulations.

    Science.gov (United States)

    Tolonen, Lasse K; Bergenstråhle-Wohlert, Malin; Sixta, Herbert; Wohlert, Jakob

    2015-04-02

    The insolubility of cellulose in ambient water and most aqueous systems presents a major scientific and practical challenge. Intriguingly though, the dissolution of cellulose has been reported to occur in supercritical water. In this study, cellulose solubility in ambient and supercritical water of varying density (0.2, 0.7, and 1.0 g cm(-3)) was studied by atomistic molecular dynamics simulations using the CHARMM36 force field and TIP3P water. The Gibbs energy of dissolution was determined between a nanocrystal (4 × 4 × 20 anhydroglucose residues) and a fully dissociated state using the two-phase thermodynamics model. The analysis of Gibbs energy suggested that cellulose is soluble in supercritical water at each of the studied densities and that cellulose dissolution is typically driven by the entropy gain upon the chain dissociation while simultaneously hindered by the loss of solvent entropy. Chain dissociation caused density augmentation around the cellulose chains, which improved water-water bonding in low density supercritical water whereas the opposite occurred in ambient and high density supercritical water.

  8. Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary

    The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.

  9. 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.

  10. Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations.

    Science.gov (United States)

    Miettinen, Markus S; Knecht, Volker; Monticelli, Luca; Ignatova, Zoya

    2012-08-30

    Polyglutamine (polyQ) diseases comprise a group of dominantly inherited pathology caused by an expansion of an unstable polyQ stretch which is presumed to form β-sheets. Similar to other amyloid pathologies, polyQ amyloidogenesis occurs via a nucleated polymerization mechanism, and proceeds through energetically unfavorable nucleus whose existence and structure are difficult to detect. Here, we use atomistic molecular dynamics simulations in explicit solvent to assess the conformation of the polyQ stretch in the nucleus that initiates polyQ fibrillization. Comparison of the kinetic stability of various structures of polyQ peptide with a Q-length in the pathological range (Q40) revealed that steric zipper or nanotube-like structures (β-nanotube or β-pseudohelix) are not kinetically stable enough to serve as a template to initiate polyQ fibrillization as opposed to β-hairpin-based (β-sheet and β-sheetstack) or α-helical conformations. The selection of different structures of the polyQ stretch in the aggregation-initiating event may provide an alternative explanation for polyQ aggregate polymorphism.

  11. Diffusion in Liquids: Equilibrium Molecular Simulations and Predictive Engineering Models

    OpenAIRE

    Liu, X.

    2013-01-01

    The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations. From a practical point of view, systems consisting more than two components are more interesting. However, experimental and simulation data on transport diffusion for such systems are scarce. There...

  12. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    Science.gov (United States)

    2014-03-28

    Approved for Public Release; Distribution Unlimited Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic...non peer-reviewed journals: Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration" Report Title In... nanoscience of multifunctional materials: atomistic exploration” PI:Inna Ponomareva We have accomplished the following. 1. We have developed a set of

  13. 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

  14. 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.

  15. Liquid crystals and their interactions with colloidal particles and phospholipid membranes: Molecular simulation studies

    Science.gov (United States)

    Kim, Evelina B.

    Experimentally, liquid crystals (LC) can be used as the basis for optical biomolecular sensors that rely on LC ordering. Recently, the use of LC as a reporting medium has been extended to investigations of molecular scale processes at lipid laden aqueous-LC interfaces and at biological cell membranes. In this thesis, we present two related studies where liquid crystals are modelled at different length scales. We examine (a) the behavior of nanoscopic colloidal particles in LC systems, using Monte Carlo (MC) molecular simulations and a mesoscopic dynamic field theory (DyFT); and (b) specific interactions of two types of mesogens with a model phospholipid bilayer, using atomistic molecular dynamics (MD) at the A-nm scale. In (a), we consider colloidal particles suspended in a LC, confined between two walls. We calculate the colloid-substrate and colloid-colloid potentials of mean force (PMF). For the MC simulations, we developed a new technique (ExEDOS or Expanded Ensemble Density Of States) that ensures good sampling of phase space without prior knowledge of the energy landscape of the system. Both results, simulation and DyFT, indicate a repulsive force acting between a colloid and a wall. In contrast, both techniques indicate an overall colloid-colloid attraction and predict a new topology of the disclination lines that arises when the particles approach each other. In (b), we find that mesogens (pentylcyanobiphenyl [5CB] or difluorophenyl-pentylbicyclohexyl [5CF]) preferentially partition from the aqueous phase into a dipalmitoylphosphatidylcholine (DPPC) bilayer. We find highly favorable free energy differences for partitioning (-18kBT for 5CB, -26k BT for 5CF). We also simulated fully hydrated bilayers with embedded 5CB or 5CF at concentrations used in recent experiments (6 mol% and 20 mol%). The presence of mesogens in the bilayer enhances the order of lipid acyl tails and changes the spatial and orientational arrangement of lipid headgroup atoms. A stronger

