WorldWideScience

Sample records for temperature-accelerated molecular dynamics

  1. Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

    Directory of Open Access Journals (Sweden)

    Cameron Abrams

    2013-12-01

    Full Text Available We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.

  2. Molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Bethke, I.

    2002-01-01

    Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is

  3. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  4. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  5. Interactive molecular dynamics

    CERN Document Server

    Schroeder, Daniel V

    2015-01-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.

  6. Accelerated Molecular Dynamics Simulations of Reactive Hydrocarbon Systems

    Energy Technology Data Exchange (ETDEWEB)

    Stuart, Steven J.

    2014-02-25

    The research activities in this project consisted of four different sub-projects. Three different accelerated dynamics techniques (parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics) were applied to the modeling of pyrolysis of hydrocarbons. In addition, parallel replica dynamics was applied to modeling of polymerization.

  7. Molecular Dynamics and Protein Function

    National Research Council Canada - National Science Library

    M. Karplus; J. Kuriyan; Bruce J. Berne

    2005-01-01

    .... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...

  8. Molecular dynamics simulation of nanoindentation

    NARCIS (Netherlands)

    Michielsen, K; Figge, MT; De Raedt, H; De Hosson, JTM; Landau, DP; Lewis, SP; Schuttler, HB

    2003-01-01

    Molecular dynamics simulations are used to investigate the nucleation and dynamics of dislocations during nanoindentation of a (111) FCC plane. The core structure around the dislocation is visualized by coloring the atoms with deviating coordination number and its Burgers vector is automatically

  9. Molecular dynamics simulation of nanoindentation

    NARCIS (Netherlands)

    Michielsen, K.; Figge, M.T.; Raedt, H. De; Hosson, J.T.M. De

    2004-01-01

    Molecular dynamics simulations are used to investigate the nucleation and dynamics of dislocations during nanoindentation of a (111) FCC plane. The core structure around the dislocation is visualized by coloring the atoms with deviating coordination number and its Burgers vector is automatically

  10. Galilei invariant molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hoermann, G. [Vienna Univ. (Austria). Mathematisches Inst.; Jaekel, C.D. [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik

    1994-04-01

    We construct a C{sup *}-dynamical model for a chemical reaction. Galilei invariance of our nonrelativistic model is demonstrated by defining it directly on a Galilean space-time fibrebundle with C{sup *}-algebra valued fibre, i.e. without reference to any coordinate system. The existence of equilibrium states in this model is established and some of their properties are discussed. (orig.)

  11. State-Dependent Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Ciann-Dong Yang

    2014-10-01

    Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.

  12. State-dependent molecular dynamics.

    Science.gov (United States)

    Yang, Ciann-Dong; Weng, Hung-Jen

    2014-10-09

    This paper proposes a new mixed quantum mechanics (QM)-molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.

  13. Oleuropein: Molecular Dynamics and Computation.

    Science.gov (United States)

    Gentile, Luigi; Uccella, Nicola A; Sivakumar, Ganapathy

    2017-09-11

    Olive oil and table olive biophenols have been shown to significantly enrich the hedonic-sensory and nutritional quality of the Mediterranean diet. Oleuropein is one of the predominate biophenols in green olives and leaves, which not only has noteworthy free-radical quenching activity but also putatively reduces the incidence of various cancers. Clinical trials suggest that the consumption of extra virgin olive oil reduces the risk of several degenerative diseases. The oleuropein-based bioactives in olive oil could reduce tumor necrosis factor α, interleukin-1β and nitric oxide. Therefore, olive bioactives quality should be preserved and even improved due to their disease-fighting properties. Understanding the molecular dynamics of oleuropein is crucial to increase olive oil and table olive quality. The objective of this review is to provide the molecular dynamics and computational mapping of oleuropein. It is a biophenol-secoiridoid expressing different functionalities such as two π-bonds, two esters, two acetals, one catechol, and four hexose hydroxyls within 540 mw. The molecular bond sequential breaking mechanisms were analyzed through unimolecular reactions under electron spray ionization, collision activated dissociations, and fast atom bombardment mass spectrometry. The oleuropein solvent-free reactivity is leading to glucose loss and bioactive aglycone-dialdehydes via secoiridoid ring opening. Oleuropein electron distribution revealed that the free-radical non-polar processes occur from its highest occupied molecular orbital, while the lowest unoccupied molecular orbital is clearly devoted to nucleophilic and base site reactivity. This molecular dynamics and computational mapping of oleuropein could contribute to the engineering of olive-based biomedicine and/or functional food. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  14. Time Integrators for Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Nawaf Bou-Rabee

    2013-12-01

    Full Text Available This paper invites the reader to learn more about time integrators for Molecular Dynamics simulation through a simple MATLAB implementation. An overview of methods is provided from an algorithmic viewpoint that emphasizes long-time stability and finite-time dynamic accuracy. The given software simulates Langevin dynamics using an explicit, second-order (weakly accurate integrator that exactly reproduces the Boltzmann-Gibbs density. This latter feature comes from adding a Metropolis acceptance-rejection step to the integrator. The paper discusses in detail the properties of the integrator. Since these properties do not rely on a specific form of a heat or pressure bath model, the given algorithm can be used to simulate other bath models including, e.g., the widely used v-rescale thermostat.

  15. Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers

    NARCIS (Netherlands)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-01-01

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and

  16. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields......A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...

  17. Fast method for quantum mechanical molecular dynamics

    Science.gov (United States)

    Niklasson, Anders M. N.; Cawkwell, Marc J.

    2012-11-01

    As the processing power available for scientific computing grows, first-principles Born-Oppenheimer molecular dynamics simulations are becoming increasingly popular for the study of a wide range of problems in materials science, chemistry, and biology. Nevertheless, the computational cost of Born-Oppenheimer molecular dynamics still remains prohibitively large for many potential applications. Here we show how to avoid a major computational bottleneck: the self-consistent-field optimization prior to force calculations. The optimization-free quantum mechanical molecular dynamics method gives trajectories that are almost indistinguishable from an “exact” microcanonical Born-Oppenheimer molecular dynamics simulation even when low-prefactor linear scaling sparse matrix algebra is used. Our findings show that the computational gap between classical and quantum mechanical molecular dynamics simulations can be significantly reduced.

  18. Thermally driven molecular linear motors - A molecular dynamics study

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

    2009-01-01

    We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

  19. Molecular dynamics based enhanced sampling of collective variables with very large time steps.

    Science.gov (United States)

    Chen, Pei-Yang; Tuckerman, Mark E

    2018-01-14

    Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

  20. Molecular dynamics based enhanced sampling of collective variables with very large time steps

    Science.gov (United States)

    Chen, Pei-Yang; Tuckerman, Mark E.

    2018-01-01

    Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

  1. Chirality in molecular collision dynamics

    Science.gov (United States)

    Lombardi, Andrea; Palazzetti, Federico

    2018-02-01

    Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

  2. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

  3. Modeling the Hydrogen Bond within Molecular Dynamics

    Science.gov (United States)

    Lykos, Peter

    2004-01-01

    The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.

  4. 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.

  5. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical...

  6. Programming an interpreter using molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2007-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the

  7. Modeling hybrid perovskites by molecular dynamics.

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  8. Exciton dynamics in molecular aggregates

    NARCIS (Netherlands)

    Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A

    2006-01-01

    The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the

  9. Molecular dynamics simulation methods revised

    NARCIS (Netherlands)

    Bekker, Hendrik

    1996-01-01

    Korte beschrijving: In this thesis, all the subjects mentioned in the previous section are revised, except neighbor searching and integration. So, the following subjects are discussed: non-bonded force calculations, bonded force calculations, constraint dynamics, and box shapes. Moreover, mapping

  10. Liouville-von Neumann molecular dynamics.

    Science.gov (United States)

    Jakowski, Jacek; Morokuma, Keiji

    2009-06-14

    We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C(2) and retinal system.

  11. Advances in molecular vibrations and collision dynamics molecular clusters

    CERN Document Server

    Bacic, Zatko

    1998-01-01

    This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

  12. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  13. Theory and application of quantum molecular dynamics

    CERN Document Server

    Zeng Hui Zhang, John

    1999-01-01

    This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

  14. Classical molecular dynamics in a nutshell.

    Science.gov (United States)

    Hug, Susanna

    2013-01-01

    This chapter provides an overview of the various techniques that are commonly used in classical molecular dynamics simulations. It describes suitable algorithms for the integration of Newton's equation of motion over many time steps for systems containing a large number of particles, different choices of boundary conditions as well as available force fields for biological systems, that is, the mathematical description of the interactions of atoms and molecules with each other. It also illustrates algorithms used to simulate systems at constant temperature and/or pressure and discusses their advantages and disadvantages. It presents a few methods to save CPU time and a summary of popular software for biomolecular molecular dynamics simulations.

  15. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.

    Science.gov (United States)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-02-21

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular

  16. Nonadiabatic electron wavepacket dynamics behind molecular autoionization.

    Science.gov (United States)

    Matsuoka, Takahide; Takatsuka, Kazuo

    2018-01-07

    A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

  17. Nonadiabatic electron wavepacket dynamics behind molecular autoionization

    Science.gov (United States)

    Matsuoka, Takahide; Takatsuka, Kazuo

    2018-01-01

    A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

  18. Molecular dynamics simulation study of methanesulfonic acid

    OpenAIRE

    Canales Gabriel, Manel; Alemán Llansó, Carlos

    2014-01-01

    A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hyd...

  19. Molecular Reaction Dynamics and Solvation.

    Science.gov (United States)

    Kim, Seong Keun

    A potential energy surface was constructed for the triatomic molecule Li_2H using a semiempirical method akin to the diatomics-in-molecules theory. Valence bond configurations were chosen to include the major ionic contributions in the ground state potential energy. Quasiclassical trajectories were run on this potential energy surface. The results of these calculations are shown to be generally in accord with the experimental investigations of analogous reactions of H atoms with bigger alkali dimer molecules. Certain aspects of chemical reaction dynamics which have been largely overlooked were examined. These involve correlations of vector properties in chemical reactions. Specifically, the strong correlation between orbital and rotational angular momenta in the product channel of this reaction was shown to be the reason for a seemingly contradictory set of distributions of different angles. Gas phase solvation of nucleic acid base molecules was studied using clusters produced by supersonic expansion. Relative stabilities of the species with different numbers of solvent molecules were studied by varying the expansion conditions. The ionization potentials were measured as a function of the number of solvent molecules. Rather distinct effects of hydration were observed for the ionization potentials of adenine and thymine.

  20. molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    KEYWORDS: Molecular dynamic simulation; iron surface; adsorption; imidazoline derivatives; quantum chemical calculations ..... break any bond. This means that the closer the nuclei of the bonding atoms are a greater supply of energy is needed to separate the atoms due to large force of attraction between the atoms.

  1. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  2. 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.)

  3. Molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

  4. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  5. Molecular Exchange Dynamics in Block Copolymer Micelles

    Science.gov (United States)

    Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy

    2012-02-01

    Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.

  6. Dynamical quenching of tunneling in molecular magnets

    Energy Technology Data Exchange (ETDEWEB)

    José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

    2015-12-15

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

  7. Exciton dynamics in perturbed vibronic molecular aggregates

    Directory of Open Access Journals (Sweden)

    C. Brüning

    2016-07-01

    Full Text Available A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states.

  8. Molecular dynamics simulation of layered double hydroxides

    Energy Technology Data Exchange (ETDEWEB)

    KALINICHEV,ANDREY G.; WANG,JIANWEI; KIRKPATRICK,R. JAMES; CYGAN,RANDALL T.

    2000-05-19

    The interlayer structure and the dynamics of Cl{sup {minus}} ions and H{sub 2}O molecules in the interlayer space of two typical LDH [Layered Double Hydroxide] phases were investigated by molecular dynamics computer simulations. The simulations of hydrocalumite, [Ca{sub 2}Al(OH){sub 6}]Cl{center_dot}2H{sub 2}O reveal significant dynamic disorder in the orientations of interlayer water molecules. The hydration energy of hydrotalcite, [Mg{sub 2}Al(0H){sub 6}]Cl{center_dot}nH{sub 2}O, is found to have a minimum at approximately n = 2, in good agreement with experiment. The calculated diffusion coefficient of Cl{sup {minus}} as an outer-sphere surface complex is almost three times that of inner-sphere Cl{sup {minus}}, but is still about an order of magnitude less than that of Cl{sup {minus}} in bulk solution. The simulations demonstrate unique capabilities of combined NMR and molecular dynamics studies to understand the structure and dynamics of surface and interlayer species in mineral/water systems.

  9. Open quantum system parameters from molecular dynamics

    CERN Document Server

    Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander

    2015-01-01

    We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...

  10. Temperature Dependent Molecular Dynamic Simulation of Friction

    OpenAIRE

    Dias, R. A.; Rapini, M.; Costa, B. V.; Coura, P. Z.

    2006-01-01

    In this work we present a molecular dynamics simulation of a FFM experiment. The tip-sample interaction is studied by varying the normal force in the tip and the temperature of the surface. The friction force, cA, at zero load and the friction coefficient, $\\mu$, were obtained. Our results strongly support the idea that the effective contact area, A, decreases with increasing temperature and the friction coefficient presents a clear signature of the premelting process of the surface.

  11. Molecular dynamics modelling of solidification in metals

    Energy Technology Data Exchange (ETDEWEB)

    Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)

    1997-12-31

    Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.

  12. Nonequilibrium molecular dynamics theory, algorithms and applications

    CERN Document Server

    Todd, Billy D

    2017-01-01

    Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

  13. Dynamic Maintenance and Visualization of Molecular Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N

    2004-12-16

    Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.

  14. 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)

  15. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  16. Molecular dynamic results on transport properties

    Energy Technology Data Exchange (ETDEWEB)

    Alder, B.J.; Alley, W.E.

    1978-06-01

    Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so.

  17. Molecular dynamics of flow in micropores

    Science.gov (United States)

    Bitsanis, I.; Magda, J. J.; Tirrell, M.; Davis, H. T.

    1987-08-01

    The method of nonequilibrium molecular dynamics is used to study the viscosity and flow properties of strongly inhomogeneous liquids, a particular case of which is a liquid confined in a micropore only a few molecular diameters wide. Fluid inhomogeneity is introduced by imposing an external potential that in one case simulates flat solid walls and in the other case causes density peaks in the middle of a thin liquid film. For comparison a homogeneous fluid is also simulated. In both types of inhomogeneous fluid, the shear stress and effective viscosity are smaller than in the homogeneous fluid. The density profiles and the diffusivities in the micropore were found to be independent of flow, even at the extremely high rates, 1010-1011 s-1 of the simulation. The Green-Kubo relation is found to be valid for the diffusivity under the flow studied. We propose a local average density model (LADM) of viscosity and diffusivity, in which the local transport coefficients are those of homogeneous fluid at a mean density obtained by averaging the local density over a molecular volume. LADM predicts qualitatively correct velocity profiles, effective viscosities, and shear stresses using only equilibrium density profiles and molecular diameters. An analogous local equilibrium version of Enskog's theory of diffusivity agrees well with the simulated pore diffusivities. Recently Vanderlick and Davis generalized Enskog's theory of diffusivity to strongly inhomogeneous fluids. Their theoretical pore diffusion coefficient is also in good agreement with simulation results.

  18. Attosecond VUV Coherent Control of Molecular Dynamics

    CERN Document Server

    Ranitovic, P; Riviere, P; Palacios, A; Tong, X M; Toshima, N; Gonzalez-Castrillo, A; Martin, L; Martin, F; Murnane, M M; Kapteyn, H C

    2014-01-01

    High harmonic light sources make it possible to access attosecond time-scales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized. This is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep ultraviolet, which have not yet been synthesized. Here, we present a novel approach using attosecond vacuum ultraviolet pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly-ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipula...

  19. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    revolution. Novel nanofabrication techniques have opened up possibilities for the development of small-scale integrated devices, such as lab-on-a-chip for biochemical synthesis and analysis, the integration is achieved by miniaturization of the functional elements e.g., of the channels transporting the fluid...... at the nanoscale are expensive and time consuming moreover the time scale associated to several nanoscale phenomena requires a very high time resolution of the devices performing nanoscale measurements. Computational nanofluidics is the enabling technology for fundamental studies, development, and design...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...

  20. Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations.

    Science.gov (United States)

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

    2015-12-07

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

  1. Molecular Dynamics: New Frontier in Personalized Medicine.

    Science.gov (United States)

    Sneha, P; Doss, C George Priya

    2016-01-01

    The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.

  2. 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.

  3. Molecular dynamics in high electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Apostol, M., E-mail: apoma@theory.nipne.ro; Cune, L.C.

    2016-06-15

    Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

  4. 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...

  5. MDLab: a molecular dynamics simulation prototyping environment.

    Science.gov (United States)

    Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A

    2010-05-01

    Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net. Copyright 2009 Wiley Periodicals, Inc.

  6. Multiple branched adaptive steered molecular dynamics

    Science.gov (United States)

    Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto

    2014-08-01

    Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient "multiple branching" (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.

  7. Color molecular dynamics for dense matter and nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Maruyama, Toshiki [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Hatsuda, T. [Kyoto Univ. (Japan). Faculty of Science

    2000-01-01

    We propose a microscopic simulation for quark many-body system based on a molecular dynamics. Using confinement potential, one-gluon exchange potential and meson exchange potentials, we can construct color-singlet nucleons, nuclei and also an infinite nuclear/quark matter. Statistical feature and the dynamical change between confinement and deconfinement phases are studied with this molecular dynamics simulation. (author)

  8. Atomistic Molecular Dynamic Simulations of Multiferroics

    Science.gov (United States)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  9. 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..

  10. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  11. Lattice gas with molecular dynamics collision operator

    Science.gov (United States)

    Parsa, M. Reza; Wagner, Alexander J.

    2017-07-01

    We introduce a lattice gas implementation that is based on coarse-graining a molecular dynamics (MD) simulation. Such a lattice gas is similar to standard lattice gases, but its collision operator is informed by an underlying MD simulation. This can be considered an optimal lattice gas implementation because it allows for the representation of any system that can be simulated with MD. We show here that equilibrium behavior of the popular lattice Boltzmann algorithm is consistent with this optimal lattice gas. This comparison allows us to make a more accurate identification of the expressions for temperature and pressure in lattice Boltzmann simulations, which turn out to be related not only to the physical temperature and pressure but also to the lattice discretization. We show that for any spatial discretization, we need to choose a particular temporal discretization to recover the lattice Boltzmann equilibrium.

  12. DMS: A Package for Multiscale Molecular Dynamics

    CERN Document Server

    Somogyi, Endre; Ortoleva, Peter J

    2013-01-01

    Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables...

  13. Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.

    Science.gov (United States)

    Schwabe, Tobias

    2015-08-20

    For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied.

  14. Molecular dynamics simulations of microscale fluid transport

    Energy Technology Data Exchange (ETDEWEB)

    Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.

    1998-02-01

    Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.

  15. An undergraduate laboratory activity on molecular dynamics simulations

    National Research Council Canada - National Science Library

    Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan

    2016-01-01

    .... Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD...

  16. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  17. A molecular dynamics approach to barrodiffusion

    Science.gov (United States)

    Cooley, James; Marciante, Mathieu; Murillo, Michael

    2016-10-01

    Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

  18. Molecular-dynamic study of liquid ethylenediamine

    Science.gov (United States)

    Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.

    2016-10-01

    Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.

  19. Molecular dynamics simulation of amorphous indomethacin.

    Science.gov (United States)

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-01-07

    Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in α- and γ-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal

  20. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

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

  1. Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation

    National Research Council Canada - National Science Library

    Lei Zhao; Jiangtao Cheng

    2017-01-01

    (ProQuest: ... denotes formulae and/or non-USASCII text omitted; see image) In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation...

  2. Thermal transpiration: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  3. Molecular dynamics study of two- and three-dimensional classical ...

    Indian Academy of Sciences (India)

    We have carried out a molecular dynamics simulation of two- and three- dimensional double Yukawa ... potential have been studied by employing the techniques of molecular dynamics simulations [6,7]. Since, with .... position vectors r(t) and velocity vectors v(t) were stored at every 10th time step for subsequent analysis.

  4. 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.

  5. Direct anharmonic correction method by molecular dynamics

    Science.gov (United States)

    Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang

    2017-04-01

    The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.

  6. Dynamics, flexibility, and allostery in molecular chaperonins.

    Science.gov (United States)

    Skjærven, Lars; Cuellar, Jorge; Martinez, Aurora; Valpuesta, José María

    2015-09-14

    The chaperonins are a family of molecular chaperones present in all three kingdoms of life. They are classified into Group I and Group II. Group I consists of the bacterial variants (GroEL) and the eukaryotic ones from mitochondria and chloroplasts (Hsp60), while Group II consists of the archaeal (thermosomes) and eukaryotic cytosolic variants (CCT or TRiC). Both groups assemble into a dual ring structure, with each ring providing a protective folding chamber for nascent and denatured proteins. Their functional cycle is powered by ATP binding and hydrolysis, which drives a series of structural rearrangements that enable encapsulation and subsequent release of the substrate protein. Chaperonins have elaborate allosteric mechanisms to regulate their functional cycle. Long-range negative cooperativity between the two rings ensures alternation of the folding chambers. Positive intra-ring cooperativity, which facilitates concerted conformational transitions within the protein subunits of one ring, has only been demonstrated for Group I chaperonins. In this review, we describe our present understanding of the underlying mechanisms and the structure-function relationships in these complex protein systems with a particular focus on the structural dynamics, allostery, and associated conformational rearrangements. Copyright © 2015. Published by Elsevier B.V.