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

    Directory of Open Access Journals (Sweden)

    Ramon Reigada

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

  17. Computer Simulation and X-ray Diffraction of Nanocrystals

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    X-ray diffraction of structure in nanocrystalline α-Fe and Cu was studied by atomistic simulation. Atomic position equilibrium was reached by using molecular dynamics method to simulate nanocrystalline structure with Finnis potentials to model interatomic interactions. lt was found that the boundary component exhibits short-range order, and the distortion in crystalline component increases with the decrease of grain size.

  18. 预应力对多晶铁冲击行为影响的微观模拟研究∗%Influence of prestress on sho ck b ehavior of p olycrystalline iron via atomistic simulations

    Institute of Scientific and Technical Information of China (English)

    任国武; 张世文; 范诚; 陈永涛

    2016-01-01

    冲击加载铁动力学响应是当前冲击波领域金属材料塑性和相变行为研究最为关注的焦点之一。本文采用分子动力学模拟方法开展预应力作用下冲击加载多晶铁的动力学行为研究。模拟结果表明,随着预应力的增加,导致弹塑转变应力(Hugoniot弹性极限)和冲击波速度提高,符合已有的理论分析结果。微观晶体结构表征则发现较大的预应力导致剪应力大于屈服应力,塑性弛豫时间缩短,加快多晶铁α→ε相转变。进一步通过与平面及柱壳纯铁冲击加载获得的自由面速度剖面对比分析,证实了模拟结果。%Plasticity behavior and phase transition of metal Fe subjected to shock loading have attracted considerable attention in shock physics community, in particular for underlying relationship between them. Experimental examinations and atomistic simulations on shocked Fe have displayed a three-wave structure: elastic wave, plastic wave and transformation wave. However, these studies are primarily limited to the one-dimensional planar case. Recently, owing to the rapid development of experimental techniques, investigating dynamic property of shocked metal has extended to the multi-dimensional loading conditions, such as cylindrical or spherical shocks. In this regard, fruitful findings are achieved, for example, twinning ratio in polycrystalline Fe under implosive compression is found to be much higher than that under planar shock, implying that the the complex stress state plays a critical role. In this paper, we explore the effects of prestress on plasticity and phase transition of shocked polycrystalline iron. The imposed presstress normal to the impact direction in one-dimensional planar shocking represents the varying deviatoric stress, and does not nearly affect the principal stress. The utilized empirical potential for iron could describe the plasticity dislocation and phase transition very well. The simulations

  19. Atomistic simulation of point defects in face centered cubic metals using MAEAM potential%面心立方金属中点缺陷的MAEAM模拟

    Institute of Scientific and Technical Information of China (English)

    宋祥磊; 张晓军; 张建民; 徐可为

    2005-01-01

    From the system energy minimization, the stable configuration and the rule of migration of mono-vacancy, di-vacancy and a single self-interstitial atom are analyzed using the modified analytical embedded atom method (MAEAM) combined with the molecular dynamics simulation in Al, Ni, Cu,Ag, Au and Pb. The results show that only the first-nearest neighbor di-vacancy is the stable configuration of di-vacancy. Compared with the mono-vacancy, the first-nearest neighbor di-vacancy is Ni, Cu, Ag and Au, but the body-centered configuration is favorable in Al and Pb. However compared with mono-vacancy, the single self-interstitial atom is also difficult to form.%将改进分析型嵌入原子法(MAEAM)模型与分子动力学模拟方法相结合,用能量最小化原理分析了面心立方金属Al、Ni、Cu、Ag、Au和Pb中的单空位、双空位及单自间隙原子3种点缺陷的稳定构型及其迁移规律.结果表明:最近邻双空位是双空位中惟一能够存在的构型,而且比单空位还容易迁移;尽管在4种构型的自间隙原子中,〈110〉哑铃状自间隙构型容易在Ni、Cu、Ag和Au中形成,体心自间隙构型也容易在Al和Pb中形成,但和单空位相比较还是较难形成的.

  20. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

    Science.gov (United States)

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

    2015-12-15

    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

  1. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    Science.gov (United States)

    Qian Xie; Tinker, Robert

    2006-01-01

    One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…

  2. 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.

  3. Molecular simulation of alkyl monolayers on the Si(111)surface

    Institute of Scientific and Technical Information of China (English)

    YUAN; Shiling; (苑世领); CAI; Zhengting; (蔡政亭); XIAO; Li; (肖莉); XU; Guiying; (徐桂英); LIU; Yongjun; (刘永军)

    2003-01-01

    The structure of twelve-carbon monolayers on the H-terminated Si(111) surface is investigated by molecular simulation method. The best substitution percent on Si(111) surface obtained via molecular mechanics calculation is equal to 50%, and the (8×8) simulated cell can be used to depict the structure of alkyl monolayer on Si surface. After two-dimensional cell containing alkyl chains and four-layer Si(111) crystal at the substitution 50% is constructed, the densely packed and well-ordered monolayer on Si(111) surface can be shown through energy minimization in the suitable-size simulation cell. These simulation results are in good agreement with the experiments. These conclusions show that molecular simulation can provide otherwise inaccessible mesoscopic information at the molecular level, and can be considered as an adjunct to experiments.

  4. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  5. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Science.gov (United States)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver

    2015-06-01

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  6. 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.

  7. Molecular dynamics simulation of diffusion of gases in a carbon-nanotube-polymer composite

    Science.gov (United States)

    Lim, Seong Y.; Sahimi, Muhammad; Tsotsis, Theodore T.; Kim, Nayong

    2007-07-01

    Extensive molecular dynamics (MD) simulations were carried out to compute the solubilities and self-diffusivities of CO2 and CH4 in amorphous polyetherimide (PEI) and mixed-matrix PEI generated by inserting single-walled carbon nanotubes into the polymer. Atomistic models of PEI and its composites were generated using energy minimizations, MD simulations, and the polymer-consistent force field. Two types of polymer composite were generated by inserting (7,0) and (12,0) zigzag carbon nanotubes into the PEI structure. The morphologies of PEI and its composites were characterized by their densities, radial distribution functions, and the accessible free volumes, which were computed with probe molecules of different sizes. The distributions of the cavity volumes were computed using the Voronoi tessellation method. The computed self-diffusivities of the gases in the polymer composites are much larger than those in pure PEI. We find, however, that the increase is not due to diffusion of the gases through the nanotubes which have smooth energy surfaces and, therefore, provide fast transport paths. Instead, the MD simulations indicate a squeezing effect of the nanotubes on the polymer matrix that changes the composite polymers’ free-volume distributions and makes them more sharply peaked. The presence of nanotubes also creates several cavities with large volumes that give rise to larger diffusivities in the polymer composites. This effect is due to the repulsive interactions between the polymer and the nanotubes. The solubilities of the gases in the polymer composites are also larger than those in pure PEI, hence indicating larger gas permeabilities for mixed-matrix PEI than PEI itself.

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

    Science.gov (United States)

    Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

    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.

  9. A test of systematic coarse-graining of molecular dynamics simulations: thermodynamic properties.

    Science.gov (United States)

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

    2012-10-28

    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

  10. 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

  11. Molecular Dynamics Simulation of Tau Peptides for the Investigation of Conformational Changes Induced by Specific Phosphorylation Patterns.

    Science.gov (United States)

    Gandhi, Neha S; Kukic, Predrag; Lippens, Guy; Mancera, Ricardo L

    2017-01-01

    The Tau protein plays an important role due to its biomolecular interactions in neurodegenerative diseases. The lack of stable structure and various posttranslational modifications such as phosphorylation at various sites in the Tau protein pose a challenge for many experimental methods that are traditionally used to study protein folding and aggregation. Atomistic molecular dynamics (MD) simulations can help around deciphering relationship between phosphorylation and various intermediate and stable conformations of the Tau protein which occur on longer timescales. This chapter outlines protocols for the preparation, execution, and analysis of all-atom MD simulations of a 21-amino acid-long phosphorylated Tau peptide with the aim of generating biologically relevant structural and dynamic information. The simulations are done in explicit solvent and starting from nearly extended configurations of the peptide. The scaled MD method implemented in AMBER14 was chosen to achieve enhanced conformational sampling in addition to a conventional MD approach, thereby allowing the characterization of folding for such an intrinsically disordered peptide at 293 K. Emphasis is placed on the analysis of the simulation trajectories to establish correlations with NMR data (i.e., chemical shifts and NOEs). Finally, in-depth discussions are provided for commonly encountered problems.