  7. Spin-diffusions and diffusive molecular dynamics

    Science.gov (United States)

    Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

    2017-12-01

    Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

  8. Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy)

    2011-01-07

    Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.

  9. Optical Microfiber Technology for Current, Temperature, Acceleration, Acoustic, Humidity and Ultraviolet Light Sensing

    Directory of Open Access Journals (Sweden)

    George Y. Chen

    2017-12-01

    Full Text Available Optical microfibers possess excellent optical and mechanical properties that have been exploited for sensing. We highlight the authors’ recent work in the areas of current, temperature, acceleration, acoustic, humidity and ultraviolet-light sensing based on this exquisite technology, and the advantages and challenges of using optical microfibers are discussed.

  10. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  11. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

    2016-01-01

    Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

  12. Molecular dynamics using quasielastic neutron scattering

    CERN Document Server

    Mitra, S

    2003-01-01

    Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)

  13. Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

    Science.gov (United States)

    Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

    2010-12-01

    Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to

  14. DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

    National Research Council Canada - National Science Library

    Lankaš, Filip; Šponer, Jiří; Langowski, Jörg; Cheatham, Thomas E

    2003-01-01

    The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d(GCCTATAAACGCCTATAA) and d(CTAGGTGGATGACTCATT...

  15. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  16. Special issue on ultrafast electron and molecular dynamics

    Science.gov (United States)

    Hishikawa, Akiyoshi; Martin, Fernando; Vrakking, Marc

    2013-07-01

    Your invitation to submit. Journal of Physics. B: Atomic Molecular and Optical Physics (JPhysB) is delighted to announce a forthcoming special issue on ultrafast electron and molecular dynamics to appear in 2014, and invites you to submit a paper. Within the last decade, a number of novel approaches have emerged, both experimental and theoretical, that allow the investigation of (time-resolved) molecular dynamics in novel ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain. Along the way, particular types of molecular dynamics, such as dynamics around conical intersections, have gained an increased prominence, sparked by an emerging realization about the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of some of the most important developments in the field, while at the same time indicating how studies of (time-resolved) molecular dynamics are likely to evolve in the coming

  17. Hardening Mechanisms of Silicon Nanospheres: A Molecular Dynamics Study

    Science.gov (United States)

    2011-05-01

    grants NSF_CMMI 0800896 and CMMI -1000415. Additional support was obtained by the Air Force through an AOARD-08-4131 program dedicated to...directly compare these types of simulations to the experimental results. The focus of this thesis is the molecular dynamics simulations related to the...response of real material response. 1.2 Experimental Background Because the molecular dynamics simulations that comprise this thesis are

  18. Next generation extended Lagrangian first principles molecular dynamics

    Science.gov (United States)

    Niklasson, Anders M. N.

    2017-08-01

    Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

  19. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  20. Molecular dynamics of histone H1

    National Research Council Canada - National Science Library

    Raghuram, Nikhil; Carrero, Gustavo; Thng, John; Hendzel, Michael J

    2009-01-01

    .... In this review, we focus on the wealth of information gathered on the molecular kinetics of histone H1 molecules using novel imaging techniques, such as fluorescence recovery after photobleaching...

  1. Molecular dynamics simulation of supercritical fluids

    Science.gov (United States)

    Branam, Richard D.

    Axisymmetric injectors appear in a multitude of applications ranging from rocket engines to biotechnology. While experimentation is limited to larger injectors, much interest has been shown in the micro- and nano-scales as well. Experimentation at these scales can be cost prohibitive if even possible. Often, the operating regime involves supercritical fluids or complex geometries. Molecular dynamics modeling provides a unique way to explore these flow regimes, calculate hard to measure flow parameters accurately, and determine the value of potential improvements before investing in costly experiments or manufacturing. This research effort modeled sub- and supercritical fluid flow in a cylindrical tube being injected into a quiescent chamber. The ability of four wall models to provide an accurate simulation was compared. The simplest model, the diffuse wall, proved useful in getting results quickly but the results for the higher density cases are questionable, especially with respect to velocity profiles and density distributions. The one zone model, three layers of an fcc solid tethered to the lattice sites with a spring, proved very useful for this research primarily because it did not need as many CPU hours to equilibrate. The two zone wall uses springs as a two body potential and has a second stationary zone to hold the wall in place. The most complicated, the three zone wall, employed a reactionary zone, a stochastic zone and a stationary zone using a Lennard-Jones two body potential. Jet simulations were conducted on argon and nitrogen for liquid tube diameters from 20 to 65 A at both sub and supercritical temperatures (Ar: 130 K and 160 K, N2: 120 K and 130 K). The simulations focused on pressures above the critical pressure (Ar: 6 MPa, N2: 4 MPa). The diffusive wall showed some variation from the analytical velocity profile in the tube while the atomistically modeled walls performed very well. The walls were all able to maintain system temperature to reach

  2. Molecular dynamics simulation of a polysorbate 80 micelle in water

    NARCIS (Netherlands)

    Amani, Amir; York, Peter; de Waard, Hans; Anwar, Jamshed

    2011-01-01

    The structure and dynamics of a single molecule of the nonionic surfactant polysorbate 80 (POE (20) sorbitan monooleate; Tween 80 (R)) as well as a micelle comprising sixty molecules of polysorbate 80 in water have been investigated by molecular dynamics simulation. In its free state in water the

  3. HYDRATION OF Cd(II): MOLECULAR DYNAMICS STUDY Ahmed M ...

    African Journals Online (AJOL)

    a

    K is estimated by the transition state theory to be 4.9 x 108 s-1, assuming a transmission coefficient of unity. KEY WORDS: Molecular dynamics, Umbrella sampling, Hydration structure, Cd(II), Water exchange, Three- body corrections. INTRODUCTION. Knowledge of the structural and dynamical properties of metal ion-water ...

  4. Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.

    Science.gov (United States)

    Spiridon, Laurentiu; Minh, David D L

    2017-10-10

    Compared to fully flexible molecular dynamics, simulations of constrained systems can use larger time steps and focus kinetic energy on soft degrees of freedom. Achieving ergodic sampling from the Boltzmann distribution, however, has proven challenging. Using recent generalizations of the equipartition principle and Fixman potential, here we implement Hamiltonian Monte Carlo based on constrained molecular dynamics as a Gibbs sampling move. By mixing Hamiltonian Monte Carlo based on fully flexible and torsional dynamics, we are able to reproduce free energy landscapes of simple model systems and enhance sampling of macrocycles.

  5. Order parameter prediction from molecular dynamics simulations in proteins

    CERN Document Server

    Perilla, Juan R

    2011-01-01

    A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter -- a reduced descriptor for the major subset of degrees of freedom -- that can be used to aid sampling for the large conformational change. We present a novel way to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that ma...

  6. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    Science.gov (United States)

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Molecular dynamics with deterministic and stochastic numerical methods

    CERN Document Server

    Leimkuhler, Ben

    2015-01-01

    This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

  8. Relativistic corrections to molecular dynamic dipole polarizabilities

    DEFF Research Database (Denmark)

    Kirpekar, Sheela; Oddershede, Jens; Jensen, Hans Jørgen Aagaard

    1995-01-01

    Using response function methods we report calculations of the dynamic isotropic polarizability of SnH4 and PbH4 and of the relativistic corrections to it in the random phase approximation and at the correlated multiconfigurational linear response level of approximation. All relativistic correctio...

  9. Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite

    NARCIS (Netherlands)

    Van den Berg, A.W.C.; Bromley, S.T.; Flikkema, E.; Wojdel, J.; Maschmeyer, T.; Jansen, J.C.

    2004-01-01

    In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the

  10. Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

    Science.gov (United States)

    Negre, Christian

    2017-06-01

    A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

  11. Molecular Dynamics and Spectra. II. Diatomic Raman.

    Science.gov (United States)

    1981-02-01

    a degeneracy factor g is introduced which depends on the symmetry of the molecule For our IT- homonuclear diatomic, z is gj, the nuclear spin...classi~a mechanical viewpoint. with some caveats for features In which anharmonicity is important, such as the de- tailed shape of Q branches. it is...to compute the Spectra of coa- plex molecular systems, for example of large molecules , clusters, liquids, solutions, and solids. Second, this

  12. Dynamics of Rarefied Gas and Molecular Gas Dynamics.

    Science.gov (United States)

    1983-08-25

    Soc. for Aeon. and Space Scienses , voL 3, No 4, 1960. 9. A. I. Bunimovich, M. L. Kagan. Free molecular flow of gas in the flat ducts and the lattices...J. La perturbation de lecoulement moleculatre libre produite par un obstacle. Bull. de L’Academic Polonaise des sciense , 1957, t. 5. n" I. 23. R. S

  13. Dynamics of Structural Phase Transformations Using Molecular Dynamics

    Science.gov (United States)

    2013-12-08

    corresponding to a universal molecular simulation method, Journal of Fluid Mechanics, (12 2011): 0. doi: 10.1017/jfm.2011.483 Amin Aghaei, Kaushik...Materials Science at the Center for Nonlinear Analysis, June 2013. -- Fluids and Materials Seminar in the School of Mathematics, University of Bristol... Mecanique des Materiaux Seminar, University of Metz, June 2010. Contributed conference proceedings: -- European Materials Research Society

  14. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics...... an improved stability with a factor of , but the overhead of computer time is a factor of at least two. The conclusion is that the second-order “Verlet”-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated...

  15. Molecular Dynamics Modeling and Simulation of Diamond Cutting of Cerium

    Science.gov (United States)

    Zhang, Junjie; Zheng, Haibing; Shuai, Maobing; Li, Yao; Yang, Yang; Sun, Tao

    2017-07-01

    The coupling between structural phase transformations and dislocations induces challenges in understanding the deformation behavior of metallic cerium at the nanoscale. In the present work, we elucidate the underlying mechanism of cerium under ultra-precision diamond cutting by means of molecular dynamics modeling and simulations. The molecular dynamics model of diamond cutting of cerium is established by assigning empirical potentials to describe atomic interactions and evaluating properties of two face-centered cubic cerium phases. Subsequent molecular dynamics simulations reveal that dislocation slip dominates the plastic deformation of cerium under the cutting process. In addition, the analysis based on atomic radial distribution functions demonstrates that there are trivial phase transformations from the γ-Ce to the δ-Ce occurred in both machined surface and formed chip. Following investigations on machining parameter dependence reveal the optimal machining conditions for achieving high quality of machined surface of cerium.

  16. Drug design benefits from molecular dynamics: some examples.

    Science.gov (United States)

    Zhang, Ji-Long; Zheng, Qing-Chuan; Chu, Wen-Ting; Zhang, Hong-Xing

    2013-12-01

    With the increasing application of various computer techniques in new drug development, molecular dynamics (MD) simulation, as a promising tool for rational drug design, is playing a more and more vital role. In this review, we initially give a brief recapitulation of relevant basic MD theories, followed by an additional introduction of the current state-of-the-art MD methodologies, mainly involving steered molecular dynamics (SMD) and constant pH molecular dynamics (CpHMD). Both of the methods extend research field of conventional MD simulations. In the end, some interesting examples using these latest MD approaches are also presented to demonstrate their practicability and validity for the study on the ligand-receptor interaction.

  17. Hydrolysis of Al3+ from constrained molecular dynamics.

    Science.gov (United States)

    Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

    2006-02-21

    We investigated the hydrolysis reactions of Al(3+) in AlCl(3) aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of DeltaG(0) approximately 8.0 kcal mol(-1) the hydrolysis constant pK(a1) is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al(3+) in acidic conditions is at least 4 kcal mol(-1) higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH.

  18. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

    OpenAIRE

    Ruggerone, Paolo; Vargiu, Attilio V.; Collu, Francesca; Fischer, Nadine; Kandt, Christian

    2013-01-01

    Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformation...

  19. Molecular reactivity dynamics in a confined environment.

    Science.gov (United States)

    Khatua, Munmun; Chattaraj, Pratim Kumar

    2013-04-21

    Time evolution of various reactivity parameters viz. hardness, electrophilicity, chemical potential, polarizability, etc. in a confined environment has been studied through quantum fluid density functional theory formalism during time dependent processes such as proton-molecule collisions and molecule-field interaction. A Dirichlet type boundary condition has been incorporated to confine the systems. Responses in the reactivity parameters of the diatomic molecules, in the dynamical context, in ground state as well as in excited state, have been reported. Harmonic spectra are generated in the cases of the external laser field interacting with H2 and N2 molecules.

  20. State-to-state dynamics of molecular energy transfer

    Energy Technology Data Exchange (ETDEWEB)

    Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

  1. Femtochemistry and femtobiology ultrafast dynamics in molecular science

    CERN Document Server

    Douhal, Abderrazzak

    2002-01-01

    This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

  2. Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E

    2017-01-01

    Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach to the de......Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...

  3. Explicit proton transfer in classical molecular dynamics simulations

    OpenAIRE

    Wolf, Maarten G.; Groenhof, Gerrit

    2014-01-01

    We present Hydrogen Dynamics (HYDYN), a method that allows explicit proton transfer in classical force field molecular dynamics simulations at thermodynamic equilibrium. HYDYN reproduces the characteristic properties of the excess proton in water, from the special pair dance, to the continuous fluctuation between the limiting Eigen and Zundel complexes, and the water reorientation beyond the first solvation layer. Advantages of HYDYN with respect to existing methods are computational efficien...

  4. Coarse-Grained Molecular Dynamics: Dissipation Due to Internal Modes

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, R E

    2001-12-21

    We describe progress on the issue of pathological elastic wave reflection in atomistic and multiscale simulation. First we briefly review Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe how Langevin dynamics arise naturally in CGMD, and we examine the implication for elastic wave scattering.

  5. Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

    Czech Academy of Sciences Publication Activity Database

    Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

    2015-01-01

    Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

  6. Electron trapping in amorphous silicon: A quantum molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Lin H.; Kalia, R.K.; Vashishta, P.

    1990-12-01

    Quantum molecular dynamics (QMD) simulations provide the real-time dynamics of electrons and ions through numerical solutions of the time-dependent Schrodinger and Newton equations, respectively. Using the QMD approach we have investigated the localization behavior of an excess electron in amorphous silicon at finite temperatures. For time scales on the order of a few picoseconds, we find the excess electron is localized inside a void of radius {approximately}3 {Angstrom} at finite temperatures. 12 refs.

  7. A fast recursive algorithm for molecular dynamics simulation

    Science.gov (United States)

    Jain, A.; Vaidehi, N.; Rodriguez, G.

    1993-01-01

    The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

  8. 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.

  9. Simplistic Coulomb Forces in Molecular Dynamics

    DEFF Research Database (Denmark)

    Hansen, Jesper Schmidt; Schrøder, Thomas; Dyre, J. C.

    2012-01-01

    measures for the convergence of the Wolf method to the Ewald summation method. The SF approximation is also tested for the SPC/Fw model of liquid water at room temperature, showing good agreement with both the Wolf and the particle mesh Ewald methods; this confirms previous findings [Fennell, C. J......In this paper we compare the Wolf method to the shifted forces (SF) method for efficient computer simulation of bulk systems with Coulomb forces, taking results from the Ewald summation and particle mesh Ewald methods as representing the true behavior. We find that for the Hansen–McDonald molten...... salt model the SF approximation overall reproduces the structural and dynamical properties as accurately as does the Wolf method. It is shown that the optimal Wolf damping parameter depends on the property in focus and that neither the potential energy nor the radial distribution function are useful...

  10. Molecular circuits for dynamic noise filtering.

    Science.gov (United States)

    Zechner, Christoph; Seelig, Georg; Rullan, Marc; Khammash, Mustafa

    2016-04-26

    The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli.

  11. A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

    NARCIS (Netherlands)

    AHLSTROM, P; BERENDSEN, HJC

    1993-01-01

    Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

  12. Projector augmented wave method: ab initio molecular dynamics ...

    Indian Academy of Sciences (India)

    http://www.ias.ac.in/article/fulltext/boms/026/01/0033-0041 ... A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends ...

  13. Molecular Dynamics Investigation of Efficient SO2 Absorption by ...

    Indian Academy of Sciences (India)

    ANIRBAN MONDAL

    Abstract. Ionic liquids are appropriate candidates for the absorption of acid gases such as SO2. Six anion- functionalized ionic liquids with different basicities have been studied for SO2 absorption capacity by employ- ing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum ...

  14. Stability of Surface Nanobubbles: A Molecular Dynamics Study

    NARCIS (Netherlands)

    Maheshwari, Shantanu; van der Hoef, Martin Anton; Zhang, Xuehua; Lohse, Detlef

    2016-01-01

    The stability and growth or dissolution of a single surface nanobubble on a chemically patterned surface are studied by molecular dynamics simulations of binary mixtures consisting of Lennard-Jones (LJ) particles. Our simulations reveal how pinning of the three-phase contact line on the surface can

  15. Ab initio molecular dynamics study of Fe-containing smectites

    NARCIS (Netherlands)

    Liu, X.; Meijer, E.J.; Lu, X.; Wang, R.

    2010-01-01

    In order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Fe-bearing smectites. The following basic properties were investigated: local structures in the clay layer,

  16. Projector augmented wave method: ab initio molecular dynamics ...

    Indian Academy of Sciences (India)

    Unknown

    Abstract. A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented.

  17. Quantum molecular dynamics approach to estimate spallation yield ...

    Indian Academy of Sciences (India)

    Keywords. Spallation reaction; neutron emission; spallation products; quantum molecular dynamics. PACS Nos 25.40.Sc; 25.40.-h; 28.20.-v. 1. Introduction. In recent years, spallation neutron sources are used extensively for material science stud- ies. Additionally, they provide an important link between the accelerator and ...

  18. Molecular dynamics simulation of a charged biological membrane

    NARCIS (Netherlands)

    López Cascales, J.J.; García de la Torre, J.; Marrink, S.J.; Berendsen, H.J.C.

    1996-01-01

    A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as counterions and water molecules. The behavior of this membrane differs from that was shown by other

  19. Molecular dynamics study of dislocation nucleation from a crack tip

    NARCIS (Netherlands)

    Hess, B; Thijsse, BJ; Van der Giessen, E; Thijsse, Barend J.

    We have performed a systematic molecular dynamics study of the competition between crack growth and dislocation emission from a crack tip. Two types of boundary conditions are adopted: either planar extension or boundary displacements according to the anisotropic mode-I asymptotic continuum

  20. A Molecular Dynamics Approach to Grain Boundary Structure and Migration

    DEFF Research Database (Denmark)

    Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans

    1974-01-01

    It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...

  1. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  2. Active site modeling in copper azurin molecular dynamics simulations

    NARCIS (Netherlands)

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    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

  3. Molecular Dynamics and Bioactivity of a Novel Mutated Human ...

    African Journals Online (AJOL)

    Purpose: To design and evaluate a novel human parathyroid hormone (hPTH) analog. Methods: Mutation stability prediction was processed on hPTH, docked the mutant hPTH with its receptor, and then proceeded with molecular dynamics using Discovery Studio 3.5 software package for the complex. The bioactivity of the ...

  4. Acidity constants of lumiflavin from first principles molecular dynamics simulations

    NARCIS (Netherlands)

    Kiliç, M.; Ensing, B.

    2014-01-01

    We have computed the free energy profiles of the deprotonation reactions of lumiflavin in the semiquinone and fully reduced oxidation states using constrained DFT-based molecular dynamics simulations. In the semiquinone state, the N5 nitrogen atom and the N1 nitrogen atom can become protonated. We

  5. 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

  6. Molecular dynamics study on the relaxation properties of bilayered ...

    Indian Academy of Sciences (India)

    2017-08-31

    Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...

  7. Molecular dynamics of a proguanil derivative | Muhammad | Bayero ...

    African Journals Online (AJOL)

    Proguanil is a prophylactic antimalarial drug that is very effective against sporozoites and works by stopping the malaria parasites from reproducing inside the red blood cells. In this work, the molecular dynamics of a derivative of Proguanil is studied. A Hydrogen atom at position 3 on the benzene ring of the molecule of ...

  8. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    African Journals Online (AJOL)

    dimensional (3D) structure of lunasin is thus far not yet fully characterized. Thus this work is aimed at exploring the conformational profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. The results obtained ...

  9. Reasoning with Atomic-Scale Molecular Dynamic Models

    Science.gov (United States)

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

    The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

  10. Molecular dynamics simulations of cluster fission and fusion processes

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...

  11. Calcium binding to the purple membrane : A molecular dynamics study

    NARCIS (Netherlands)

    Wassenaar, Tsjerk A.; Daura, Xavier; Padros, Esteve; Mark, Alan E.

    2009-01-01

    The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a

  12. Free energy from molecular dynamics with multiple constraints

    NARCIS (Netherlands)

    den Otter, Wouter K.; Briels, Willem J.

    2000-01-01

    In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to

  13. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.

    1996-01-01

    of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...

  14. 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...

  15. Coarse-grained molecular dynamics simulations of biomolecules

    Directory of Open Access Journals (Sweden)

    Ken Takahashi

    2014-03-01

    Full Text Available Coarse-grained molecular dynamics (CGMD simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.