  12. Molecular Dynamics Simulation of Amyloid Beta Dimer Formation

    CERN Document Server

    Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V

    2004-01-01

    Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...

  13. Prototyping Bio-Nanorobots using Molecular Dynamics Simulation

    OpenAIRE

    Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos

    2005-01-01

    Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...

  14. 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.

  15. 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.

  16. Multiscale coupling of molecular dynamics and peridynamics

    Science.gov (United States)

    Tong, Qi; Li, Shaofan

    2016-10-01

    We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.

  17. Effects of oxidation on tensile deformation of iron nanowires: Insights from reactive molecular dynamics simulations

    Science.gov (United States)

    Aral, Gurcan; Wang, Yun-Jiang; Ogata, Shigenobu; van Duin, Adri C. T.

    2016-10-01

    The influence of oxidation on the mechanical properties of nanostructured metals is rarely explored and remains poorly understood. To address this knowledge gap, in this work, we systematically investigate the mechanical properties and changes in the metallic iron (Fe) nanowires (NWs) under various atmospheric conditions of ambient dry O2 and in a vacuum. More specifically, we focus on the effect of oxide shell layer thickness over Fe NW surfaces at room temperature. We use molecular dynamics (MD) simulations with the variable charge ReaxFF force field potential model that dynamically handles charge variation among atoms as well as breaking and forming of the chemical bonds associated with the oxidation reaction. The ReaxFF potential model allows us to study large length scale mechanical atomistic deformation processes under the tensile strain deformation process, coupled with quantum mechanically accurate descriptions of chemical reactions. To study the influence of an oxide layer, three oxide shell layer thicknesses of ˜4.81 Å, ˜5.33 Å, and ˜6.57 Å are formed on the pure Fe NW free surfaces. It is observed that the increase in the oxide layer thickness on the Fe NW surface reduces both the yield stress and the critical strain. We further note that the tensile mechanical deformation behaviors of Fe NWs are dependent on the presence of surface oxidation, which lowers the onset of plastic deformation. Our MD simulations show that twinning is of significant importance in the mechanical behavior of the pure and oxide-coated Fe NWs; however, twin nucleation occurs at a lower strain level when Fe NWs are coated with thicker oxide layers. The increase in the oxide shell layer thickness also reduces the external stress required to initiate plastic deformation.

  18. Impact of ionic liquids in aqueous solution on bacterial plasma membranes studied with molecular dynamics simulations.

    Science.gov (United States)

    Lim, Geraldine S; Zidar, Jernej; Cheong, Daniel W; Jaenicke, Stephan; Klähn, Marco

    2014-09-04

    The impact of five different imidazolium-based ionic liquids (ILs) diluted in water on the properties of a bacterial plasma membrane is investigated using molecular dynamics (MD) simulations. Cations considered are 1-octyl-3-methylimidazolium (OMIM), 1-octyloxymethyl-3-methylimidazolium (OXMIM), and 1-tetradecyl-3-methylimidazolium (TDMIM), as well as the anions chloride and lactate. The atomistic model of the membrane bilayer is designed to reproduce the lipid composition of the plasma membrane of Gram-negative Escherichia coli. Spontaneous insertion of cations into the membrane is observed in all ILs. Substantially more insertions of OMIM than of OXMIM occur and the presence of chloride reduces cation insertions compared to lactate. In contrast, anions do not adsorb onto the membrane surface nor diffuse into the bilayer. Once inserted, cations are oriented in parallel to membrane lipids with cation alkyl tails embedded into the hydrophobic membrane core, while the imidazolium-ring remains mostly exposed to the solvent. Such inserted cations are strongly associated with one to two phospholipids in the membrane. The overall order of lipids decreased after OMIM and OXMIM insertions, while on the contrary the order of lipids in the vicinity of TDMIM increased. The short alkyl tails of OMIM and OXMIM generate voids in the bilayer that are filled by curling lipids. This cation induced lipid disorder also reduces the average membrane thickness. This effect is not observed after TDMIM insertions due to the similar length of cation alkyl chain and the fatty acids of the lipids. This lipid-mimicking behavior of inserted TDMIM indicates a high membrane affinity of this cation that could lead to an enhanced accumulation of cations in the membrane over time. Overall, the simulations reveal how cations are inserted into the bacterial membrane and how such insertions change its properties. Moreover, the different roles of cations and anions are highlighted and the fundamental

  19. Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study.

    Science.gov (United States)

    Shao, Qing; Hall, Carol K

    2016-08-09

    A better understanding of the binding preference of amino acids for gold nanoparticles of different diameters could aid in the design of peptides that bind specifically to nanoparticles of a given diameter. Here we identify the binding preference of 19 natural amino acids for three gold nanoparticles with diameters of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. We calculate potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force determines the amino acids' nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. We also use atomistic molecular dynamics simulations to investigate how water molecules near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water molecules in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is determined mainly by their ability to replace or to reorient water molecules in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water molecules are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water molecules prefer a smaller nanoparticle and tend to have more complex side chain structures.

  20. Shock initiated thermal and chemical responses of HMX crystal from ReaxFF molecular dynamics simulation.

    Science.gov (United States)

    Zhou, Tingting; Song, Huajie; Liu, Yi; Huang, Fenglei

    2014-07-21

    To gain an atomistic-level understanding of the thermal and chemical responses of condensed energetic materials under thermal shock, we developed a thermal shock reactive dynamics (TS-RD) computational protocol using molecular dynamics simulation coupled with ReaxFF force field. β-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) was selected as a a target explosive due to its wide usage in the military and industry. The results show that a thermal shock initiated by a large temperature gradient between the "hot" region and the "cold" region results in thermal expansion of the particles and induces a thermal-mechanical wave propagating back and forth in the system with an averaged velocity of 3.32 km s(-1). Heat propagating along the direction of thermal shock leads to a temperature increment of the system and thus chemical reaction initiation. Applying a continuum reactive heat conduction model combined with the temperature distribution obtained from the RD simulation, a heat conduction coefficient is derived as 0.80 W m(-1) K(-1). The chemical reaction mechanisms during thermal shock were analyzed, showing that the reaction is triggered by N-NO2 bond breaking followed by HONO elimination and ring fission. The propagation rates of the reaction front and reaction center are obtained to be 0.069 and 0.038 km s(-1), based on the time and spatial distribution of NO2. The pressure effect on the thermal shock was also investigated by employing uniaxial compression before the thermal shock. We find that compression significantly accelerates thermal-mechanical wave propagation and heat conduction, resulting in higher temperature and more excited molecules and thus earlier initiation and faster propagation of chemical reactions.

  1. 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

  2. Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

    Science.gov (United States)

    Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

    2016-09-01

    Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

  3. Atomic motions in poly(vinyl methyl ether): A combined study by quasielastic neutron scattering and molecular dynamics simulations in the light of the mode coupling theory.

    Science.gov (United States)

    Capponi, S; Arbe, A; Alvarez, F; Colmenero, J; Frick, B; Embs, J P

    2009-11-28

    Quasielastic neutron scattering experiments (time-of-flight, neutron spin echo, and backscattering) on protonated poly(vinyl methyl ether) (PVME) have revealed the hydrogen dynamics above the glass-transition temperature. Fully atomistic molecular dynamics simulations properly validated with the neutron scattering results have allowed further characterization of the atomic motions accessing the correlation functions directly in real space. Deviations from Gaussian behavior are found in the high-momentum transfer range, which are compatible with the predictions of mode coupling theory (MCT). We have applied the MCT phenomenological version to the self-correlation functions of PVME atoms calculated from our simulation data, obtaining consistent results. The unusually large value found for the lambda-exponent parameter is close to that recently reported for polybutadiene and simple polymer models with intramolecular barriers.

  4. Complex molecular assemblies at hand via interactive simulations.

    Science.gov (United States)

    Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

    2009-11-30

    Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example.