  16. 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

  17. Vibrational frequencies in Car-Parrinello molecular dynamics.

    Science.gov (United States)

    Ong, Sheau Wei; Tok, Eng Soon; Kang, Hway Chuan

    2010-12-07

    Car-Parrinello molecular dynamics (CPMD) are widely used to investigate the dynamical properties of molecular systems. An important issue in such applications is the dependence of dynamical quantities such as molecular vibrational frequencies upon the fictitious orbital mass μ. Although it is known that the correct Born-Oppenheimer dynamics are recovered at zero μ, it is not clear how these dynamical quantities are to be rigorously extracted from CPMD calculations. Our work addresses this issue for vibrational frequencies. We show that when the system is sufficiently close to the ground state the calculated ionic vibrational frequencies are ω(M) = ω(0M)[1 -C(μ/M)] for small μ/M, where ω(0M) is the Born-Oppenheimer ionic frequency, M the ionic mass, and C a constant that depends upon the ion-orbital coupling force constants. Our analysis also provides a quantitative understanding of the orbital oscillation amplitudes, leading to a relationship between the adiabaticity of a system and the ion-orbital coupling constants. In particular, we show that there is a significant systematic dependence of calculated vibrational frequencies upon how close the CPMD trajectory is to the Born-Oppenheimer surface. We verify our analytical results with numerical simulations for N(2), Sn(2), and H/Si(100)-(2×1).

  18. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

    Science.gov (United States)

    Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

    2015-12-08

    Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

  19. On the Vibration of Single-Walled Carbon Nanocones: Molecular Mechanics Approach versus Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    R. Ansari

    2014-01-01

    Full Text Available The vibrational behavior of single-walled carbon nanocones is studied using molecular structural method and molecular dynamics simulations. In molecular structural approach, point mass and beam elements are employed to model the carbon atoms and the connecting covalent bonds, respectively. Single-walled carbon nanocones with different apex angles are considered. Besides, the vibrational behavior of nanocones under various types of boundary conditions is studied. Predicted natural frequencies are compared with the existing results in the literature and also with the ones obtained by molecular dynamics simulations. It is found that decreasing apex angle and the length of carbon nanocone results in an increase in the natural frequency. Comparing the vibrational behavior of single-walled carbon nanocones under different boundary conditions shows that the effect of end condition on the natural frequency is more prominent for nanocones with smaller apex angles.

  20. Constrained dynamics and extraction of normal modes from ab initio molecular dynamics: application to ammonia.

    Science.gov (United States)

    Siddick, M M; Ackland, G J; Morrison, C A

    2006-08-14

    We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.

  1. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

    Science.gov (United States)

    2014-01-01

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

  2. Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

    Science.gov (United States)

    Fogarty, Aoife C; Laage, Damien

    2014-07-17

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

  3. Molecular dynamics computer simulation of permeation in solids

    Energy Technology Data Exchange (ETDEWEB)

    Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-31

    In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.

  4. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik

    2010-03-17

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  5. Multiscale molecular dynamics simulations of rotary motor proteins.

    Science.gov (United States)

    Ekimoto, Toru; Ikeguchi, Mitsunori

    2017-12-04

    Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

  6. Special issue on ultrafast electron and molecular dynamics

    Science.gov (United States)

    Martin, Fernando; Hishikawa, Akiyoshi; Vrakking, Marc

    2014-06-01

    In the last few years, the advent of novel experimental and theoretical approaches has made possible the investigation of (time-resolved) molecular dynamics in ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation (HHG) and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain, thus opening completely new avenues for imaging electronic and nuclear dynamics in molecules. Along the way, particular types of molecular dynamics, e.g., dynamics around conical intersections, have gained an increased prominence, sparked by the realization of the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. In the short term, this will allow one to uncover and control the dynamics of elementary chemical processes such as, e.g., ultrafast charge migration, proton transfer, isomerization or multiple ionization, and to address new key questions about the role of attosecond coherent electron dynamics in chemical reactivity. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules, including biomolecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of the current

  7. Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, F

    2007-08-15

    The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

  8. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    Energy Technology Data Exchange (ETDEWEB)

    Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

    2010-03-14

    Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

  9. Stretching siloxanes: An ab initio molecular dynamics study

    Science.gov (United States)

    Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.

    2005-10-01

    We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.

  10. Molecular dynamics simulations: from structure function relationships to drug discovery.

    Science.gov (United States)

    Nair, Pramod C; Miners, John O

    2014-01-01

    Molecular dynamics (MD) simulation is an emerging in silico technique with potential applications in diverse areas of pharmacology. Over the past three decades MD has evolved as an area of importance for understanding the atomic basis of complex phenomena such as molecular recognition, protein folding, and the transport of ions and small molecules across membranes. The application of MD simulations in isolation and in conjunction with experimental approaches have provided an increased understanding of protein structure-function relationships and demonstrated promise in drug discovery.

  11. Benefits of Considering More than Temperature Acceleration for GaN HEMT Life Testing

    Directory of Open Access Journals (Sweden)

    Ronald A. Coutu

    2016-06-01

    Full Text Available The purpose of this work was to investigate the validity of Arrhenius accelerated-life testing when applied to gallium nitride (GaN high electron mobility transistors (HEMT lifetime assessments, where the standard assumption is that only critical stressor is temperature, which is derived from operating power, device channel-case, thermal resistance, and baseplate temperature. We found that power or temperature alone could not explain difference in observed degradation, and that accelerated life tests employed by industry can benefit by considering the impact of accelerating factors besides temperature. Specifically, we found that the voltage used to reach a desired power dissipation is important, and also that temperature acceleration alone or voltage alone (without much power dissipation is insufficient to assess lifetime at operating conditions.

  12. A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

    Science.gov (United States)

    Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

    2010-01-01

    As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

  13. Molecular dynamics and the phase transition in solid C60

    Science.gov (United States)

    Tycko, R.; Dabbagh, G.; Fleming, R. M.; Haddon, R. C.; Makhija, A. V.; Zahurak, S. M.

    1991-09-01

    The molecular reorientational dynamics in two phases of solid C60 with C-13 NMR measurements are characterized. A change in the nature of the dynamics, indicated by a change in kinetic parameters extracted from spin-lattice relaxation data, occurs at the phase transition at 260 K. Above the transition, the molecules appear to execute continuous rotational diffusion; below the transition, they appear to jump between symmetry-equivalent orientations. This interpretation is consistent with the X-ray-diffraction results of Heiney et al. (1991) as well as the NMR relaxation and spectral data.

  14. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    Science.gov (United States)

    Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

  15. Advanced molecular dynamics simulation methods for kinase drug discovery.

    Science.gov (United States)

    Aci-Sèche, Samia; Ziada, Sonia; Braka, Abdennour; Arora, Rohit; Bonnet, Pascal

    2016-04-01

    Interest in the application of molecular dynamics (MD) simulations has increased in the field of protein kinase (PK) drug discovery. PKs belong to an important drug target class because they are directly involved in a number of diseases, including cancer. MD methods simulate dynamic biological and chemical events at an atomic level. This information can be combined with other in silico and experimental methods to efficiently target selected receptors. In this review, we present common and advanced methods of MD simulations and we focus on the recent applications of MD-based methodologies that provided significant insights into the elucidation of biological mechanisms involving PKs and into the discovery of novel kinase inhibitors.

  16. Molecular dynamics simulation of d-Benzedrine transmitting through molecular channels within D3R.

    Science.gov (United States)

    Xie, Wei; Wang, Ming; Li, Aijing; Xu, Si-Chuan

    2017-06-01

    Dex-Benzedrine (known as d-Benzedrine or SAT) acts in dopamine receptors of central nerve cell system. In clinic, SAT is used to treat a variety of diseases; meanwhile, it has dependence and addiction. In order to investigate the pharmacology and addiction mechanisms of SAT as a medicine, in this paper, we have studied the structure of D3R complex protein with SAT, and based on which, using potential mean force with umbrella samplings and the simulated phospholipid bilayer membrane (or POPC bilayer membrane), the molecular dynamics simulation was performed to obtain free energy changes upon the trajectories for SAT moving along the molecular channels within D3R. The free energy change for SAT transmitting toward the outside of cell along the functional molecular channel within D3R is 83.5 kJ mol(-1). The change of free energy for SAT to permeate into the POPC bilayer membrane along the protective molecular channel within D3R is 87.7 kJ mol(-1). Our previous work gave that the free energy for Levo-Benzedrine (RAT) transmitting toward the outside of cell along the functional molecular channel within D3R is 91.4 kJ mol(-1), while it is 117.7 kJ mol(-1) for RAT to permeate into the POPC bilayer membrane along the protective molecular channel within D3R. The values of free energy suggest that SAT relatively prefers likely to pass through the functional molecular channel within D3R for increasing the release of dopamine molecules resulting in a variety of functional effects for SAT. The obtained results show that the pharmacology and addiction mechanisms of SAT as a drug are closely related to the molecular dynamics and mechanism for SAT transmitting along molecular channels within D3R.

  17. A Review of Enhanced Sampling Approaches for Accelerated Molecular Dynamics

    Science.gov (United States)

    Tiwary, Pratyush; van de Walle, Axel

    Molecular dynamics (MD) simulations have become a tool of immense use and popularity for simulating a variety of systems. With the advent of massively parallel computer resources, one now routinely sees applications of MD to systems as large as hundreds of thousands to even several million atoms, which is almost the size of most nanomaterials. However, it is not yet possible to reach laboratory timescales of milliseconds and beyond with MD simulations. Due to the essentially sequential nature of time, parallel computers have been of limited use in solving this so-called timescale problem. Instead, over the years a large range of statistical mechanics based enhanced sampling approaches have been proposed for accelerating molecular dynamics, and accessing timescales that are well beyond the reach of the fastest computers. In this review we provide an overview of these approaches, including the underlying theory, typical applications, and publicly available software resources to implement them.

  18. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

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

  19. Excitation Dynamics and Relaxation in a Molecular Heterodimer

    CERN Document Server

    Balevicius, V; Abramavicius, D; Mancal, T; Valkunas, L

    2011-01-01

    The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the energy gap of the molecular excitation, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

  20. Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar

    This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB......) in water and organic solvents. The effects of solvent on structural and dynamical enzyme properties are studied, and special attention is given to how enzyme properties in organic solvents are affected by the hydration level, which is shown to be related to the water activity. In experimental studies...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining...

  1. Optical spectra and lattice dynamics of molecular crystals

    CERN Document Server

    Zhizhin, GN

    1995-01-01

    The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

  2. Kinetic distance and kinetic maps from molecular dynamics simulation

    CERN Document Server

    Noe, Frank

    2015-01-01

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...

  3. Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.

    Science.gov (United States)

    Fidelis, Krzysztof Andrzej

    1990-08-01

    The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.

  4. Quantum tunneling splittings from path-integral molecular dynamics

    Science.gov (United States)

    Mátyus, Edit; Wales, David J.; Althorpe, Stuart C.

    2016-03-01

    We illustrate how path-integral molecular dynamics can be used to calculate ground-state tunnelling splittings in molecules or clusters. The method obtains the splittings from ratios of density matrix elements between the degenerate wells connected by the tunnelling. We propose a simple thermodynamic integration scheme for evaluating these elements. Numerical tests on fully dimensional malonaldehyde yield tunnelling splittings in good overall agreement with the results of diffusion Monte Carlo calculations.

  5. Lattice Dynamics and Intermolecular Forces in Organic Molecular Crystals

    OpenAIRE

    Bougeard, D.

    1988-01-01

    Recent developments in the theory and the application of determination of intermolecular forces are discussed for the computer simulation of the lattice dynamics of organic molecular crystals. Different atom-atom potentials for carbon, hydrogen, halogens, oxygen and nitrogen are presented. The influences of hydrogen bonds and multipolar forces are illustrated with some examples. Such potentials are applied to glutaric and squaric acid, hexachloroethane, malononitrile and parachlorobenzamide.

  6. Molecular dynamics study of acoustic emission from individual lattice defects

    Science.gov (United States)

    Nikonov, A. Yu.

    2017-12-01

    The paper reports on a molecular dynamics study of acoustic emission in an indented iron crystal for analyzing the effect of dislocations on its signal. The acoustic response of the system to loading is evaluated as forces acting on sensors which represent separate atomic areas located on the specimen surface. The analysis of acoustic emission and internal specimen structure shows a significant change in the emission signal due to the emergence of dislocations on the specimen surface.

  7. Fragmentation dynamics of molecular hydrogen in strong ultrashort laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Rudenko, A; Feuerstein, B; Zrost, K; Jesus, V L B de; Ergler, T; Dimopoulou, C; Schroeter, C D; Moshammer, R; Ullrich, J [Max-Planck-Institut fuer Kernphysik, D-69029 Heidelberg (Germany)

    2005-03-14

    We present the results of a systematic experimental study of dissociation and Coulomb explosion of molecular hydrogen induced by intense ultrashort (7-25 fs) laser pulses. Using coincident recoil-ion momentum spectroscopy we can distinguish the contributions from dissociation and double ionization even if they result in the same kinetic energies of the fragments. The dynamics of all fragmentation channels drastically depends on the pulse duration, and for 7 fs pulses becomes extremely sensitive to the pulse shape.

  8. Thermodynamics of small clusters of atoms: A molecular dynamics simulation

    DEFF Research Database (Denmark)

    Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J

    1974-01-01

    The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...... was found to be icosahedral in the 55-atom system and face centered cubic for the two larger systems. ©1974 American Institute of Physics...

  9. Structure prediction of subtilisin BPN' mutants using molecular dynamics methods

    OpenAIRE

    Heiner, Andreas P.; Berendsen, Herman J.C.; van Gunsteren, Wilfred F.

    2017-01-01

    In this paper we describe the achievements and pitfalls encountered in doing structure predictions of protein mutants using molecular dynamics simulation techniques in which properties of atoms are slowly changed as a function of time. Basically the method consists of a thermodynamic integration (slow growth) calculation used for free energy determination, but aimed at structure prediction; this allows for a fast determination of the mutant structure. We compared the calculated structure of t...

  10. Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part I

    OpenAIRE

    Jenkins, S.; Kirk, S. R.; Persson, M.; Carlen, J.; Abbas, Z.

    2007-01-01

    Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles in aqueous solution, of diameter 4.4 nm with four different background electrolyte concentrations, to extract the mean force acting between the pair of silica nanoparticles. Dependences of the interparticle forces with separation and the background electrolyte concentration were demonstrated. The nature of the interaction of the counter-ions with charged silica surface sites (deprotonated silanols...

  11. Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part II

    OpenAIRE

    Jenkins, S.; Kirk, S. R.; Persson, M.; Carlen, J.; Abbas, Z.

    2007-01-01

    Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles of diameter 3.2 nm immersed in a background electrolyte. Mean forces acting between the pair of silica nanoparticles were extracted at four different background electrolyte concentrations. Dependence of the inter-particle potential of mean force on the separation and the silicon to sodium ratio, as well as on the background electrolyte concentration, are demonstrated. The pH was indirectly account...

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

    Science.gov (United States)

    Rapaport, D C

    2009-04-01

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

  13. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  14. Molecular Dynamics Simulations for Anisotropic Thermal Conductivity of Borophene

    OpenAIRE

    Jia, Yue; Li, Chun; Jiang, Jin-Wu; Wei, Ning; Chen, Yang; Zhang, Yongjie Jessica

    2017-01-01

    The present work carries out molecular dynamics simulations to compute the thermal conductivity of the borophene nanoribbon and the borophene nanotube using the Muller-Plathe approach. We investigate the thermal conductivity of the armchair and zigzag borophenes, and show the strong anisotropic thermal conductivity property of borophene. We compare the results of the borophene nanoribbon and the borophene nanotube, and find the thermal conductivity of the borophene is structure dependent.

  15. Molecular Dynamics Simulations of Solutions at Constant Chemical Potential

    OpenAIRE

    Perego, C; Salvalaglio, M; Parrinello, M.

    2015-01-01

    Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Gran...

  16. 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.

  17. Insights from molecular dynamics simulations for computational protein design

    Science.gov (United States)

    Childers, Matthew Carter; Daggett, Valerie

    2017-01-01

    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. PMID:28239489

  18. Molecular dynamics simulations of electron irradiated PVDF nanofibers

    Science.gov (United States)

    Miao, Jiayuan; Bhatta, Ram; Kisielowski, Christian; Lolla, Dinesh; Reneker, Darrell; Tsige, Mesfin; Taylor, Philip

    2014-03-01

    High-resolution, aberration corrected transmission electron microscopy was used to observe morphological changes and segmental motion of electrospun poly(vinylidene fluoride) nanofibers in an 80 kilovolt electron beam. Atomic and molecular scale high-resolution images of fibers were made with an aberration corrected electron microscope. Chemical and morphological changes, which include the breaking of the fiber, loss of fluorine atoms and cross-linking of chains, caused by the high-energy electron beam were observed. We present the results of molecular dynamics (MD) simulations of such atomic and molecular level observations. The calculational models include the influence of chain scission, chain recoiling, and torsional defects on the morphology of a nanofiber. The effects of the loss of fluorine atoms and the applied tension on the morphology of the fibers were also investigated. Work supported by the Petroleum Research Fund of the American Chemical Society.

  19. Molecular Dynamics Studies on the Buffalo Prion Protein

    CERN Document Server

    Zhang, Jiapu

    2015-01-01

    It was reported that buffalo is a low susceptibility species resisting to TSEs (Transmissible Spongiform Encephalopathies) (same as rabbits, horses and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (in humans prion diseases are (v)CJDs, GSS, FFI, and kulu etc). It was reported that buffalo is a low susceptibility species resisting to prion diseases (as rabbits, dogs, horses). In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to find out the reason why buffaloes are resistant to prion diseases. We first did molecular modeling a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonanc...

  20. NMR Studies and Molecular Dynamic Simulation of Synthetic Dendritic Antigens

    Directory of Open Access Journals (Sweden)

    Ezequiel Perez-Inestrosa

    2011-09-01

    Full Text Available A series of synthetic benzylpenicillinoylated dendrimers has been prepared using up to 4th generation PAMAM dendrimers. These nanoconjugates, as nanosized Dendritic Antigens, are useful in the diagnostic evaluation of drug allergy due to specific molecular recognition with the Human Immunological System (IgE. The morphology and dimensions of the conjugates coupled to the orientation of the peripheral benzylpenicillin residues in the dendrimers may play key roles in such molecular recognition processes. Herein, the characterization and conformation of these structures are studied by a detailed analysis of 1D (1H and 13C NMR and 2D NMR (1H,1H-NOESY spectra. These dendrimers in explicit solvent were studied by the atomistic forcefield-based molecular dynamics. Structural properties such as shape, radius-of-gyration and distribution of the monomers will be discussed in relation to the experimental observations.

  1. Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2017-07-01

    Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.

  2. Molecular dynamics simulations of solutions at constant chemical potential.

    Science.gov (United States)

    Perego, C; Salvalaglio, M; Parrinello, M

    2015-04-14

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  3. MDVRY: a polarizable classical molecular dynamics package for biomolecules

    Science.gov (United States)

    Souaille, M.; Loirat, H.; Borgis, D.; Gaigeot, M. P.

    2009-02-01

    The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a 'Car-Parrinello' dynamical approach. In this latter, the induced dipoles are calculated at each time step of the dynamics through the dynamics of additional degrees of freedom associated with the dipoles. This method saves computer time and allows to study polarized solvated proteins at a very low CPU cost. The program is written in C-language and runs on LINUX machines. A detailed manual of the code is given. The main features of the package are illustrated taking on examples of proteins in the gas phase or immersed in liquid water. Program summaryProgram title: MDVRY Catalogue identifier: AEBY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 39 156 No. of bytes in distributed program, including test data, etc.: 277 197 Distribution format: tar.bz2 Programming language: C Computer: Linux machines with FFTW Fourier Transform package installed Operating system: Linux machines, SUSE & RedHat distributions Classification: 3, 16.13, 23 External routines: FFTW ( http://www.fftw.org/) Nature of problem: Molecular Dynamics Software package. Solution method: Velocity Verlet algorithm. The implemented force field is composed of intra-molecular interactions and inter-molecular interactions (electrostatics, polarization, van der Waals). Polarization is accounted through induced point dipoles at each atomic site. Supplementary degrees of freedom are

  4. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise.

    Science.gov (United States)

    Cheatham, T E; Young, M A

    In the last five years we have witnessed a significant increase in the number publications describing accurate and reliable all-atom molecular dynamics simulations of nucleic acids. This increase has been facilitated by the development of fast and efficient methods for treating the long-range electrostatic interactions, the availability of faster parallel computers, and the development of well-validated empirical molecular mechanical force fields. With these technologies, it has been demonstrated that simulation is not only capable of consistently reproducing experimental observations of sequence specific fine structure of DNA, but also can give detailed insight into prevalent problems in nucleic acid structure, ion association and specific hydration of nucleic acids, polyadenine tract bending, and the subtle environmental dependence of the A-DNA-B-DNA duplex equilibrium. Despite the advances, there are still issues with the methods that need to be resolved through rigorous controlled testing. In general, these relate to deficiencies of the underlying molecular mechanical potentials or applied methods (such as the imposition of true periodicity in Ewald simulations and the need for energy conservation), and significant limits in effective conformational sampling. In this perspective, we provide an overview of our experiences, provide some cautionary notes, and provide recommendations for further study in molecular dynamics simulation of nucleic acids. Copyright 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 232-256, 2001

  5. Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

    Energy Technology Data Exchange (ETDEWEB)

    Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

    2017-04-04

    The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

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

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... 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....

  7. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering

    Science.gov (United States)

    Zaccai, Giuseppe; Natali, Francesca; Peters, Judith; Řihová, Martina; Zimmerman, Ella; Ollivier, J.; Combet, J.; Maurel, Marie-Christine; Bashan, Anat; Yonath, Ada

    2016-11-01

    Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.