  5. Molecular dynamics investigation on the deviation from stoichiometry in martensitic transformation

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Tetsuro, E-mail: tetsuro.suzuki@nifty.com [National Institute for Materials Science (Japan); Shimno, Masato; Otsuka, Kazuhiro; Ren, Xiaobing [National Institute for Materials Science (Japan); Saxena, Avadh [National Institute for Materials Science (Japan); Los Alamos National Laboratory (United States)

    2013-11-15

    Highlights: ► We have studied the martensitic transformation in Ti–Ni alloy near 50:50 stoichiometry. ► The atomistic process of the martensitic transformation is simulated by use of the molecular dynamics based on the 8-4 Lennard–Jones potential. ► The molecular dynamics provide atomistic picture when the formation of the martensite is suppressed for the deviation from 50:50 stoichiometry. -- Abstract: How the martensitic transformation in Ti–Ni alloy depends on the deviation from the stoichiometry is investigated by use of the molecular dynamics based on a simple model potential.

  6. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp

    2012-06-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

  7. A stochastic quasi Newton method for molecular simulations

    NARCIS (Netherlands)

    Chau, Chun Dong

    2010-01-01

    In this thesis the Langevin equation with a space-dependent alternative mobility matrix has been considered. Simulations of a complex molecular system with many different length and time scales based on the fundamental equations of motion take a very long simulation time before capturing the functio

  8. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    NARCIS (Netherlands)

    De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut

    2011-01-01

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices c

  9. Active site modeling in copper azurin molecular dynamics simulations

    NARCIS (Netherlands)

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    2004-01-01

    Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po

  10. Molecular Simulations of Nanoscale Transformations in Ionic Semiconductor Nanocrystals

    NARCIS (Netherlands)

    Fan, Z.

    2016-01-01

    The aim of the study described in this thesis is to obtain a profound understanding of transformations in NCs at the atomic level, by performing molecular simulations for such transformations, and by comparing the simulation results with available experimental high resolution transmission electron m

  11. Atomistic modeling at experimental strain rates and timescales

    Science.gov (United States)

    Yan, Xin; Cao, Penghui; Tao, Weiwei; Sharma, Pradeep; Park, Harold S.

    2016-12-01

    Modeling physical phenomena with atomistic fidelity and at laboratory timescales is one of the holy grails of computational materials science. Conventional molecular dynamics (MD) simulations enable the elucidation of an astonishing array of phenomena inherent in the mechanical and chemical behavior of materials. However, conventional MD, with our current computational modalities, is incapable of resolving timescales longer than microseconds (at best). In this short review article, we briefly review a recently proposed approach—the so-called autonomous basin climbing (ABC) method—that in certain instances can provide valuable information on slow timescale processes. We provide a general summary of the principles underlying the ABC approach, with emphasis on recent methodological developments enabling the study of mechanically-driven processes at slow (experimental) strain rates and timescales. Specifically, we show that by combining a strong physical understanding of the underlying phenomena, kinetic Monte Carlo, transition state theory and minimum energy pathway methods, the ABC method has been found to be useful in a variety of mechanically-driven problems ranging from the prediction of creep-behavior in metals, constitutive laws for grain boundary sliding, void nucleation rates, diffusion in amorphous materials to protein unfolding. Aside from reviewing the basic ideas underlying this approach, we emphasize some of the key challenges encountered in our own personal research work and suggest future research avenues for exploration.

  12. Neutron Star Crust and Molecular Dynamics Simulation

    CERN Document Server

    Horowitz, C J; Schneider, A; Berry, D K

    2011-01-01

    In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.

  13. Molecular Simulations of Nanoscale Transformations in Ionic Semiconductor Nanocrystals

    OpenAIRE

    Fan, Z

    2016-01-01

    The aim of the study described in this thesis is to obtain a profound understanding of transformations in NCs at the atomic level, by performing molecular simulations for such transformations, and by comparing the simulation results with available experimental high resolution transmission electron microscopy (HRTEM) data to validate the simulations and to reveal underlying physical mechanisms. These transformations include structural and morphological transitions and cation exchange processes...

  14. 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.