  8. Molecular dynamics simulations of lysozyme in water/sugar solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2008-04-18

    Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.

  9. Dynamic coherence in excitonic molecular complexes under various excitation conditions

    Science.gov (United States)

    Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš

    2014-08-01

    We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity - an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna-Matthews-Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

  10. A rotary nano ion pump: a molecular dynamics study.

    Science.gov (United States)

    Lohrasebi, A; Feshanjerdi, M

    2012-09-01

    The dynamics of a rotary nano ion pump, inspired by the F (0) part of the F(0)F(1)-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.

  11. Subpicosecond dynamics of the molecular polyalanine dipole moment

    Directory of Open Access Journals (Sweden)

    Tatiana I. Zezina

    2017-12-01

    Full Text Available Instantaneous dipole moments of polyalanine peptides in vacuum and in the aqueous medium have been calculated on the picosecond time scale in order to evaluate the external influence of temperature, of the electrostatic field's amplitude and direction. Computer simulation was performed using the molecular dynamics method. The dynamic scenarios induced by the external electrostatic field above 100 MV/m were obtained for polyalanine molecules of different lengths (from 2 to 24 groups placed in vacuum and in aqueous medium, the time step of 1 fs and the simulation time up to 100 ns being taken. The simulated scenarios can be used for a further analysis and a generalized description of structural properties and conformational dynamics of molecules. The mastered software packages are appropriate for computing the representational scenarios of biomolecular behavior under various conditions.

  12. Molecular imaging with dynamic contrast-enhanced computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Miles, K.A., E-mail: k.a.miles@bsms.ac.u [Clinical Imaging Sciences Centre, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton (United Kingdom)

    2010-07-15

    Dynamic contrast-enhanced computed tomography (DCE-CT) is a quantitative technique that employs rapid sequences of CT images after bolus administration of intravenous contrast material to measure a range of physiological processes related to the microvasculature of tissues. By combining knowledge of the molecular processes underlying changes in vascular physiology with an understanding of the relationship between vascular physiology and CT contrast enhancement, DCE-CT can be redefined as a molecular imaging technique. Some DCE-CT derived parameters reflect tissue hypoxia and can, therefore, provide information about the cellular microenvironment. DCE-CT can also depict physiological processes, such as vasodilatation, that represent the physiological consequences of molecular responses to tissue hypoxia. To date the main applications have been in stroke and oncology. Unlike some other molecular imaging approaches, DCE-CT benefits from wide availability and ease of application along with the use of contrast materials and software packages that have achieved full regulatory approval. Hence, DCE-CT represents a molecular imaging technique that is applicable in clinical practice today.

  13. Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies

    Science.gov (United States)

    St. John, Alexander; Wexler, Carlos

    2015-03-01

    Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.

  14. 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.

  15. Machine learning molecular dynamics for the simulation of infrared spectra.

    Science.gov (United States)

    Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

    2017-10-01

    Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.

  16. Accelerated molecular dynamics methods: introduction and recent developments

    Energy Technology Data Exchange (ETDEWEB)

    Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO

    2009-01-01

    A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what

  17. Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu H. G.; Muckerman, J.T.

    2012-05-29

    The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

  18. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  19. Molecular Dynamics Simulation of Carbon Nanotube Based Gears

    Science.gov (United States)

    Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

    1996-01-01

    We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

  20. Validating clustering of molecular dynamics simulations using polymer models

    Directory of Open Access Journals (Sweden)

    Phillips Joshua L

    2011-11-01

    Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

  1. Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics.

    Science.gov (United States)

    Vijaykumar, Adithya; Ouldridge, Thomas E; Ten Wolde, Pieter Rein; Bolhuis, Peter G

    2017-03-21

    The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

  2. Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

    Science.gov (United States)

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

    2017-03-01

    The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

  3. Directly calculating electrical conductivities of dense hydrogen from molecular dynamics

    Science.gov (United States)

    Ma, Qian; Kang, Dongdong; Dai, Jiayu

    2017-10-01

    The transport properties are important in warm and hot dense matter in which the Coulomb interaction is dominated in the scattering process. Density functional theory (DFT) is considered as an effective method to investigate the transport properties, but the dynamical collisions between particles are missed. Here we use an electron force field (eFF) method based molecular dynamics (MD) to include the electronic quantum effects to investigate the transport properties of warm dense hydrogen. The eFF method can be regarded as the development of wave packets molecular dynamics and it has been successfully used to describe the thermodynamics of hydrogen, Auger process in diamondoids, the equation of states for dense lithium. The most important point of eFF method is assuming that each electron is considered as a Gaussian wave packet controlled by position and size while ions are still charged points. The electrical conductivity is calculated via the correlation of electrical current. The results show that electronic quantum effects are important for the transport properties in warm dense hydrogen such as diffusion coefficient and electrical conductivity, which are much smaller than the results from DFT calculations.

  4. Error and efficiency of replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Rosta, Edina; Hummer, Gerhard

    2009-10-28

    We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water.

  5. Hydrotropic Solubilization by Urea Derivatives: A Molecular Dynamics Simulation Study

    Directory of Open Access Journals (Sweden)

    Yong Cui

    2013-01-01

    Full Text Available Hydrotropy is a phenomenon where the presence of a large quantity of one solute enhances the solubility of another solute. The mechanism of this phenomenon remains a topic of debate. This study employed molecular dynamics simulation to investigate the hydrotropic mechanism of a series of urea derivatives, that is, urea (UR, methylurea (MU, ethylurea (EU, and butylurea (BU. A poorly water-soluble compound, nifedipine (NF, was used as the model solute that was solubilized. Structural, dynamic, and energetic changes upon equilibration were analyzed to supply insights to the solubilization mechanism. The study demonstrated that NF and urea derivatives underwent significant nonstoichiometric molecular aggregation in the aqueous solution, a result consistent with the self-aggregation of urea derivatives under the same conditions. The analysis of hydrogen bonding and energy changes revealed that the aggregation was driven by the partial restoration of normal water structure. The energetic data also suggested that the promoted solubilization of NF is favored in the presence of urea derivatives. While the solutes aggregated to a varying degree, the systems were still in single-phase liquid state as attested by their active dynamics.

  6. Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

    Science.gov (United States)

    Rydzewski, J; Nowak, W

    2017-12-01

    Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. 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.

  8. Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

    Science.gov (United States)

    Graziani, F R; Bauer, J D; Murillo, M S

    2014-09-01

    Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD

  9. Symplectic molecular dynamics simulations on specially designed parallel computers.

    Science.gov (United States)

    Borstnik, Urban; Janezic, Dusanka

    2005-01-01

    We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

  10. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding.

    Science.gov (United States)

    Loco, Daniele; Lagardère, Louis; Caprasecca, Stefano; Lipparini, Filippo; Mennucci, Benedetta; Piquemal, Jean-Philip

    2017-09-12

    We present the implementation of a Born-Oppenheimer (BO) hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) strategy using density functional theory (DFT) and the polarizable AMOEBA force field. This approach couples the Gaussian and Tinker suite of programs through a variational formalism allowing for a full self-consistent relaxation of both the AMOEBA induced dipoles and the DFT electron density at each MD step. As the DFT SCF cycles are the limiting factor in terms of computational efforts and MD stability, we focus on the latter aspect and compare the time-reversible BO (TR-BO) and the extended BO Lagrangian approaches (XL-BO) to the MD propagation. The XL-BO approach allows for stable, energy-conserving trajectories offering various perspectives for hybrid simulations using polarizable force fields.

  11. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...... efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from...

  12. Sugar transport across lactose permease probed by steered molecular dynamics

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Yin, Ying; Tajkhorshid, Emad

    2007-01-01

    Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic......, forcing it to interact with channel lining residues. Lactose forms a multitude of direct sugar-channel hydrogen bonds, predominantly with residues of the flexible N-domain, which is known to contribute a major part of LacY's affinity for lactose. In the periplasmic half-channel lactose predominantly...... interacts with hydrophobic channel lining residues, whereas in the cytoplasmic half-channel key protein-substrate interactions are mediated by ionic residues. A major energy barrier against transport is found within a tight segment of the periplasmic half-channel where sugar hydration is minimal and protein-sugar...

  13. Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms

    Directory of Open Access Journals (Sweden)

    Christian R. Trott

    2012-09-01

    Full Text Available Classical equilibrium molecular dynamics (MD simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC and TIP4P water models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based accelerator MD-GRAPE 3 was used to accelerate substantially the computation of non-bonded forces, while GPU-based platforms were also used in conjunction with CUDA-enabled versions of the LAMMPS MD software packages to reduce computational time dramatically. The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance relative to power consumption, it is seen that GPU-based computing is quite attractive.

  14. MOLECULAR DYNAMICS SIMULATION OF LYSINE DENDRIMER AND SEMAX PEPTIDES INTERACTION

    Directory of Open Access Journals (Sweden)

    E. V. Popova

    2016-07-01

    Full Text Available The paper deals with the possibility of complex formation of therapeutic Semax peptides with lysine dendrimer by molecular modeling methods. Dendrimers are often used for delivery of drugs and biological molecules (e.g., DNA, peptides and polysaccharides. Since lysine dendrimers are less toxic than conventional synthetic dendrimers (e.g., polyamidoamine (PAMAM dendrimer, we chose them and studied two systems containing dendrimer and the different number of Semax peptides. The study was carried out by molecular dynamics method. It was obtained that the stable complexes were formed in both cases. The equilibrium structures of these complexes were investigated. These complexes can be used in the future in therapy of various diseases as Semax peptides have significant antioxidant, antihypoxic and neuroprotecting action.

  15. Comparative Molecular Dynamics Studies of Human DNA Polymerase η

    Science.gov (United States)

    2015-01-01

    High-energy ultraviolet radiation damages DNA through the formation of cyclobutane pyrimidine dimers, which stall replication. When the lesion is a thymine–thymine dimer (TTD), human DNA polymerase η (Pol η) assists in resuming the replication process by inserting nucleotides opposite the damaged site. We performed extensive molecular dynamics (MD) simulations to investigate the structural and dynamical effects of four different Pol η complexes with or without a TTD and with either dATP or dGTP as the incoming base. No major differences in the overall structures and equilibrium dynamics were detected among the four systems, suggesting that the specificity of this enzyme is due predominantly to differences in local interactions in the binding regions. Analysis of the hydrogen-bonding interactions between the enzyme and the DNA and dNTP provided molecular-level insights. Specifically, the TTD was observed to engage in more hydrogen-bonding interactions with the enzyme than its undamaged counterpart of two normal thymines. The resulting greater rigidity and specific orientation of the TTD are consistent with the experimental observation of higher processivity and overall efficiency at TTD sites than at analogous sites with two normal thymines. The similarities between the systems containing dATP and dGTP are consistent with the experimental observation of relatively low fidelity with respect to the incoming base. Moreover, Q38 and R61, two strictly conserved amino acids across the Pol η family, were found to exhibit persistent hydrogen-bonding interactions with the TTD and cation-π interactions with the free base, respectively. Thus, these simulations provide molecular level insights into the basis for the selectivity and efficiency of this enzyme, as well as the roles of the two most strictly conserved residues. PMID:26562587

  16. Quantum-Accurate Molecular Dynamics Potential for Tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Mitchell; Thompson, Aidan P.

    2017-03-01

    The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-He binary system.

  17. Characterization of Molecular Dynamics in Ultrashort Laser Fields

    Science.gov (United States)

    Feuerstein, B.; Ergler, T.; Rudenko, A.; Moshammer, R.; Ullrich, J.; Niederhausen, T.; Thumm, U.

    2008-05-01

    Reaction Microscope-based, complete, and time-resolved Coulomb explosion imaging of vibrating and dissociating D2^2+ molecules with femtosecond time-resolution allowed us to perform an internuclear distance (R-)dependent Fourier analysis of the corresponding wave packets. Our wave packet propagation calculations demonstrate that the obtained two-dimensional R-dependent frequency spectra enable the complete characterization of the wave packet dynamics and directly visualize the field-modified molecular potential curves in intense, ultrashort laser pulses, cf., Phys. Rev. Lett. 99 153002 (2007).

  18. Entropy of liquid water from ab initio molecular dynamics.

    Science.gov (United States)

    Zhang, Cui; Spanu, Leonardo; Galli, Giulia

    2011-12-08

    We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations. We present the results obtained with semilocal, hybrid, and van der Waals density functionals. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. The underestimate is more severe for the PBE and PBE0 functionals than for several van der Waals functionals. © 2011 American Chemical Society

  19. Thermal transport properties of uranium dioxide by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Taku; Sinnott, Susan B. [Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611 (United States); Tulenko, James S. [Department of Nuclear and Radiological Engineering, University of Florida, Gainesville, FL 32611 (United States); Grimes, Robin W. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Schelling, Patrick K. [AMPAC and Department of Physics, University of Central Florida, Orlando, FL 32816 (United States); Phillpot, Simon R. [Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611 (United States)], E-mail: sphil@mse.ufl.edu

    2008-04-30

    The thermal conductivities of single crystal and polycrystalline UO{sub 2} are calculated using molecular dynamics simulations, with interatomic interactions described by two different potential models. For single crystals, the calculated thermal conductivities are found to be strongly dependent on the size of the simulation cell. However, a scaling analysis shows that the two models predict essentially identical values for the thermal conductivity for infinite system sizes. By contrast, simulations with the two potentials for identical fine polycrystalline structures yield estimated thermal conductivities that differ by a factor of two. We analyze the origin of this difference.

  20. Interfacial interaction between polypropylene and nanotube: A molecular dynamics simulation

    Science.gov (United States)

    Zhang, Danhui; Yang, Houbo; Liu, Zhongkui; Liu, Anmin; Li, Yunfang

    2017-09-01

    The interfacial interaction between polypropylene (PE) and single walled carbon nanotube (SWCNT) was studied using molecular dynamics (MD) simulations. The result showed that the PE chain could stabilize the SWCNT and then extended along the direction of SWCNT. The mechanism of interfacial interaction between PE and SWCNT was also discussed. Furthermore, the interfacial interaction between more PE and SWCNT was also investigated and the position also deeply influenced the interaction. This will be beneficial to understanding the interfacial interaction between polymer and CNT in solution, and also guiding the fabrication of high performance polymer/CNT nanocomposites.

  1. Molecular dynamics simulations of oscillatory flows in microfluidic channels

    DEFF Research Database (Denmark)

    Hansen, J.S.; Ottesen, Johnny T.

    2006-01-01

    In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system...

  2. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    Science.gov (United States)

    Xia, Kelin; Wei, Guo-Wei

    2014-01-01

    This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365

  3. Charge Carrier Dynamics at Silver Nanocluster-Molecular Acceptor Interfaces

    KAUST Repository

    Almansaf, Abdulkhaleq

    2017-07-01

    A fundamental understanding of interfacial charge transfer at donor-acceptor interfaces is very crucial as it is considered among the most important dynamical processes for optimizing performance in many light harvesting systems, including photovoltaics and photo-catalysis. In general, the photo-generated singlet excitons in photoactive materials exhibit very short lifetimes because of their dipole-allowed spin radiative decay and short diffusion lengths. In contrast, the radiative decay of triplet excitons is dipole forbidden; therefore, their lifetimes are considerably longer. The discussion in this thesis primarily focuses on the relevant parameters that are involved in charge separation (CS), charge transfer (CT), intersystem crossing (ISC) rate, triplet state lifetime, and carrier recombination (CR) at silver nanocluster (NCs) molecular-acceptors interfaces. A combination of steady-state and femto- and nanosecond broadband transient absorption spectroscopies were used to investigate the charge carrier dynamics in various donor-acceptor systems. Additionally, this thesis was prolonged to investigate some important factors that influence the charge carrier dynamics in Ag29 silver NCs donor-acceptor systems, such as the metal doping and chemical structure of the nanocluster and molecular acceptors. Interestingly, clear correlations between the steady-state measurements and timeresolved spectroscopy results are found. In the first study, we have investigated the interfacial charge transfer dynamics in positively charged meso units of 5, 10, 15, 20-tetra (1- methyl-4-pyridino)-porphyrin tetra (p-toluene sulfonate) (TMPyP) and neutral charged 5, 10, 15, 20-tetra (4-pyridyl)-porphyrin (TPyP), with negatively charged undoped and gold (Au)- doped silver Ag29 NCs. Moreover, this study showed the impact of Au doping on the charge carrier dynamics of the system. In the second study, we have investigated the interfacial charge transfer dynamics in [Pt2 Ag23 Cl7 (PPh3

  4. Molecular-dynamics simulations with explicit hydrodynamics II: on the collision of polymers with molecular obstacles.

    Science.gov (United States)

    Kenward, M; Slater, G W

    2006-06-01

    We present a study of the dynamics of single polymers colliding with molecular obstacles using Molecular-dynamics simulations. In concert with these simulations we present a generalized polymer-obstacle collision model which is applicable to a number of collision scenarios. The work focusses on three specific problems: i) a polymer driven by an external force colliding with a fixed microscopic post; ii) a polymer driven by a (plug-like) fluid flow colliding with a fixed microscopic post; and iii) a polymer driven by an external force colliding with a free polymer. In all three cases, we present a study of the length-dependent dynamics of the polymers involved. The simulation results are compared with calculations based on our generalized collision model. The generalized model yields analytical results in the first two instances (cases i) and ii)), while in the polymer-polymer collision example (case iii)) we obtain a series solution for the system dynamics. For the case of a polymer-polymer collision we find that a distinct V-shaped state exists as seen in experimental systems, though normally associated with collisions with multiple polymers. We suggest that this V-shaped state occurs due to an effective hydrodynamic counter flow generated by a net translational motion of the two-chain system.

  5. First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations

    CERN Document Server

    Kastner, Oliver

    2012-01-01

    Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and  covers  thermodynamical, micro-mechanical  and crystallographical aspects. It addresses scientists in these research fields and thei...

  6. RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    KAUST Repository

    Suleimanov, Yu.V.

    2013-03-01

    We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

  7. Homogeneous Nucleation of Methane Hydrate in Microsecond Molecular Dynamics Simulations.

    Science.gov (United States)

    Sarupria, Sapna; Debenedetti, Pablo G

    2012-10-18

    We report atomistically detailed molecular dynamics simulations of homogeneous nucleation of methane hydrate in bulk aqueous phase in the absence of any interface. Subcritical clusters of water and methane molecules are formed in the initial segment of the simulations, which then aggregate to give the critical hydrate nucleus. This occurs over time scales of several hundred nanoseconds, indicating that the formation and aggregation of subcritical clusters can contribute significantly to the overall rate of hydrate nucleation. The clusters have elements of sI hydrate structure, such as 5(12) and 5(12)6(2) cages as well as other uncommon 5(12)6(3) and 5(12)6(4) cages, but do not possess long-range order. Clusters are dynamic in nature and undergo continuous structural rearrangements.

  8. Liquid dimethyl carbonate: a quantum chemical and molecular dynamics study.

    Science.gov (United States)

    Reddy, Sandeep K; Balasubramanian, Sundaram

    2012-12-27

    A density functional theory based Car-Parrinello molecular dynamics simulation of liquid dimethyl carbonate, an environmentally benign solvent, has been carried out to study its structure and dynamics. Conformational excitations of the molecule have been probed in both its gas and liquid phases. While the cis-cis conformer is the global energy minimum and, thus, the most predominant, at ambient conditions a few percent of molecules are present in the cis-trans conformation as well. The latter possesses a dipole moment of around 4.5 D in the liquid state, a value that is nearly five times as large as that for the cis-cis conformer. Dipole-dipole interactions play a crucial role in the formation of small hydrogen bonded clusters of cis-trans conformers in the liquid. The vibrational spectrum of liquid dimethyl carbonate has been obtained from the trajectory and is shown to agree quite well with available experimental data.

  9. Nonlinear dynamics of zigzag molecular chains (in Russian)

    DEFF Research Database (Denmark)

    Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth

    1999-01-01

    models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...... types (such as extension and compression varieties) develop simultaneously in the chain. Accordingly, the inclusion of chain geometry is necessary if physical phenomena are to be described in terms of solitary waves...

  10. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  11. 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.

  12. 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%.

  13. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...... in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces...... the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show...

  14. Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics.

    Science.gov (United States)

    Rauer, Clemens; Nogueira, Juan J; Marquetand, Philipp; González, Leticia

    2016-12-14

    The formation of cyclobutane thymine dimers is one of the most important DNA carcinogenic photolesions induced by ultraviolet irradiation. The long debated question whether thymine dimerization after direct light excitation involves singlet or triplet states is investigated here for the first time using nonadiabatic molecular dynamics simulations. We find that the precursor of this [2 + 2] cycloaddition reaction is the singlet doubly π(2)π*(2) excited state, which is spectroscopically rather dark. Excitation to the bright (1)ππ* or dark (1)nπ* excited states does not lead to thymine dimer formation. In all cases, intersystem crossing to the triplet states is not observed during the simulated time, indicating that ultrafast dimerization occurs in the singlet manifold. The dynamics simulations also show that dimerization takes place only when conformational control happens in the doubly excited state.

  15. Advanced techniques for constrained internal coordinate molecular dynamics.

    Science.gov (United States)

    Wagner, Jeffrey R; Balaraman, Gouthaman S; Niesen, Michiel J M; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

    2013-04-30

    Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle, and torsional coordinates instead of a Cartesian coordinate representation. Freezing high-frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be developed to make the CICMD method robust and widely usable. In this article, we have designed a new framework for (1) initializing velocities for nonindependent CICMD coordinates, (2) efficient computation of center of mass velocity during CICMD simulations, (3) using advanced integrators such as Runge-Kutta, Lobatto, and adaptive CVODE for CICMD simulations, and (4) cancelling out the "flying ice cube effect" that sometimes arises in Nosé-Hoover dynamics. The Generalized Newton-Euler Inverse Mass Operator (GNEIMO) method is an implementation of a CICMD method that we have developed to study protein dynamics. GNEIMO allows for a hierarchy of coarse-grained simulation models based on the ability to rigidly constrain any group of atoms. In this article, we perform tests on the Lobatto and Runge-Kutta integrators to determine optimal simulation parameters. We also implement an adaptive coarse-graining tool using the GNEIMO Python interface. This tool enables the secondary structure-guided "freezing and thawing" of degrees of freedom in the molecule on the fly during molecular dynamics simulations and is shown to fold four proteins to their native topologies. With these advancements, we envision the use of the GNEIMO method in protein structure prediction, structure refinement, and in studying domain motion. Copyright © 2013 Wiley Periodicals, Inc.

  16. Light-induced nonadiabatic dynamics in molecular assemblies and nanostructures

    Science.gov (United States)

    Mitric, Roland

    The combination of mixed quantum-classical dynamics with efficient electronic structure methods was developed in order to simulate the light-induced processes in complex molecules, multichromophoric aggregates and metallic nanostructures. We will demonstrate how the combination of nonadiabatic dynamics with experimental pump-probe techniques such as time-resolved photoelectron imaging (TRPEI) allows to fully resolve the mechanism of excited state relaxation through conical intersections in several prototype organic- and biomolecules. Specifically, the role of the solvent in the excited state relaxation in microsolvated and fully solvated systems will be addressed. Currently there is growing evidence that nonadiabatic relaxation processes also play a fundamental role in determining the efficiency of excitonic transfer or charge injection in multichromophoric assemblies. Since such systems are currently out of the reach of the state-of-the-art quantum chemistry a development of even more efficient quantum chemical approaches is necessary in order to describe the excited state dynamics in such assemblies. For this purpose we have recently developed long-range corrected time-dependent density functional tight binding (LC-TDDFTB) nonadiabatic dynamics and combined it with the QM/MM approach in order to simulate exciton relaxation in complex systems. The applications of the method to the investigation of the optical properties and dynamics in multichromophoric assemblies including stacked pi-conjugated organic chromophores, model molecular crystals as well as self-organized dye aggregates will be presented. Finally, we will address exciton transport dynamics coupled with the light propagation in hybrid exciton-plasmon nanostructures, which represent promising materials fort the development of novel light-harvesting systems.

  17. Dynamic coherence in excitonic molecular complexes under various excitation conditions

    Energy Technology Data Exchange (ETDEWEB)

    Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

    2014-08-17

    Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

  18. Effects of molecular symmetry on quantum reaction dynamics: novel aspects of photoinduced nonadiabatic dynamics.

    Science.gov (United States)

    Al-Jabour, Salih; Leibscher, Monika

    2015-01-15

    Nonadiabatic coupling terms (NACTs) between different electronic states lead to fast radiationless decay in photoexcited molecules. Using molecular symmetry, i.e., symmetry with respect to permutation of identical nuclei and inversion of the molecule in space, the irreducible representations of the NACTs can be determined with a combination of molecular symmetry arguments and quantization rules. Here, we extend these symmetry rules for electronic states and coupling elements and demonstrate the importance of molecular symmetry for nonadiabatic nuclear dynamics. As an example, we consider the NACTs related to the torsion around the CN bond in C5H4NH. We present the results of quantum dynamical simulations of the photoinduced large amplitude torsion on three coupled electronic states and show how the interference between wavepackets leads to radiationless decay, which depends on the symmetry of the NACTs. Moreover, we show that the nuclear spin of the system determines the symmetry of the initial nuclear wave function and thus influences the torsional dynamics. This may open new possibilities for nuclear spin selective laser control of nuclear dynamics.

  19. Huge-scale molecular dynamics simulation of multibubble nuclei

    KAUST Repository

    Watanabe, Hiroshi

    2013-12-01

    We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.

  20. Molecular Dynamics Approach in Designing Thermostable Aspergillus niger Xylanase

    Science.gov (United States)

    Malau, N. D.; Sianturi, M.

    2017-03-01

    Molecular dynamics methods we have applied as a tool in designing thermostable Aspergillus niger Xylanase, by examining Root Mean Square Deviation (RMSD) and The Stability of the Secondary Structure of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Aspergillus niger xylanase (ANX) have been carried at 400K (optimum catalytic temperature) for 2.5 ns and 500K (ANX reported inactive temperature) for 2.5 ns. Analysis have shown that the Root Mean Square Deviation (RMSD) significant increase at higher temperatures compared at optimum temperature and some of the secondary structures of ANX that have been damaged at high temperature. Structural analysis revealed that the fluctuations of the α-helix and β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature.

  1. 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. © 2014 The Protein Society.

  2. Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces

    Science.gov (United States)

    Frankland, Sarah-Jane V.; Clancy, Thomas C.; Hinkley, J. A.; Gates. T. S.

    2008-01-01

    The effect of moisture on adhesives used in aerospace applications can be modeled with chemically specific techniques such as molecular dynamics simulation. In the present study, the surface energy and work of adhesion are calculated for epoxy surfaces and interfaces, respectively, by using molecular dynamics simulation. Modifications are made to current theory to calculate the work of adhesion at the epoxy-epoxy interface with and without water. Quantitative agreement with experimental values is obtained for the surface energy and work of adhesion at the interface without water. The work of adhesion agrees qualitatively with the experimental values for the interface with water: the magnitude is reduced 15% with respect to the value for the interface without water. A variation of 26% in the magnitude is observed depending on the water configuration at a concentration of 1.6 wt%. The methods and modifications to the method that are employed to obtain these values are expected to be applicable for other epoxy adhesives to determine the effects of moisture uptake on their work of adhesion.

  3. Prediction of purification of biopharmeceuticals with molecular dynamics

    Science.gov (United States)

    Ustach, Vincent; Faller, Roland

    Purification of biopharmeceuticals remains the most expensive part of protein-based drug production. In ion exchange chromatography (IEX), prediction of the elution ionic strength of host cell and target proteins has the potential to reduce the parameter space for scale-up of protein production. The complex shape and charge distribution of proteins and pores complicates predictions of the interactions in these systems. All-atom molecular dynamics methods are beyond the scope of computational limits for mass transport regimes. We present a coarse-grained model for proteins for prediction of elution pH and ionic strength. By extending the raspberry model for colloid particles to surface shapes and charge distributions of proteins, we can reproduce the behavior of proteins in IEX. The average charge states of titratatable amino acid residues at relevant pH values are determined by extrapolation from all-atom molecular dynamics at pH 7. The pH specific all-atom electrostatic field is then mapped onto the coarse-grained surface beads of the raspberry particle. The hydrodynamics are reproduced with the lattice-Boltzmann scheme. This combination of methods allows very long simulation times. The model is being validated for known elution procedures by comparing the data with experiments. Defense Threat Reduction Agency (Grant Number HDTRA1-15-1-0054).

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

    Science.gov (United States)

    Bolhuis, Peter

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

  5. Vision-Augmented Molecular Dynamics Simulation of Nanoindentation

    Directory of Open Access Journals (Sweden)

    Rajab Al-Sayegh

    2015-01-01

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

  6. The Art of Molecular Dynamics Simulation (by D. C. Rapaport)

    Science.gov (United States)

    Molner, Stephen P.

    1999-02-01

    Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95. This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a

  7. EDITORIAL: 18th European Conference on Dynamics of Molecular Systems 18th European Conference on Dynamics of Molecular Systems

    Science.gov (United States)

    Varandas, A. J. C.

    2011-08-01

    This special section of Comments on Atomic, Molecular and Optical Physics (CAMOP) in Physica Scripta collects some of the papers that have been presented at the 18th European Conference on Dynamics of Molecular Systems MOLEC 2010 held in September 2010 in Curia, Portugal, as part of a series of biennial MOLEC conferences. This started in 1976 in Trento, Italy, and has continued, visiting 17 cities in 11 countries, namely Denmark, The Netherlands, Israel, France, Italy, Germany, Czech Republic, Spain, United Kingdom, Turkey and Russia. Following the MOLEC tradition, the scientific programme of the Curia meeting focused on experimental and theoretical studies of molecular interactions, collision dynamics, spectroscopy, and related fields. It included invited speakers from 22 countries, who were asked to summarize the problems reported in their presentations with the objective of revealing the current thinking of leading researchers in atomic, molecular and optical physics. It is hoped that their authoritative contributions presented in this CAMOP special section will also appeal to non-specialists through their clear and broad introductions to the field as well as references to the accessible literature. This CAMOP special section comprises ten contributions, which cover theoretical studies on the electronic structure of molecules and clusters as well as dynamics of elastic, inelastic and reactive encounters between atoms, molecules, ions, clusters and surfaces. Specifically, it includes electronic structure calculations using the traditional coupled-cluster method (Barreto et al 028111), the electron-attached equation-of-motion coupled cluster method (Hansen et al 028110), the diffusion Monte Carlo method (López-Durán et al 028107) and the path-integral Monte Carlo method (Barragán et al 028109). The contributions on molecular dynamics include on-the-fly quasi-classical trajectories on a five-atom molecule (Yu 028104), quantum reaction dynamics on triatomics

  8. Combining optimal control theory and molecular dynamics for protein folding.

    Directory of Open Access Journals (Sweden)

    Yaman Arkun

    Full Text Available A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD. In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  9. Ultrafast Vibrational Dynamics of Water Disentangled by Reverse Nonequilibrium Ab Initio Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Yuki Nagata

    2015-04-01

    Full Text Available Water is a unique solvent with strong, yet highly dynamic, intermolecular interactions. Many insights into this distinctive liquid have been obtained using ultrafast vibrational spectroscopy of water’s O-H stretch vibration. However, it has been challenging to separate the different contributions to the dynamics of the O-H stretch vibration in H_{2}O. Here, we present a novel nonequilibrium molecular dynamics (NEMD algorithm that allows for a detailed picture of water vibrational dynamics by generating nonequilibrium vibrationally excited states at targeted vibrational frequencies. Our ab initio NEMD simulations reproduce the experimentally observed time scales of vibrational dynamics in H_{2}O. The approach presented in this work uniquely disentangles the effects on the vibrational dynamics of four contributions: the delocalization of the O-H stretch mode, structural dynamics of the hydrogen bonded network, intramolecular coupling within water molecules, and intermolecular coupling between water molecules (near-resonant energy transfer between O-H groups. Our results illustrate that intermolecular energy transfer and the delocalization of the O-H stretch mode are particularly important for the spectral diffusion in H_{2}O.

  10. Molecular dynamics study of naturally existing cavity couplings in proteins.

    Science.gov (United States)

    Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier

    2015-01-01

    Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.

  11. Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

    Energy Technology Data Exchange (ETDEWEB)

    Fattebert, J.-L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Richards, D.F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Glosli, J.N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2012-12-01

    We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·106 particles on 65,536 MPI tasks.

  12. Introduction to practice of molecular simulation molecular dynamics, Monte Carlo, Brownian dynamics, lattice Boltzmann and dissipative particle dynamics

    CERN Document Server

    Satoh, Akira

    2010-01-01

    This book presents the most important and main concepts of the molecular and microsimulation techniques. It enables readers to improve their skills in developing simulation programs by providing physical problems and sample simulation programs for them to use. Provides tools to develop skills in developing simulations programs Includes sample simulation programs for the reader to use Appendix explains Fortran and C languages in simple terms to allow the non-expert to use them.

  13. Molecular model and ReaxFF molecular dynamics simulation of coal vitrinite pyrolysis.

    Science.gov (United States)

    Li, Wu; Zhu, Yan-ming; Wang, Geoff; Wang, Yang; Liu, Yu

    2015-08-01

    Vitrinite in coal, the mainly generating methane maceral, plays an important role in hydrocarbon generation of coal. This study aims at obtaining products formation mechanism of vitrinite pyrolysis, and hence determining the chemical bond, molecular liquefaction activity, and reactions mechanism of methane and C2-4 during pyrolysis. The ReaxFF molecular dynamics (MD) simulation was carried out at temperature of 1500 K in order to investigate the mechanism of vitrinite pyrolysis. Initially, a minimum energy conformational structure model was constrained by a combination of elemental and carbon-13 nuclear magnetic resonance ((13)C NMR) literature data. The model analysis shows the chemical and physical parameters of vitrinite pyrolysis are broadly consistent with the experimental data. Based on the molecular model, ReaxFF MD simulations further provide information of unimolecule such as bond length, and chemical shift, and hence the total population and energy of main products. Molecules bond and pyrolysis fragments, based on active bond analyzed, revealed pyrolysis products of single vitrinite molecule with aliphatic C-C bond, especially ring and chain aliphatic as liquefaction activity. The molecular cell whose density is 0.9 g/cm(3) with lowest energy accords with the experimental density 1.33 g/cm(3). The content of main products after pyrolysis, classifying as CH4, H2O, and H2, was changed along with the increasing temperature. The gas molecule, fragments and generation pathways of CO2, H2, CH4, and C2H6 were also elucidated. These results show agreement with experimental observations, implying that MD simulation can provide reasonable explanation for the reaction processes involved in coal vitrinite pyrolysis. Thus the mechanism of coal hydrocarbon generation was revealed at the molecular level.

  14. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Science.gov (United States)

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

    2015-10-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  15. Molecular dynamics characterization of as-implanted damage in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Ivan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)]. E-mail: ivasan@ele.uva.es; Marques, Luis A. [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Pelaz, Lourdes [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Lopez, Pedro [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Aboy, Maria [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Barbolla, Juan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)

    2005-12-05

    We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions.

  16. Interactions in charged colloidal suspensions: A molecular dynamics simulation study

    Science.gov (United States)

    Padidela, Uday Kumar; Behera, Raghu Nath

    2017-07-01

    Colloidal suspensions are extensively used in everyday life and find several applications in the pharmaceutical, chemical, food industries, etc. We present the classical molecular dynamics simulation results of the structural and transport properties of charged colloidal suspensions as a function of its size, charge and concentration. The system is viewed as a two-component (colloids and counterions) primitive model consisting of spherical colloid particle (macroion) and the counterions (micro-particles), which are treated explicitly. The solvent is treated as dielectric continuum. A systematic trend in the radial distribution functions g(r), potential of mean force W(r), different thermodynamic properties and diffusion coefficients is obtained as a function of colloid charge, size and concentration. An attractive minimum in W(r) is obtained at short interparticle distance.

  17. Molecular dynamic simulations of the sputtering of multilayer organic systems

    CERN Document Server

    Postawa, Z; Piaskowy, J; Krantzman, K; Winograd, N; Garrison, B J

    2003-01-01

    Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag left brace 1 1 1 right brace surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.

  18. Thermal conductivity of penta-graphene from molecular dynamics study.

    Science.gov (United States)

    Xu, Wen; Zhang, Gang; Li, Baowen

    2015-10-21

    Using classical equilibrium molecular dynamics simulations and applying the original Tersoff interatomic potential, we study the thermal transport property of the latest two dimensional carbon allotrope, penta-graphene. It is predicted that its room-temperature thermal conductivity is about 167 W/mK, which is much lower than that of graphene. With normal mode decomposition, the accumulated thermal conductivity with respect to phonon frequency and mean free path is analyzed. It is found that the acoustic phonons make a contribution of about 90% to the thermal conductivity, and phonons with mean free paths larger than 100 nm make a contribution over 50%. We demonstrate that the remarkably lower thermal conductivity of penta-graphene compared with graphene results from the lower phonon group velocities and fewer collective phonon excitations. Our study highlights the importance of structure-property relationship and provides better understanding of thermal transport property and valuable insight into thermal management of penta-graphene.

  19. Dynamical image-charge effect in molecular tunnel junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun; Thygesen, Kristian Sommer

    2014-01-01

    When an electron tunnels between two metal contacts it temporarily induces an image charge (IC) in the electrodes which acts back on the tunneling electron. It is usually assumed that the IC forms instantaneously such that a static model for the image potential applies. Here we investigate how...... the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z(2), where Z is the quasiparticle renormalization factor, compared to the static IC approximation...... that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels....

  20. Molecular dynamics simulation of membrane in room temperature ionic liquids

    Science.gov (United States)

    Theng, Soong Guan; Jumbri, Khairulazhar bin; Wirzal, Mohd Dzul Hakim

    2017-10-01

    The polyvinylidene difluoride (PVDF) membrane has been a popular material in membrane separation process. In this work, molecular dynamic simulation was done on the PVDF membrane with 100 wt% IL and 50 wt% IL in GROningen MAchine for Chemical Simulations (GROMACS). The results was evaluated based on potential energy, root mean square deviation (RMSD) and radial distribution function (RDF). The stability and interaction of PVDF were evaluated. Results reveal that PVDF has a stronger interaction to [C2bim]+ cation compared to water and bromine anion. Both potential energy and RMSD were lower when the weight percentage of IL is higher. This indicates that the IL is able to stabilize the PVDF structure. RMSD reveals that [C2bim]+ cation is dominant at short distance (less than 1 nm), indicating that strong interaction of cation to PVDF. This understanding of the behavior of PVDF-IL could be used as a reference for future development of stronger membrane.

  1. Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes. Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...... of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...

  2. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes.1,2,3 Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...... computations of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems.3,16,17,18 For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence...

  3. Molecular Dynamics on FPGA Based Accelerated Processing Units

    Directory of Open Access Journals (Sweden)

    Maliţa Mihaela

    2017-01-01

    Full Text Available One of the main problems in providing the amount of computation requested by the Molecular Dynamic domain is to offer an appropriate architectural environment for solving all the aspects of the intense parts of the involved computation. Current solutions accelerate only partially the intense computation – forces com putation & position and speed updates, which represents around 75% from the total computational effort – thus limiting the help provided by the parallel computing resources involved. The aim of this paper is to introduce a parallel accelerator featured with functions able to add to the accelerated functions the neighbourhood list building, which represent around 25% from the total computation. Thus, accelerations higher than the current ~ 4× are expected. Our proposal, the MapReduce Accelerator, is evaluated using the Gromacs system. The Martini water example, running on a cycle accurate simulator, is used to evaluate the speed-up and the energy.

  4. Isomorphic phase transformation in shocked cerium using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Dupont, Virginie [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Chen, Shao - Ping [Los Alamos National Laboratory

    2010-08-12

    Cerium (Ce) undergoes a significant ({approx}16%) volume collapse associated with an isomorphic fcc-fcc phase transformation when subject to compressive loading. We present here a new Embedded Atom Method (EAM) potential for Cerium that models two minima for the two fcc phases. We show results from its use in Molecular Dynamics (MD) simulations of Ce samples subjected to shocks with pressures ranging from 0.5 to 25 GPa. A split wave structure is observed, with an elastic precursor followed by a plastic wave. The plastic wave causes the expected fcc-fcc phase transformation. Comparisons to experiments and MD simulations on Cesium (Cs) indicate that three waves could be observed. The construction of the EAM potential may be the source of the difference.

  5. Molecular dynamics of shock loading of metals with defects

    Energy Technology Data Exchange (ETDEWEB)

    Belak, J.F. [Lawrence Livermore National Lab., CA (United States)

    1997-12-31

    The finite rise time of shock waves in metals is commonly attributed to dissipative or viscous behavior of the metal. This viscous or plastic behavior is commonly attributed to the motion of defects such as dislocations. Despite this intuitive understanding, the experimental observation of defect motion or nucleation during shock loading has not been possible due to the short time scales involved. Molecular dynamics modeling with realistic interatomic potentials can provide some insight into defect motion during shock loading. However, until quite recently, the length scale required to accurately represent a metal with defects has been beyond the scope of even the most powerful supercomputers. Here, the author presents simulations of the shock response of single defects and indicate how simulation might provide some insight into the shock loading of metals.

  6. Water response to intense electric fields: A molecular dynamics study.

    Science.gov (United States)

    Marracino, Paolo; Liberti, Micaela; d'Inzeo, Guglielmo; Apollonio, Francesca

    2015-07-01

    This paper investigated polarization properties of water molecules in close proximity to an ionic charge in the presence of external electric fields by using an approach based on simulations at the atomic level. We chose sodium and chloride ions in water as examples of dilute ionic solutions and used molecular dynamics simulations to systematically investigate the influence of an external static electric field on structural, dipolar, and polarization properties of water near charged ions. Results showed that a threshold electric field higher than 10(8) V/m is needed to affect water polarization and increase mean dipole moment of water molecules close to the ion. A similar threshold holds for water permittivity profiles, although a field 10× higher is needed to ensure that water permittivity is almost constant independently of the position close to the ion. Electric fields of such intensities can greatly enhance polarizability of water in hydration shells around ions. © 2015 Wiley Periodicals, Inc.