  15. ADATOM, VACANCY AND SPUTTERING YIELDS OF ENERGETIC Pt ATOMS IMPACTING ON Pt(100) BY MOLECULAR DYNAMICS SIMULATION

    Institute of Scientific and Technical Information of China (English)

    YE ZI-YAN; ZHANG QING-YU

    2001-01-01

    We have studied the influence of incident atoms with low energy on the Pt(100) surface by molecular dynamics simulation. The interaction potential obtained by the embedded atom method (EAM) was used in the simulation. The incident energy changes from 0.leV to 200eV, and the target temperature ranges from 100 to 500 K. The target scales are 6×6×4 and 8×8×4 fcc cells for lower and higher incident energies, respectively. The adatom, sputtering, vacancy and backscattering yields are calculated. It was found that there is a sputtering threshold for the incident energy. When the incident energy is higher than the sputtering threshold, the sputtering yield increases with the increase of incident energy, and the sputtering shows a symmetrical pattern. We found that the adatom and vacancy yields increase as the incident energy increases. The vacancy yields are much higher than those obtained by Monte Carlo simulation. The dependence of the adatom and sputtering yields on the incident energy and the relative atomistic mechanisms are discussed.

  16. 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.

  17. Experimental and molecular dynamics simulation study of structure of liquid and amorphous Ni62Nb38 alloy

    Science.gov (United States)

    Zhang, Y.; Ashcraft, R.; Mendelev, M. I.; Wang, C. Z.; Kelton, K. F.

    2016-11-01

    The state-of-the-art experimental and atomistic simulation techniques were utilized to study the structure of the liquid and amorphous Ni62Nb38 alloy. First, the ab initio molecular dynamics (AIMD) simulation was performed at rather high temperature where the time limitations of the AIMD do not prevent to reach the equilibrium liquid structure. A semi-empirical potential of the Finnis-Sinclair (FS) type was developed to almost exactly reproduce the AIMD partial pair correlation functions (PPCFs) in a classical molecular dynamics simulation. This simulation also showed that the FS potential well reproduces the bond angle distributions. The FS potential was then employed to elongate the AIMD PPCFs and determine the total structure factor (TSF) which was found to be in excellent agreement with X-ray TSF obtained within the present study demonstrating the reliability of the AIMD for the simulation of the structure of the liquid Ni-Nb alloys as well as the reliability of the developed FS potential. The glass structure obtained with the developed potential was also found to be in excellent agreement with the X-ray data. The analysis of the structure revealed that a network of the icosahedra clusters centered on Ni atoms is forming during cooling the liquid alloy down to Tg and the Nb Z14, Z15, and Z16 clusters are attached to this network. This network is the main feature of the Ni62Nb38 alloy and further investigations of the properties of this alloy should be based on study of the behavior of this network.

  18. Computer simulation in materials science

    Energy Technology Data Exchange (ETDEWEB)

    Arsenault, R.J.; Beeler, J.R.; Esterling, D.M.

    1988-01-01

    This book contains papers on the subject of modeling in materials science. Topics include thermodynamics of metallic solids and fluids, grain-boundary modeling, fracture from an atomistic point of view, and computer simulation of dislocations on an atomistic level.

  19. M3B: A coarse grain model for the simulation of oligosaccharides and their water mixtures.

    Science.gov (United States)

    Goddard, William A.; Cagin, Tahir; Molinero, Valeria

    2003-03-01

    Water and sugar dynamics in concentrated carbohydrate solutions is of utmost importance in food and pharmaceutical technology. Water diffusion in concentrated sugar mixtures can be slowed down many orders of magnitude with respect to bulk water [1], making extremely expensive the simulation of these systems with atomistic detail for the required time-scales. We present a coarse grain model (M3B) for malto-oligosaccharides and their water mixtures. M3B speeds up molecular dynamics simulations about 500-1000 times with respect to the atomistic model while retaining enough detail to be mapped back to the atomistic structures with low uncertainty in the positions. The former characteristic allows the study of water and carbohydrate dynamics in supercooled and polydisperse mixtures with characteristic time scales above the nanosecond. The latter makes M3B well suited for combined atomistic-mesoscale simulations. We present the parameterization of M3B force field for water and a family of technologically relevant glucose oligosaccharides, the alpha-(1->4) glucans. The coarse grain force field is completely parameterized from atomistic simulations to reproduce the density, cohesive energy and structural parameters of amorphous sugars. We will show that M3B is capable to describe the helical character of the higher oligosaccharides, and that the water structure in low moisture mixtures shows the same features obtained with the atomistic and M3B models. [1] R Parker, SG Ring: Carbohydr. Res. 273 (1995) 147-55.

  20. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori

    2011-09-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.