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

    Science.gov (United States)

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

    2017-10-01

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

  8. Molecular dynamics simulation of gold cluster growth during sputter deposition

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, J. W., E-mail: abraham@theo-physik.uni-kiel.de; Bonitz, M., E-mail: bonitz@theo-physik.uni-kiel.de [Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, Leibnizstraße 15, D-24098 Kiel (Germany); Strunskus, T.; Faupel, F. [Institut für Materialwissenschaft, Lehrstuhl für Materialverbunde, Christian-Albrechts-Universität zu Kiel, Kaiserstraße 2, D-24143 Kiel (Germany)

    2016-05-14

    We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

  9. Substrate recognition by norovirus polymerase: microsecond molecular dynamics study

    Science.gov (United States)

    Maláč, Kamil; Barvík, Ivan

    2013-04-01

    Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP ( C5' -O5'-C4'-O4'), cocCTP ( C5' -O5'-C4'- C4'') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP—substrate, 2dCTP—poor substrate, coCTP—chain terminator, cocCTP—inhibitor). Moreover, extremely rare events—as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement—were captured.

  10. 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.

  11. Determination of Reference Chemical Potential Using Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Krishnadeo Jatkar

    2010-01-01

    Full Text Available A new method implementing molecular dynamics (MD simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining Δ0, the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.

  12. Molecular dynamics study of a polymeric reverse osmosis membrane.

    Energy Technology Data Exchange (ETDEWEB)

    Harder, E.; Walters, D. E.; Bodnar, Y. D.; Faibish, R. S.; Roux, B. (Nuclear Engineering Division); (Univ. of Chicago); (Rosalind Franklin Univ. of Medicine and Science)

    2009-07-30

    Molecular dynamics (MD) simulations are used to investigate the properties of an atomic model of an aromatic polyamide reverse osmosis membrane. The monomers forming the polymeric membrane are cross-linked progressively on the basis of a heuristic distance criterion during MD simulations until the system interconnectivity reaches completion. Equilibrium MD simulations of the hydrated membrane are then used to determine the density and diffusivity of water within the membrane. Given a 3 MPa pressure differential and a 0.125 {micro}m width membrane, the simulated water flux is calculated to be 1.4 x 10{sup -6} m/s, which is in fair agreement with an experimental flux measurement of 7.7 x 10{sup -6} m/s.

  13. Molecular dynamics study of the thermal expansion coefficient of silicon

    Science.gov (United States)

    Nejat Pishkenari, Hossein; Mohagheghian, Erfan; Rasouli, Ali

    2016-12-01

    Due to the growing applications of silicon in nano-scale systems, a molecular dynamics approach is employed to investigate thermal properties of silicon. Since simulation results rely upon interatomic potentials, thermal expansion coefficient (TEC) and lattice constant of bulk silicon have been obtained using different potentials (SW, Tersoff, MEAM, and EDIP) and results indicate that SW has a better agreement with the experimental observations. To investigate effect of size on TEC of silicon nanowires, further simulations are performed using SW potential. To this end, silicon nanowires of different sizes are examined and their TEC is calculated by averaging in different directions ([100], [110], [111], and [112]) and various temperatures. Results show that as the size increases, due to the decrease of the surface effects, TEC approaches its bulk value.

  14. Guiding lead optimization with GPCR structure modeling and molecular dynamics.

    Science.gov (United States)

    Heifetz, Alexander; James, Tim; Morao, Inaki; Bodkin, Michael J; Biggin, Philip C

    2016-10-01

    G-protein coupled receptor (GPCR) modeling approaches are widely used in the hit-to-lead and lead optimization stages of drug discovery. Modern protocols that involve molecular dynamics simulation can address key issues such as the free energy of binding (affinity), ligand-induced GPCR flexibility, ligand binding kinetics, conserved water positions and their role in ligand binding and the effects of mutations. The goals of these calculations are to predict the structures of the complexes between existing ligands and their receptors, to understand the key interactions and to utilize these insights in the design of new molecules with improved binding, selectivity or other pharmacological properties. In this review we present a brief survey of various computational approaches illustrated through a hierarchical GPCR modeling protocol and its prospective application in three industrial drug discovery projects. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Isomorphic phase transformation in shocked Cerium using molecular dynamics

    Directory of Open Access Journals (Sweden)

    Germann T.C.

    2011-01-01

    Full Text Available Cerium (Ce undergoes a significant (∼16% volume collapse associated with an isomorphic fcc-fcc phase transformation when subject to compressive loading. We present here a new Embedded Atom Method (EAM potential for Cerium that models two minima for the two fcc phases. We show results from its use in Molecular Dynamics (MD simulations of Ce samples subjected to shocks with pressures ranging from 0.5 to 25 GPa. A split wave structure is observed, with an elastic precursor followed by a plastic wave. The plastic wave causes the expected fcc-fcc phase transformation. Comparisons to experiments and MD simulations on Cesium (Cs indicate that three waves could be observed. The construction of the EAM potential may be the source of the difference.

  16. Extension of variational space in the antisymmetrized molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hirata, Yuichi; Ohnishi, Akira [Hokkaido Univ., Sapporo (Japan). Faculty of Science; Nara, Yasushi; Harada, Toru

    1997-05-01

    With starting from a framework of AMD (antisymmetrized molecular dynamics), {Xi}{sup -} reaction at rest was simulated by extended AMD which the width of Gauss wave packet of a particle wave function was applied to the time-dependence vibrational parameter. The results by AMD showed to produce many amount of complex nucleus with bounded two {Lambda}-particles, but that by extended AMD approached the experimental result which {Lambda}-particle was easily released from the complex nuclei. However, AMD and the extended AMD were able to describe only emission of {Lambda}-particle and not fragmentation of reaction ({Xi}{sup -}+{sup 12}C{yields}{sub {Lambda}}{sup 4}H+{sub {Lambda}}{sup 9}Be). (S.Y.)

  17. A hybrid algorithm for parallel molecular dynamics simulations

    Science.gov (United States)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  18. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  19. Molecular dynamics of poly(N-vinylcaprolactam) hydrate

    CERN Document Server

    Lebedev, V T; Toeroek, G; Cser, L; Kali, G

    2002-01-01

    Poly(N-vinylcaprolactam)-D sub 2 O has been studied by Neutron Spin Echo (NSE) in the temperature range from -60 C to +40 C. Hydration (propor to 7 D sub 2 O molecules per chain unit) transforms the rigid-chain polymer into an elastomer, making the glass-transition temperature drop from T sub G =147 C (dry polymer) to T sub G =-20 C. The hydration shell, created by hydrogen bonds of water molecules with C=O groups, remains stable up to propor to 50 C. The molecular mobility is enhanced by the addition of water, showing a maximum in the window T=-20 to +5 C. The anomalous dynamics was studied in the time domain t=0.003-5 ns (momentum transfer q=0.55 nm sup - sup 1), and demonstrated the hybridisation of transversal modes and reputations of the chains. (orig.)

  20. Molecular dynamics simulations on the ionic current through charged nanopores

    Science.gov (United States)

    Xue, J. M.; Zou, X. Q.; Xie, Y. B.; Wang, Y. G.

    2009-05-01

    Molecular dynamics (MD) simulation was performed to investigate the ionic current through charged nanopores, and the results were compared with the calculation of Poisson-Nernst-Planck (PNP) equations based on the continuum theory. Results show that the current obtained by MD simulation is lower than the current calculated by PNP equations, and the discrepancy depends on the surface charge density of the nanopores. Also, MD simulation shows that the contribution of the electro-osmotic flow effect on ionic current could be 10% higher than the results obtained by solving PNP equations. Since the PNP equations do not take the effect of the pore wall into consideration, we suggest that adjusting the diffusion coefficient in the PNP equations can obtain more accurate results when calculating the ionic current through charged nanopores.

  1. Molecular dynamics study of shock compression in porous silica glass

    Science.gov (United States)

    Jones, Keith; Lane, J. Matthew D.; Vogler, Tracy J.

    2017-06-01

    The shock response of porous amorphous silica is investigated using classical molecular dynamics, over a range of porosity ranging from fully dense (2.21 g/cc) down to 0.14 g/cc. We observe an enhanced densification in the Hugoniot response at initial porosities above 50 %, and the effect increases with increasing porosity. In the lowest initial densities, after an initial compression response, the systems expand with increased pressure. These results show good agreement with experiments. Mechanisms leading to enhanced densification will be explored, which appear to differ from mechanisms observed in similar studies in silicon. Sandia National Laboratories is a multi mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  2. Molecular dynamics simulation of deformation twin in rocksalt vanadium nitride

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Tao [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); Peng, Xianghe, E-mail: xhpeng@cqu.edu.cn [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044 (China); Zhao, Yinbo [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); Li, Tengfei [College of Materials Science and Engineering, Chongqing University, Chongqing 400044 (China); Li, Qibin [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); Wang, Zhongchang, E-mail: zcwang@wpi-aimr.tohoku.ac.jp [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan)

    2016-08-05

    We perform molecular dynamics simulation of nano-indentation with a cylindrical indenter to investigate the formation mechanism of deformation twin in vanadium nitride (VN) with a rocksalt structure. We find that the deformation twins occur during the loading stage, and subsequently conduct a systematic analysis of nucleation, propagation and thickening of a deformation twin. We find that the nucleation of a partial dislocation and its propagation to form a stacking fault are premise of deformation twin formation. The sequential nucleation and propagation of partial dislocation on adjacent parallel {111} planes are found to cause the thickening of the deformation twin. Moreover, the deformation twins can exist in VN at room temperature. - Highlights: • MD simulations of indentation are performed to study the deformation twin in VN. • The deformation twins can occur in VN during the loading stage. • The nucleation, propagation and thickening of a deformation twin are analyzed. • The deformation twins can exist in VN at room temperature.

  3. Isentropic compression of deuterium by quantum molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Chentsov, A.V. [Joint Institute for High Temperatures, Moscow (Russian Federation); Levashov, P.R. [Joint Institute for High Temperatures, Moscow (Russian Federation); Moscow Intitute of Physics and Technology, State University, Moscow (Russian Federation)

    2012-01-15

    In this work we present our calculations of the compression isentrope of deuterium. We use an ab initio molecular dynamics approach to compute pressure and internal energy of dense deuterium in the range of temperatures 293-25000 K and densities 0.9-4.3 g/cm{sup 3}. We then restore the isentrope and compare the results with experimental data and other theories. The position of the calculated isentrope slightly depends on the initial point and agrees with the low-pressure part and the highest-pressure point of the measurements. However, we do not observe the density jump registered experimentally at P{approx}130 GPa (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  4. Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

    Directory of Open Access Journals (Sweden)

    Sposito Garrison

    2002-09-01

    Full Text Available Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

  5. Molecular dynamics study of enhanced Man5B enzymatic activity.

    Science.gov (United States)

    Bernardi, Rafael C; Cann, Isaac; Schulten, Klaus

    2014-01-01

    Biofuels are a well-known alternative to the largely used fossil-derived fuels, however the competition with food production is an ethical dilemma. Fortunately a solution is offered by second-generation biofuels which can be produced from agricultural waste or, more specifically, from plant cell wall polysaccharides. The conversion process involves typically enzymatic hydrolysis of lignocellulosic biomass and then separation of its constituent sugars that are further fermented to produce ethanol. Over the years several technologies have been developed that allow this conversion process to occur and the objective is now to make this process cost-competitive in today's markets. We observe that reduction of enzymatic efficiency in the presence of gluco-oligosaccharides is associated with a loss of the enzyme's flexibility, the latter being required to bind new substrate, while the presence of manno-oligosaccharides does not pose this problem. Molecular dynamics simulations identify key contacts between substrates and the enzyme catalytic pocket that might be modified through site-directed mutagenesis to prevent loss of enzymatic efficiency. Based on previous experimental studies and the new molecular dynamics data, we suggest that cellohexaose in the active site pocket slows down or even inhibits Man5B enzymatic activity. The assumption of such a mechanism is reasonable since when the gluco-oligosaccharide substrate is attached to the catalytic pocket it takes much longer to leave the pocket and thus prevents other substrates from reaching the active site. The insight is of crucial importance since the inhibition of enzymes by the enzymatic product or by an unsuitable substrate is a major technological problem in reducing the competitiveness of second-generation biofuel production.

  6. A domain specific language for performance portable molecular dynamics algorithms

    Science.gov (United States)

    Saunders, William Robert; Grant, James; Müller, Eike Hermann

    2018-03-01

    Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

  7. Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups.

    Science.gov (United States)

    Kurbatov, A O; Balabaev, N K; Mazo, M A; Kramarenko, E Yu

    2018-01-07

    Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.

  8. Polarizable molecular dynamics in a polarizable continuum solvent.

    Science.gov (United States)

    Lipparini, Filippo; Lagardère, Louis; Raynaud, Christophe; Stamm, Benjamin; Cancès, Eric; Mennucci, Benedetta; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip

    2015-02-10

    We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.

  9. Multiscale implementation of infinite-swap replica exchange molecular dynamics

    Science.gov (United States)

    Yu, Tang-Qing; Lu, Jianfeng; Abrams, Cameron F.; Vanden-Eijnden, Eric

    2016-01-01

    Replica exchange molecular dynamics (REMD) is a popular method to accelerate conformational sampling of complex molecular systems. The idea is to run several replicas of the system in parallel at different temperatures that are swapped periodically. These swaps are typically attempted every few MD steps and accepted or rejected according to a Metropolis–Hastings criterion. This guarantees that the joint distribution of the composite system of replicas is the normalized sum of the symmetrized product of the canonical distributions of these replicas at the different temperatures. Here we propose a different implementation of REMD in which (i) the swaps obey a continuous-time Markov jump process implemented via Gillespie’s stochastic simulation algorithm (SSA), which also samples exactly the aforementioned joint distribution and has the advantage of being rejection free, and (ii) this REMD-SSA is combined with the heterogeneous multiscale method to accelerate the rate of the swaps and reach the so-called infinite-swap limit that is known to optimize sampling efficiency. The method is easy to implement and can be trivially parallelized. Here we illustrate its accuracy and efficiency on the examples of alanine dipeptide in vacuum and C-terminal β-hairpin of protein G in explicit solvent. In this latter example, our results indicate that the landscape of the protein is a triple funnel with two folded structures and one misfolded structure that are stabilized by H-bonds. PMID:27698148

  10. Excipient-assisted vinpocetine nanoparticles: experiments and molecular dynamic simulations.

    Science.gov (United States)

    Li, Cai-Xia; Wang, Hao-Bo; Oppong, Daniel; Wang, Jie-Xin; Chen, Jian-Feng; Le, Yuan

    2014-11-03

    Hydrophilic excipients can be used to increase the solubility and bioavailability of poorly soluble drugs. In this work, the conventional water-soluble pharmaceutical excipients hydroxypropylmethylcellulose (HPMC), polyvinylpyrrolidone (PVP), and lactose (LAC) were used as solid supports to prevent drug nanoparticles from aggregation and enhance drug dissolution. Excipient-assisted vinpocetine (VIN) nanoparticles were prepared by reactive precipitation. The analysis results indicated that HPMC was a suitable excipient to prepare VIN nanoparticles. VIN/HPMC nanoparticles had a mean size of 130 nm within a narrow distribution. The dissolution rate of VIN nanoparticles was significantly faster than those of a physical mixture of VIN/HPMC and raw VIN. VIN/HPMC nanoparticles had a higher dissolution profile than VIN/PVP and VIN/LAC nanoparticles. Besides, molecular dynamics (MD) simulation was applied to investigate the molecular interactions between VIN and excipients. The calculated results revealed that VIN interacted with excipients by Coulomb and Lennard-Jones (LJ) interactions. Few hydrogen bonds were formed between VIN and excipients. The HPMC affording smaller particle size may be a result of the stronger interactions between VIN and HPMC (mainly LJ interaction) and the property of HPMC. These characteristics may greatly influence the adsorption behavior and may be the crucial parameter for the better performance of HPMC.

  11. 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...

  12. Molecular dynamics simulation of pervaporation in zeolite membranes

    Science.gov (United States)

    Jia, W.; Murad, S.

    The pervaporation separation of liquid mixtures of water/ethanol and water/methanol using three zeolite (Silicalite, NaA and Chabazite) membranes has been examined using the method of molecular dynamics. The main goal of this study was to identify intermolecular interactions between water, methanol, ethanol and the membrane surface that play a critical role in the separations. This would then allow better membranes to be designed more efficiently and systematically than the trial-and-error procedures often being used. Our simulations correctly exhibited all the qualitative experimental observations for these systems, including the hydrophobic or hydrophilic behaviour of zeolite membranes. The simulations showed that, for Silicalite zeolite, the separation is strongly influenced by the selective adsorption of ethanol. The separation factor, as a consequence, increases almost exponentially as the ethanol composition decreases. For ethanol dehydration in NaA and Chabazite, pore size was found to play a very important role in the separation; very high separation factors were therefore possible. Simulations were also used to investigate the effect of pore structure, feed compositions and operating conditions on the pervaporation efficiency. Finally, our simulations also demonstrated that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential pervaporation separation applications. Simulations can cost only a small fraction of an experiment, and can therefore be used to design experiments most likely to be successful.

  13. Molecular Dynamics study on the Micellization of Rhamnolipids.

    Science.gov (United States)

    Munusamy, Elango; Schwartz, Steven D.

    2015-03-01

    Oil spills have become one of the most serious environmental and ecological problems owing to the growth of oil exploration, production and transportation. Millions of gallons of crude oil and refined products are spilled into marine waters worldwide each year. Large volumes of surfactants are applied to the ocean as a remediation strategy. Environmental and toxicity issues arise when such a voluminous amounts of chemical surfactants are applied. One prospective solution to this problem is to use greener surfactants that possess excellent biodegradation and toxicity characteristics relative to existing classes of commonly used surfactants. In this context, we are interested in designing and developing greener surfactants that are patterned after naturally occurring glycolipids. In the present work, we concentrate on one of the more commonly studied glycolipid, rhamnolipid (Rha1C10C10) . Despite the available experimental data, the molecular structure, shape and geometry of micelles formed by rhamnolipid is unknown. Molecular Dynamics (MD) simulations were performed to understand the aggregation behavior of rhamnolipids in aqueous solution and at air-water interface. All calculations were performed in NPT ensembles at 300 K using NAMD 2.8, a parallel code designed for high-performance simulation of large biological macromolecule using the CHARMM force field. The results obtained from MD simulations on the aggregation of rhamnolipids in water and at air-water interface will be presented.

  14. Study of thermal scattering for organic tissues through molecular dynamics

    Directory of Open Access Journals (Sweden)

    Ramos Ricardo

    2017-01-01

    Full Text Available Boron Neutron Capture Therapy (BNCT is an experimental therapy for tumors which is based on the nuclear reaction that occurs when 10B is irradiated with thermal neutrons. Calculations for BNCT with Monte Carlo N-Particle (MCNP take into account the thermal scattering treatment for hydrogen bound in bulk water for any organic tissue. However, in these tissues, hydrogen is also present in macromolecules (protein, lipids, etc. and in confined water. Thermal scattering cross section for hydrogen in an organic tissue can be determined by calculating the scattering law S(α,β. This function can be obtained with the nuclear data processing system NJOY from the vibrational frequency spectrum of an atom in a molecular system. We performed calculations of the frequency spectrum from molecular dynamics simulations using the program GROMACS. Systems composed of a peptide in a water box were considered, with different proportions of water molecules. All-atom potentials for modeling this molecules were used in order to represent the internal vibrational normal modes for the atoms of hydrogen. The results showed several internal normal modes that in the case of hydrogen bound in bulk water do not appear.

  15. Study of thermal scattering for organic tissues through molecular dynamics

    Science.gov (United States)

    Ramos, Ricardo; Cantargi, Florencia; Marquez Damian, Jose Ignacio; Gonçalves-Carralves, Manuel Sztejnberg

    2017-09-01

    Boron Neutron Capture Therapy (BNCT) is an experimental therapy for tumors which is based on the nuclear reaction that occurs when 10B is irradiated with thermal neutrons. Calculations for BNCT with Monte Carlo N-Particle (MCNP) take into account the thermal scattering treatment for hydrogen bound in bulk water for any organic tissue. However, in these tissues, hydrogen is also present in macromolecules (protein, lipids, etc.) and in confined water. Thermal scattering cross section for hydrogen in an organic tissue can be determined by calculating the scattering law S(α,β). This function can be obtained with the nuclear data processing system NJOY from the vibrational frequency spectrum of an atom in a molecular system. We performed calculations of the frequency spectrum from molecular dynamics simulations using the program GROMACS. Systems composed of a peptide in a water box were considered, with different proportions of water molecules. All-atom potentials for modeling this molecules were used in order to represent the internal vibrational normal modes for the atoms of hydrogen. The results showed several internal normal modes that in the case of hydrogen bound in bulk water do not appear.

  16. Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Nivedita Rai

    2015-01-01

    Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

  17. Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

    Science.gov (United States)

    Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

    2017-08-30

    Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  18. Molecular Dynamics of the ZIKA Virus NS3 Helicase

    Science.gov (United States)

    Raubenolt, Bryan; Rick, Steven; The Rick Group Team

    The recent outbreaks of the ZIKA virus (ZIKV) and its connection to microcephaly in newborns has raised its awareness as a global threat and many scientific research efforts are currently underway in attempt to create a vaccine. Molecular Dynamics is a powerful method of investigating the physical behavior of protein complexes. ZIKV is comprised of 3 structural and 7 nonstructural proteins. The NS3 helicase protein appears to play a significant role in the replication complex and its inhibition could be a crucial source of antiviral drug design. This research primarily focuses on studying the structural dynamics, over the course of few hundred nanoseconds, of NS3 helicase in the free state, as well as in complex form with human ssRNA, ATP, and an analogue of GTP. RMSD and RMSF plots of each simulation will provide details on the forces involved in the overall stability of the active and inactive states. Furthermore, free energy calculations on a per residue level will reveal the most interactive residues between states and ultimately the primary driving force behind these interactions. Together these analyses will provide highly relevant information on the binding surface chemistry and thus serve as the basis for potential drug design.

  19. Molecular Wavepacket Dynamics at a Jahn-Teller Conical Intersection

    Science.gov (United States)

    Makhija, Varun; Veyrinas, Kevin; Boguslavskiy, Andrey E.; Forbes, Ruaridh; Wilkinson, Iain; Moffatt, Doug; Neville, Simon; Schuurman, Michael; Lausten, Rune; Stolow, Albert

    2017-04-01

    According to the Jahn-Teller theorem, any symmetric configuration of atoms in an electronically degenerate molecular state is unstable and distorts to a configuration of lower symmetry, hence lifting the degeneracy. Jahn-Teller dynamics feature in numerous, highly symmetric systems, such as fullerenes and in doped rare-earth magnetites where they underly the phenomenon of ``colossal magneto-resistance''. Here, we use ultrafast time-resolved photoelectron velocity-map imaging (VMI) to study the fundamental Jahn-Teller dynamics in an excited state of isolated ammonia (NH3) molecules. Supersonically cooled NH3 is resonantly excited by a 160 nm, 80 fs pump pulse. A time delayed 400 nm, 40 fs probe pulse photoionizes the molecule and the kinetic energy and angular distribution of the ejected photoelectron is measured as a function of time. Dramatic changes in the time-dependent angular distributions are observed, which reveal details of non-adiabatic wavepacket propagation on the coupled Jahn-Teller potential surfaces.

  20. Peptide dimerization-dissociation rates from replica exchange molecular dynamics

    Science.gov (United States)

    Leahy, Cathal T.; Kells, Adam; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

    2017-10-01

    We show how accurate rates of formation and dissociation of peptide dimers can be calculated using direct transition counting (DTC) from replica-exchange molecular dynamics (REMD) simulations. First, continuous trajectories corresponding to system replicas evolving at different temperatures are used to assign conformational states. Second, we analyze the entire REMD data to calculate the corresponding rates at each temperature directly from the number of transition counts. Finally, we compare the kinetics extracted directly, using the DTC method, with indirect estimations based on trajectory likelihood maximization using short-time propagators and on decay rates of state autocorrelation functions. For systems with relatively low-dimensional intrinsic conformational dynamics, the DTC method is simple to implement and leads to accurate temperature-dependent rates. We apply the DTC rate-extraction method to all-atom REMD simulations of dimerization of amyloid-forming NNQQ tetrapetides in explicit water. In an assessment of the REMD sampling efficiency with respect to standard MD, we find a gain of more than a factor of two at the lowest temperature.

  1. Short-time dynamics of molecular junctions after projective measurement

    Science.gov (United States)

    Tang, Gaomin; Xing, Yanxia; Wang, Jian

    2017-08-01

    In this work, we study the short-time dynamics of a molecular junction described by Anderson-Holstein model using full-counting statistics after projective measurement. The coupling between the central quantum dot (QD) and two leads was turned on at remote past and the system is evolved to steady state at time t =0 , when we perform the projective measurement in one of the lead. Generating function for the charge transfer is expressed as a Fredholm determinant in terms of Keldysh nonequilibrium Green's function in the time domain. It is found that the current is not constant at short times indicating that the measurement does perturb the system. We numerically compare the current behaviors after the projective measurement with those in the transient regime where the subsystems are connected at t =0 . The universal scaling for high-order cumulants is observed for the case with zero QD occupation due to the unidirectional transport at short times. The influences of electron-phonon interaction on short-time dynamics of electric current, shot noise, and differential conductance are analyzed.

  2. Energy conservation in molecular dynamics simulations of classical systems.

    Science.gov (United States)

    Toxvaerd, Søren; Heilmann, Ole J; Dyre, Jeppe C

    2012-06-14

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.

  3. Molecular Dynamics with the massively parallel APE computers

    Science.gov (United States)

    La Penna, G.; Minicozzi, V.; Morante, S.; Rossi, G. C.; Salina, G.

    1997-10-01

    In this paper we discuss the general question of the portability of Molecular Dynamics codes for diffusive systems (liquids) on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from the CPU to individual nodes puts strong constraints on the possible programming strategies. As a test case, we report the results of the simulation of the dynamics of 512 molecules of liquid butane (C 4H 10) ta room temperature. After 30 to 50 ps of equilibrium, the system was followed along four long trajectories, each one more than 1.3 ns. The effective CPU time corresponding to the simulation of a trajectory of 1 ns on the Torre (512 nodes ≈ 25 Gigaflops) was ≈ 50 hours. The CPU time can be substantially reduced (by almost a factor 3), if the APE- assembler micro-code of the most time-consuming part of the program is carefully optimized.

  4. A molecular dynamics study of human serum albumin binding sites.

    Science.gov (United States)

    Artali, Roberto; Bombieri, Gabriella; Calabi, Luisella; Del Pra, Antonio

    2005-01-01

    A 2.0 ns unrestrained Molecular Dynamics was used to elucidate the geometric and dynamic properties of the HSA binding sites. The structure is not stress affected and the rmsds calculated from the published crystallographic data are almost constant for all the simulation time, with an averaged value of 2.4A. The major variability is in the C-terminus region. The trajectory analysis of the IIA binding site put in evidence fast oscillations for the Cgamma@Leu203...Cgamma@Leu275 and Cgamma@Leu219...Cgamma@Leu260 distances, with fluctuations around 250 ps, 1000 ps and over for the first, while the second is smoothly increasing with the simulation time from 7 to 10A. These variations are consistent with a volume increase up to 20% confirmed by the inter-domain contacts analysis, in particular for the pair O@Pro148...Ogamma@Ser283, representing the change of distance between IB-h9 and IIA-h6, O@Glu149...Ogamma@Ser189 for sub-domains IB-h9/IIA-h1 and N@Val339...Odelta2@Asp447 sub-domains IIB-h9/IIIA-h1. These inter-domain motions confirm the flexibility of the unfatted HSA with possible binding site pre-formation.

  5. Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions.

    Directory of Open Access Journals (Sweden)

    Natalie S Scholes

    2016-05-01

    Full Text Available Transcriptional activation domains (ADs are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators.

  6. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Jianjun [University of South Florida, Tampa (USF); Cheng, Xiaolin [ORNL; Monticelli, Luca [Institut National de la Santé et de la Recherche Médicale (INSERM) and INTS, France; Heberle, Frederick A [ORNL; Kucerka, Norbert [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,; Tieleman, D. Peter [University of Calgary, ALberta, Canada; Katsaras, John [ORNL

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  7. Molecular dynamics simulation of a synthetic ion channel.

    Science.gov (United States)

    Zhong, Q; Jiang, Q; Moore, P B; Newns, D M; Klein, M L

    1998-01-01

    A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four alpha-helical peptides, each of which is composed of the amino acids leucine (L) and serine (S), with the sequence Ac-(LSLLLSL)3-CONH2. This four-helix bundle has been shown experimentally to act as a proton-conducting channel in a membrane environment. In the present simulation, the channel was initially assembled as a parallel bundle in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. An explicit reversible multiple-time-step integrator was used to generate a dynamical trajectory, a few nanoseconds in duration for this composite system on a parallel computer, under ambient conditions. After more than 1 ns, the four helices were found to adopt an associated dimer state with twofold symmetry, which evolved into a coiled-coil tetrameric structure with a left-handed twist. In the coiled-coil state, the polar serine side chains interact to form a layered structure with the core of the bundle filled with H2O. The dipoles of these H2O molecules tended to align opposite the net dipole of the peptide bundle. The calculated dipole relaxation function of the pore H2O molecules exhibits two reorientation times. One is approximately 3.2 ps, and the other is approximately 100 times longer. The diffusion coefficient of the pore H2O is about one-third of the bulk H2O value. The total dipole moment and the inertia tensor of the peptide bundle have been calculated and reveal slow (300 ps) collective oscillatory motions. Our results, which are based on a simple united atom force-field model, suggest that the function of this synthetic ion channel is likely inextricably coupled to its dynamical behavior.

  8. Thermal neutron scattering law calculations using ab initio molecular dynamics

    Science.gov (United States)

    Wormald, Jonathan; Hawari, Ayman I.

    2017-09-01

    In recent years, methods for the calculation of the thermal scattering law (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables, respectively) were developed based on ab initio lattice dynamics (AILD) and/or classical molecular dynamics (CMD). While these methods are now mature and efficient, further advancement in the application of such atomistic techniques is possible using ab initio molecular dynamics (AIMD) methods. In this case, temperature effects are inherently included in the calculation, e.g. phonon density of states (DOS), while using ab initio force fields that eliminate the need for parameterized semi-empirical force fields. In this work, AIMD simulations were performed to predict the phonon spectra as a function of temperature for beryllium and graphite, which are representative nuclear reactor moderator and reflector materials. Subsequently, the calculated phonon spectra were utilized to predict S(α,β) using the LEAPR module of the NJOY code. The AIMD models of beryllium and graphite were 5 × 5 × 5 crystal unit cells (250 atoms and 500 atoms respectively). Electronic structure calculations for the prediction of Hellman-Feynman forces were performed using density functional theory with a GGA exchange correlation functional and corresponding core electron pseudopotentials. AIMD simulations of 1000-10,000 time-steps were performed with the canonical ensemble (NVT thermostat) for several temperatures between 300 K and 900 K. The phonon DOS were calculated as the power spectrum of the AIMD predicted velocity autocorrelation functions. The resulting AIMD phonon DOS and corresponding inelastic thermal neutron scattering cross sections at 300 K, where anharmonic effects are expected to be small, were found to be in reasonable agreement with the results generated using traditional AILD. This illustrated the validity of the AIMD approach. However, since the impact of the temperature on the phonon DOS (e.g. broadening of

  9. Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

    Science.gov (United States)

    Wu, Bin

    Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and

  10. Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations.

    Science.gov (United States)

    Soares, Rosemberg O; Torres, Pedro H M; da Silva, Manuela L; Pascutti, Pedro G

    2016-08-01

    The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Mixtures of protic ionic liquids and molecular cosolvents: a molecular dynamics simulation.

    Science.gov (United States)

    Docampo-Álvarez, Borja; Gómez-González, Víctor; Méndez-Morales, Trinidad; Carrete, Jesús; Rodríguez, Julio R; Cabeza, Óscar; Gallego, Luis J; Varela, Luis M

    2014-06-07

    In this work, the effect of molecular cosolvents (water, ethanol, and methanol) on the structure of mixtures of these compounds with a protic ionic liquid (ethylammonium nitrate) is analyzed by means of classical molecular dynamics simulations. Included are as-yet-unreported measurements of the densities of these mixtures, used to test our parameterized potential. The evolution of the structure of the mixtures throughout the concentration range is reported by means of the calculation of coordination numbers and the fraction of hydrogen bonds in the system, together with radial and spatial distribution functions for the various molecular species and molecular ions in the mixture. The overall picture indicates a homogeneous mixing process of added cosolvent molecules, which progressively accommodate themselves in the network of hydrogen bonds of the protic ionic liquid, contrarily to what has been reported for their aprotic counterparts. Moreover, no water clustering similar to that in aprotic mixtures is detected in protic aqueous mixtures, but a somehow abrupt replacing of [NO3](-) anions in the first hydration shell of the polar heads of the ionic liquid cations is registered around 60% water molar concentration. The spatial distribution functions of water and alcohols differ in the coordination type, since water coordinates with [NO3](-) in a bidentate fashion in the equatorial plane of the anion, while alcohols do it in a monodentate fashion, competing for the oxygen atoms of the anion. Finally, the collision times of the different cosolvent molecules are also reported by calculating their velocity autocorrelation functions, and a caging effect is observed for water molecules but not in alcohol mixtures.

  12. RECOGNITION DYNAMICS OF ESCHERICHIA COLI THIOREDOXIN PROBED USING MOLECULAR DYNAMICS AND BINDING FREE ENERGY CALCULATIONS

    Directory of Open Access Journals (Sweden)

    M. S. Shahul Hameed

    2016-03-01

    Full Text Available E. coli thioredoxin has been regarded as a hub protein as it interacts with, and regulates, numerous target proteins involved in a wide variety of cellular processes. Thioredoxin can form complexes with a variety of target proteins with a wide range of affinity, using a consensus binding surface. In this study an attempt to deduce the molecular basis for the observed multispecificity of E. coli thioredoxin has been made. In this manuscript it has been shown that structural plasticity, adaptable and exposed hydrophobic binding surface, surface electrostatics, closely clustered multiple hot spot residues and conformational changes brought about by the redox status of the protein have been shown to account for the observed multispecificity and molecular recognition of thioredoxin. Dynamical differences between the two redox forms of the enzyme have also been studied to account for their differing interactions with some target proteins.

  13. Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

    Energy Technology Data Exchange (ETDEWEB)

    Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

    2014-10-15

    The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

  14. Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams

    Science.gov (United States)

    Ohya, Kaoru

    2017-03-01

    The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.

  15. Molecular dynamics simulation studies of structural and dynamical properties of rapidly quenched Al

    Energy Technology Data Exchange (ETDEWEB)

    Shen, B.; Liu, C. Y.; Jia, Y.; Yue, G. Q.; Ke, F. S.; Zhao, H. B.; Chen, L. Y.; Wang, S. Y.; Wang, C. Z.; Ho, K. M.

    2014-01-01

    The structural and dynamical properties of rapidly quenched Al are studied by molecular dynamics simulations. The pair-correlation function of high temperature liquid Al agrees well with the experimental results. Different cooling rates are applied with high cooling rates leading to glass formation, while low cooling rates leading to crystallization. The local structures are characterized by Honeycutt–Andersen indices and Voronoi tessellation analysis. The results show that for high cooling rates, the local structures of the liquid and glassy Al are predominated by icosahedral clusters, together with considerable amount of face-centered cubic and hexagonal close packed short-range orders. These short-range order results are further confirmed using the recently developed atomic cluster alignment method. Moreover, the atomic cluster alignment clearly shows the crystal nucleation process in supercooled liquid of Al. Finally, the mean square displacement for the liquid is also analyzed, and the corresponding diffusion coefficient as a function of temperature is calculated.

  16. Finite-size effects on the lattice dynamics in spin crossover nanomaterials. II. Molecular dynamics simulations

    Science.gov (United States)

    Mikolasek, Mirko; Nicolazzi, William; Terki, Férial; Molnár, Gábor; Bousseksou, Azzedine

    2017-07-01

    In the first part of this work, an experimental study of the lattice dynamics of spin crossover nanoparticles was performed using the nuclear inelastic scattering (NIS). A size dependence of low energy phonon modes appears under 10 nm, but its origin is not well understood. In this paper, we investigate the phonon confinement effects in the framework of molecular dynamics simulations by modeling three-dimensional nanoparticles considering a cubic lattice with an octahedral pattern. The vibrational density of states is computed and compared to the experiment. The simulations allow one to highlight both the role of the phonon quantification and the role of the size and shape distributions of particles on the extracted parameters leading to a better understanding of the experimental results.

  17. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations

    Science.gov (United States)

    Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.

    2016-04-01

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.

  18. Nucleation rate analysis of methane hydrate from molecular dynamics simulations.

    Science.gov (United States)

    Yuhara, Daisuke; Barnes, Brian C; Suh, Donguk; Knott, Brandon C; Beckham, Gregg T; Yasuoka, Kenji; Wu, David T; Sum, Amadeu K

    2015-01-01

    Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP) methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates calculated by MFPT and SP methods are within 5%, and the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.

  19. Molecular dynamics modelling of radiation damage in zircon

    Science.gov (United States)

    Grechanovsky, A. E.

    2009-04-01

    Zircon (ZrSiO4) is among actinide-bearing phases which has been proposed as a crystalline confinement matrix for nuclear waste management, especially for weapon-grade plutonium and UO2 spent fuel in the USA. Zircon is also widely used in geochronology. But, with accumulating α-decay damage, zircon undergoes a radiation induced transition to an amorphous (or metamict) state. So, in the present work molecular dynamics simulations (MD simulations) of zircon structure have been performed to study radiation damage in zircon. In this technique, one simulates the propagation of an energetic particle in a system of atoms interacting via model potentials, by integrating the Newton equations of motion. Author has used version 3.09 of the DL_POLY molecular simulation package. Zircon structure containing 181944 atoms (19x19x21 unit cells) was equilibrated at 300 K for 10 ps, and one Zr atom (usually called the primary knock-on atom, PKA) was given a velocity corresponding to an implantation energy of about 20 keV. MD simulations were performed in the microcanonical ensemble that is under conditions of constant particle number, volume and energy. Results of the MD simulations show that the number of interstitials is equal to 840 atoms. This is very close (4000-5000 atoms for 70 keV recoil atom 234Th) to what is measured in the diffuse x-ray scattering and NMR experiments on amorphous metamict samples (damaged by natural irradiation) of geological age. It has been shown that the damaged structure contains several depleted regions with characteristic sized up to 2,5 nm after single event and up to 4,5 nm after three overlapping events. Furthermore, these events produce channels of depleted matter between the overlapping damaged regions. These channels provide a high-diffusivity path for radiogenic Pb (percolation effect). Loss of radiogenic Pb may result in to incorrect dating of rocks.

  20. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

    Directory of Open Access Journals (Sweden)

    Beata Szefler

    2016-10-01

    Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

  1. Equilibration of experimentally determined protein structures for molecular dynamics simulation.

    Science.gov (United States)

    Walton, Emily B; Vanvliet, Krystyn J

    2006-12-01

    Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often equilibrated with respect to an initial configuration. This so-called equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to artifactual trajectories of protein dynamics. The time at which nonequilibrium effects from the initial configuration are minimized-what we will call the equilibration time-marks the beginning of equilibrium phase-space exploration. Note that the identification of this time does not imply exploration of the entire equilibrium phase space. We have found that current equilibration methodologies contain ambiguities that lead to uncertainty in determining the end of the equilibration stage of the trajectory. This results in equilibration times that are either too long, resulting in wasted computational resources, or too short, resulting in the simulation of molecular trajectories that do not accurately represent the physical system. We outline and demonstrate a protocol for identifying the equilibration time that is based on the physical model of Normal Mode Analysis. We attain the computational efficiency required of large-protein simulations via a stretched exponential approximation that enables an analytically tractable and physically meaningful form of the root-mean-square deviation of atoms comprising the protein. We find that the fitting parameters (which correspond to physical properties of the protein) fluctuate initially but then stabilize for increased simulation time, independently of the simulation duration or sampling frequency. We define the end of the equilibration stage--and thus the equilibration time--as the point in the simulation when these parameters attain constant values. Compared to existing methods, our approach provides the objective identification of the time at

  2. Relaxation dynamics of lysozyme in solution under pressure: Combining molecular dynamics simulations and quasielastic neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Calandrini, V. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Synchrotron Soleil, L' Orme de Merisiers, B.P. 48, 91192 Gif-sur-Yvette (France); Hamon, V. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Hinsen, K. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Synchrotron Soleil, L' Orme de Merisiers, B.P. 48, 91192 Gif-sur-Yvette (France); Calligari, P. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Institut Laue-Langevin, 6 Rue Jules Horowitz, B.P. 156, 38042 Grenoble (France); Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France); Bellissent-Funel, M.-C. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France); Kneller, G.R. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Synchrotron Soleil, L' Orme de Merisiers, B.P. 48, 91192 Gif-sur-Yvette (France)], E-mail: kneller@cnrs-orleans.fr

    2008-04-18

    This paper presents a study of the influence of non-denaturing hydrostatic pressure on the relaxation dynamics of lysozyme in solution, which combines molecular dynamics simulations and quasielastic neutron scattering experiments. We compare results obtained at ambient pressure and at 3 kbar. Experiments have been performed at pD 4.6 and at a protein concentration of 60 mg/ml. For both pressures we checked the monodispersity of the protein solution by small angle neutron scattering. To interpret the simulation results and the experimental data, we adopt the fractional Ornstein-Uhlenbeck process as a model for the internal relaxation dynamics of the protein. On the experimental side, global protein motions are accounted for by the model of free translational diffusion, neglecting the much slower rotational diffusion. We find that the protein dynamics in the observed time window from about 1 to 100 ps is slowed down under pressure, while its fractal characteristics is preserved, and that the amplitudes of the motions are reduced by about 20%. The slowing down of the relaxation is reduced with increasing q-values, where more localized motions are seen.

  3. Structural and Dynamical Properties of Polyethylene/Graphene Nanocomposites through Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Anastassia N. Rissanou

    2015-02-01

    Full Text Available Detailed atomistic (united atoms molecular dynamics simulations of several graphene based polymer (polyethylene, PE nanocomposite systems have been performed. Systems with graphene sheets of different sizes have been simulated at the same graphene concentration (~3%. In addition, a periodic graphene layer (“infinite sheet” has been studied. Results concerning structural and dynamical properties of PE chains are presented for the various systems and compared to data from a corresponding bulk system. The final properties of the material are the result of a complex effect of the graphene’s sheet size, mobility and fluctuations. A detailed investigation of density, structure and dynamics of the hybrid systems has been conducted. Particular emphasis has been given in spatial heterogeneities due to the PE/graphene interfaces, which were studied through a detailed analysis based on radial distances form the graphene’s center-of-mass. Chain segmental dynamics is found to be slower, compared to the bulk one, at the PE/graphene interface by a factor of 5 to 10. Furthermore, an analysis on the graphene sheets characteristics is presented in terms of conformational properties (i.e., wrinkling and mobility.

  4. Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries.

    Science.gov (United States)

    Sasselli, I R; Moreira, I P; Ulijn, R V; Tuttle, T

    2017-08-09

    There is significant interest in the use of unmodified self-assembling peptides as building blocks for functional, supramolecular biomaterials. Recently, dynamic peptide libraries (DPLs) have been proposed to select self-assembling materials from dynamically exchanging mixtures of dipeptide inputs in the presence of a nonspecific protease enzyme, where peptide sequences are selected and amplified based on their self-assembling tendencies. It was shown that the results of the DPL of mixed sequences (e.g. starting from a mixture of dileucine, L 2 , and diphenylalanine, F 2 ) did not give the same outcome as the separate L 2 and F 2 libraries (which give rise to the formation of F 6 and L 6 ), implying that interactions between these sequences could disrupt the self-assembly. In this study, coarse grained molecular dynamics (CG-MD) simulations are used to understand the DPL results for F 2 , L 2 and mixed libraries. CG-MD simulations demonstrate that interactions between precursors can cause the low formation yield of hexapeptides in the mixtures of dipeptides and show that this ability to disrupt is influenced by the concentration of the different species in the DPL. The disrupting self-assembly effect between the species in the DPL is an important effect to take into account in dynamic combinatorial chemistry as it affects the possible discovery of new materials. This work shows that combined computational and experimental screening can be used complementarily and in combination providing a powerful means to discover new supramolecular peptide nanostructures.

  5. Folding of small proteins using constrained molecular dynamics.

    Science.gov (United States)

    Balaraman, Gouthaman S; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

    2011-06-16

    The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched toward "native-like" structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement. It is computationally expensive to perform all-atom simulations of protein folding because the processes occur on a time scale of microseconds. Compared to the all-atom MD simulation, constrained MD methods have the advantage that stable dynamics can be achieved for larger time steps and the number of degrees of freedom is an order of magnitude smaller, leading to a decrease in computational cost. We have developed a generalized constrained MD method that allows the user to "freeze and thaw" torsional degrees of freedom as fit for the problem studied. We have used this method to perform all-torsion constrained MD in implicit solvent coupled with the replica exchange method to study folding of small proteins with various secondary structural motifs such as, α-helix (polyalanine, WALP16), β-turn (1E0Q), and a mixed motif protein (Trp-cage). We demonstrate that constrained MD replica exchange method exhibits a wider conformational search than all-atom MD with increased enrichment of near-native structures. "Hierarchical" constrained MD simulations, where the partially formed helical regions in the initial stretch of the all-torsion folding simulation trajectory of Trp-cage were frozen, showed a better sampling of near-native structures than all-torsion constrained MD simulations. This is in agreement with the zipping-and-assembly folding model put forth by Dill and co-workers for folding proteins. The use of hierarchical "freeze and thaw" clustering schemes in constrained MD simulation can be used to sample conformations that contribute significantly to folding of proteins. © 2011 American Chemical Society

  6. Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Sanders

    Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of

  7. Hybrid molecular dynamics simulation for plasma induced damage analysis

    Science.gov (United States)

    Matsukuma, Masaaki

    2016-09-01

    In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam

  8. Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-nitro-2-phenoxymethyl benzimidazole

    Science.gov (United States)

    Menon, Vidya V.; Foto, Egemen; Mary, Y. Sheena; Karatas, Esin; Panicker, C. Yohannan; Yalcin, Gözde; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Yildiz, Ilkay

    2017-02-01

    FT-IR and FT-Raman spectra of 5-nitro-2-phenoxymethylbenzimidazole were recorded and analyzed theoretically and experimentally. The splitting of Nsbnd H stretching mode in the IR spectrum with a red shift from the calculated value indicates the weakening of the NH bond. The theoretical calculations give the phenyl ring breathing modes at 999 cm-1 for mono substituted benzene ring and at 1040 cm-1 for tri-substituted benzene ring. The theoretical NMR chemical shifts are in agreement with the experimental chemical shifts. The most reactive sites for electrophilic and nucleophilic attack are predicted from the MEP analysis. HOMO of π nature is delocalized over the entire molecule whereas the LUMO is located over the complete molecule except mono-substituted phenyl ring and oxygen atom. Reactive sites of the title molecule have been located with the help of ALIE surfaces and Fukui functions. In order to determine locations prone to autoxidation and locations interesting for starting of degradation, bond dissociation energies have been calculated for all single acyclic bonds. For the determination of atoms with pronounced interactions with water we have calculated radial distribution functions obtained after molecular dynamics simulations. The calculated first hyperpolarizability of the title compound is 58.03 times that of standard nonlinear optical material urea. The substrate binding site interactions of the title compound with Topo II enzyme is reported by using molecular docking study. Biological activity studies show that the title compound can be leaded for developing new anticancer agents.

  9. Extended Lagrangian quantum molecular dynamics simulations of shock-induced chemistry in hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Sanville, Edward J [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, William M [Los Alamos National Laboratory; Cawkwell, Marc J [Los Alamos National Laboratory; Niklasson, Anders M N [Los Alamos National Laboratory; Dattelbaum, Dana M [Los Alamos National Laboratory; Sheffield, Stephen [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI

    2010-01-01

    A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.

  10. Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets

    Directory of Open Access Journals (Sweden)

    Renata Rachide Nunes

    Full Text Available The main challenge in the control of malaria has been the emergence of drug-resistant parasites. The presence of drug-resistant Plasmodium sp. has raised the need for new antimalarial drugs. Molecular modelling techniques have been used as tools to develop new drugs. In this study, we employed virtual screening of a pyrazol derivative (Tx001 against four malaria targets: plasmepsin-IV, plasmepsin-II, falcipain-II, and PfATP6. The receiver operating characteristic curves and area under the curve (AUC were established for each molecular target. The AUC values obtained for plasmepsin-IV, plasmepsin-II, and falcipain-II were 0.64, 0.92, and 0.94, respectively. All docking simulations were carried out using AutoDock Vina software. The ligand Tx001 exhibited a better interaction with PfATP6 than with the reference compound (-12.2 versus -6.8 Kcal/mol. The Tx001-PfATP6 complex was submitted to molecular dynamics simulations in vacuum implemented on an NAMD program. The ligand Tx001 docked at the same binding site as thapsigargin, which is a natural inhibitor of PfATP6. Compound TX001 was evaluated in vitro with a P. falciparum strain (W2 and a human cell line (WI-26VA4. Tx001 was discovered to be active against P. falciparum (IC50 = 8.2 µM and inactive against WI-26VA4 (IC50 > 200 µM. Further ligand optimisation cycles generated new prospects for docking and biological assays.

  11. Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations.

    Science.gov (United States)

    Lousa, Diana; Baptista, António M; Soares, Cláudio M

    2012-02-27

    One of the drawbacks of nonaqueous enzymology is the fact that enzymes tend to be less stable in organic solvents than in water. There are, however, some enzymes that display very high stabilities in nonaqueous media. In order to take full advantage of the use of nonaqueous solvents in enzyme catalysis, it is essential to elucidate the molecular basis of enzyme stability in these media. Toward this end, we performed μs-long molecular dynamics simulations using two homologous proteases, pseudolysin, and thermolysin, which are known to have considerably different stabilities in solutions containing ethanol. The analysis of the simulations indicates that pseudolysin is more stable than thermolysin in ethanol/water mixtures and that the disulfide bridge between C30 and C58 is important for the stability of the former enzyme, which is consistent with previous experimental observations. Our results indicate that thermolysin has a higher tendency to interact with ethanol molecules (especially through van der Waals contacts) than pseudolysin, which can lead to the disruption of intraprotein hydrophobic interactions and ultimately result in protein unfolding. In the absence of the C30-C58 disulfide bridge, pseudolysin undergoes larger conformational changes, becoming more open and more permeable to ethanol molecules which accumulate in its interior and form hydrophobic interactions with the enzyme, destroying its structure. Our observations are not only in good agreement with several previous experimental findings on the stability of the enzymes studied in ethanol/water mixtures but also give an insight on the molecular determinants of this stability. Our findings may, therefore, be useful in the rational development of enzymes with increased stability in these media.

  12. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

  13. Ultrafast High Harmonic, Soft X-Ray Probing of Molecular Dynamics

    Science.gov (United States)

    2013-04-30

    photochemistry and molecular dynamics of ionic liquids in vapor phase and aerosol is completed. The photochemistry and thermodynamics of ionic liquids...are studied using the quasi-continuous vacuum ultraviolet light of the Advanced Light Source at Lawrence Berkeley National Laboratory. The molecular...34), the method of high order harmonic generation of ultrashort vacuum ultraviolet pulses was used to investigate molecular photodissociation, ultrafast

  14. Hydrogen diffusion in tungsten: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yi-Nan [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Wu, Tiefeng [Shanghai Aircraft Design and Research Institute, Shanghai 201210 (China); Yu, Yi [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Li, Xiao-Chun [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Shu, Xiaolin, E-mail: shuxlin@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Lu, Guang-Hong, E-mail: lgh@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China)

    2014-12-15

    The diffusion behavior of hydrogen (H) in tungsten (W) has been studied by molecular dynamics simulations. The diffusivities from 200 K to 3000 K are calculated and the diffusion equation is fitted to D = 5.13 × 10{sup −8}exp(−0.21 eV/kT) m{sup 2}/s. The diffusion equations in different temperature ranges of 200–500 K, 500–2400 K and 2400–3000 K are also given separately and the results imply different H diffusion modes in different temperature ranges, which is proved by analyzing equilibrium H positions at low and high temperatures. The H atom jumps between different tetrahedral interstitial sites (TISs) at lower temperatures, but the transition to octahedral interstitial sites (OISs) is also observed at high temperatures. Moreover, with a vacancy present in the W system, vacancy trapping of H is observed, and it is shown that the vacancy trapping reduces with the increasing temperature. The H binding energy to monovacancy is obtained using three different methods including NEB and fitting both H diffusivity and time for H to detrap from the vacancy, which provides more information of the H behaviors with the existence of defects.

  15. Cleavage Energies of Modified Layered Silicates by Molecular Dynamics Simulation

    Science.gov (United States)

    Fu, Yao-Tsung; Heinz, Hendrik

    2009-03-01

    The cleavage energy of organically modified layered silicates indicates the thermodynamic propensity of exfoliation in polymer matrices. We find substantial cleavage energy differences upon variation in cation exchange capacity (CEC) (90 and 145 meq/100g), head groups (-NH3 and --NMe3), and chain length of the surfactants (C2 to C14) due to layering effects of the surfactants in the galleries using molecular dynamics simulation. Model systems of full atomistic detail are periodic in the xy plane, open in the z direction, are subjected to sheet separation starting at equilibrium distance. Overall, the cleavage energy, consistent with experimentally measured surface tensions and previous calculations for selected organoclays, shows complex fluctuations as a function of chain length and head group structure. Computed cleavage energies are in the range 25-50 mJ/m^2 for C2˜C14 (-NH3 headgroup) and 40-200 mJ/m^2 for C2˜C14 (--NMe3 headgroup) at two CEC layered silicates. The progression is not linear and related to the packing density of the interlayer of self-assembled surfactant chains and surface reconstruction of the modified layered silicates upon cleavage.

  16. Mechanical properties of irradiated nanowires – A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Figueroa, Emilio [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente, Universidad Tecnológica Metropolitana, Santiago 7800002 (Chile); Tramontina, Diego [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina); Instituto de Bioingeniería, Universidad de Mendoza, 5500 Mendoza (Argentina); Gutiérrez, Gonzalo, E-mail: gonzalo@fisica.ciencias.uchile.cl [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Bringa, Eduardo [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina)

    2015-12-15

    In this work we study, by means of molecular dynamics simulation, the change in the mechanical properties of a gold nanowire with pre-existing radiation damage. The gold nanowire is used as a simple model for a nanofoam, made of connected nanowires. Radiation damage by keV ions leads to the formation of a stacking fault tetrahedron (SFT), and this defect leads to a reduced plastic threshold, as expected, when the nanowire is subjected to tension. We quantify dislocation and twin density during the deformation, and find that the early activation of the SFT as a dislocation source leads to reduced dislocation densities compared to the case without radiation damage. In addition, we observed a total destruction of the SFT, as opposed to a recent simulation study where it was postulated that SFTs might act as self-generating dislocation sources. The flow stress at large deformation is also found to be slightly larger for the irradiated case, in agreement with recent experiments. - Highlights: • Stacking Fault Tetrahedra (SFT) formation proceeds by cascades, containing typically a vacancy cluster and interstitials. • Applied tension leads to the destruction of the SFT, in contrast to a recently reported case of a SFT which soften the NW. • After the initial dislocation activity, strength is controlled by a few surviving dislocations.

  17. Effective particle size from molecular dynamics simulations in fluids

    Science.gov (United States)

    Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

    2017-12-01

    We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

  18. Constrained molecular dynamics for quantifying intrinsic ductility versus brittleness

    Science.gov (United States)

    Tanguy, D.

    2007-10-01

    Evaluating the critical load levels for intrinsic ductility and brittle propagation is a first, but necessary, step for modeling semibrittle crack propagation. In the most general case, the calculations have to be fully atomistic because the details of the crack tip structure cannot be captured by continuum mechanics. In this paper, we present a method to explore ductile and brittle configurations, within the same force field, giving a quantitative estimate of the proximity of a transition from intrinsic ductility to brittleness. The shear localization is characterized by a centrosymmetry criterion evaluated on each atom in the vicinity of the crack tip. This provides an efficient order parameter to track the nucleation and propagation of dislocations. We show that it can be used as a holonomic constraint within molecular dynamics simulations, giving a precise control over plasticity during crack propagation. The equations of motion are derived and applied to crack propagation in the [112¯] direction of an fcc crystal loaded in mode I along [111]. The critical loads for dislocation emission and for brittle propagation are computed. The key point is that the generalized forces of constraint are not dissipative. Therefore, they do not spoil the critical elastic energy release rates (the Griffith criterion is preserved). As an example of the possibilities of the method, the response of blunted tips is investigated for three configurations: a slab of vacancies, an elliptical hole, and a circular hole. Brittle propagation by an alternative mechanism to cleavage, called “vacancy injection,” is reported.

  19. Molecular dynamics simulations of radon accumulation in water and oil

    Energy Technology Data Exchange (ETDEWEB)

    Pafong, Elvira; Drossel, Barbara [Institut fuer Festkoerperphysik, Technische Universitaet Darmstadt (Germany)

    2016-07-01

    Radon is a radioactive gas that can enter the human body from air or from ground water. Radon can accumulate to levels that considerably rise the risk of lung cancer while it is also known as a a treatment of various ailments, most notably rheumatoid arthritis. The accumulation of radon differs between tissues, with particularly high concentrations in fatty cells. In order to understand the mechanisms responsible for the different solubility of radon in water and fat, we perform molecular dynamics simulations of radon gas at ambient conditions in contact with a bulk material consisting either of water or oil. We evaluate the diffusion coefficient of radon in both media as well as the equilibrium concentration. The crucial point here is to understand the hydrophobic interaction between water and radon as compared to the dispersive interaction between radon and oil. Therefore, we artificially vary the water charges (i.e., the hydrophobicity) as well as the parameters of the van-der-Waals interaction.

  20. Elucidating nitric oxide synthase domain interactions by molecular dynamics.

    Science.gov (United States)

    Hollingsworth, Scott A; Holden, Jeffrey K; Li, Huiying; Poulos, Thomas L

    2016-02-01

    Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis. © 2015 The Protein Society.

  1. Molecular dynamics study of thermal-driven methane hydrate dissociation.

    Science.gov (United States)

    English, Niall J; Phelan, Gráinne M

    2009-08-21

    Nonequilibrium molecular dynamics simulations have been performed to investigate the thermal-driven breakup of both spherical methane hydrate nanocrystallites (with radii of approximately 18 and 21 A) and planar methane hydrate interfaces in liquid water at 280-340 K. The melting temperatures of each cluster were estimated, and dissociation was observed to be strongly dependent on temperature, with higher dissociation rates at larger overtemperatures vis-a-vis melting. For the 18 and 21 A radius nanocrystals, breakup was also seen to be dependent on cluster size, and different methane compositions (85%, 95%, and 100% of maximum theoretical occupation) in the planar case also lead to slight differences in the initial dissociation rate. In all cases, the diffusion of the methane into the surrounding liquid water was found to be an important step limiting the overall rate of breakup. A simple coupled mass and heat transfer model has been devised for both the spherical and planar hydrate systems that explains these findings, and distinguishes between the role of the overall thermal driving force and methane diffusional mass transfer in controlling the break-up rate.

  2. Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition.

    Science.gov (United States)

    Alavi, Saman; Ripmeester, J A

    2010-04-14

    Nonequilibrium, constant energy, constant volume (NVE) molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed.

  3. Fluorine environment in bioactive glasses: ab initio molecular dynamics simulations.

    Science.gov (United States)

    Christie, Jamieson K; Pedone, Alfonso; Menziani, Maria Cristina; Tilocca, Antonio

    2011-03-10

    Fluorinated bioactive glasses (FBGs) combine the antibacterial properties of fluorine with the biological activity of phosphosilicate glasses. Because their biomedical application depends on the release of fluorine, the detailed characterization of the fluorine environment in FBGs is the key to understand their properties. Car-Parrinello molecular dynamics (CPMD) simulations have been performed on a 45S5 Bioglass composition in which 10 mol % of the CaO has been replaced with CaF(2), and have allowed us to resolve some longstanding issues about the atomic structure of fluorinated bioglasses, with particular regard to the structural role of fluorine. F is coordinated almost entirely to the modifier ions Na and Ca, with a very small amount of residual Si-F bonds, whose fraction only becomes significant in the melt precursor. High temperature leads to Si-F bonds in both tetra- (SiO(3)F) and, less frequently, penta-coordinated (SiO(4)F and SiO(3)F(2)) complexes, showing that formation of these bonds through the expansion of the SiO(4) coordination shell is generally less favored. There is no evidence for preferential bonding of F to either modifier ion: almost all F atoms are coordinated to both calcium and sodium in a "mixed state", rather than exclusively to either, as had been conjectured. We discuss the consequences of these findings on the properties of fluorine-containing bioglasses. © 2011 American Chemical Society

  4. Molecular Dynamics Simulations of Nanoparticles Coated with Charged Polymers

    Science.gov (United States)

    Wen, Chengyuan; Cheng, Shengfeng

    Polymer coating is frequently used to stabilize colloidal and nano-sized particles. We employ molecular dynamics simulations to study nanoparticles coated with polymer chains that contain ionizable groups. In a polar solvent, the chains become charged with counterions dissociated. In the computational model, we treat the solvent as a uniform dielectric background and use the bead-spring model for the polymer chains. Counterions are explicitly included as mobile beads. The nanoparticle is modeled as a layer of sites uniformly distributed on a spherical surface with a certain fraction of sites serving as the tether points of the grafted polymer brush. We vary the grafting density and calculate the distribution of polymer beads and counterions around the nanoparticle. Our results indicate that charged chains adopt extended conformations because of their mutual repulsions. We further study the interactions between two polymer-coated nanoparticles and obtain the potential of mean force. We also find an interesting transition of a confined single layer of such polymer-coated nanoparticles into two layers when the confinement is removed. Results show that the brush-brush contact has a nonuniform distribution and the nanoparticles tend to form dipole-like structures.

  5. Modeling of aging in plutonium by molecular dynamics

    CERN Document Server

    Pochet, P

    2003-01-01

    The origin of aging in plutonium lies in the extra formation of defects due to self-decay of sup 2 sup 3 sup 9 Pu. The modeling of the formation of these defects is achieved by molecular dynamics (MD). In this work a simple EAM potential has been used to study defects formation in fcc plutonium and a 2 keV cascade is analyzed. A large pressure wave is generated around the cascade core. In the used MD code the pressure wave is not absorbed at the box boundaries and due to the periodic boundary conditions, the use of a very large box is crucial in order to avoid interaction of the cascade with itself. More than 800 000 atoms are needed to deal with this small 2 keV cascade without any artifacts. This effect comes from the very low bulk modulus of fcc Pu. The relative long time to achieve the annealing is also connected to the bulk modulus. These results are discussed in terms of large pressure wave: alloying effects are predicted using that viewpoint.

  6. Porting of a serial molecular dynamics code on MIMD platforms

    Energy Technology Data Exchange (ETDEWEB)

    Celino, M. [ENEA Centro Ricerche Casaccia, S. Maria di Galeria, RM (Italy). HPCN Project

    1999-07-01

    A molecular dynamics (MD) code, utilized for the study of atomistic models of metallic systems has been parallelized for MIMD (multiple instructions multiple data) parallel platforms by means of the parallel virtual machine (PVM) message passing library. Since the parallelization implies modifications of the sequential algorithms, these are described from the point of view of the statistical mechanical theory. Furthermore, techniques and parallelization strategies utilized and the MD parallel code are described in detail. Benchmarks on several MIMD platforms (IBM SP1, SP2, Cray T3D, cluster of workstations) allow performances evaluation of the code versus the different characteristics of the parallel platforms. [Italian] Un codice seriale di dinamica molecolare (MD) utilizzato per lo studio di modelli atomici di materiali metallici e' stato parallelizzato per piattaforme parallele MIMD (multiple instructions multiple data) utilizzando librerie del parallel virtual machine (PVM). Poiche' l'operazione di parallelizzazione ha implicato la modifica degli algoritmi seriali del codice, questi vengono descritti ripercorrendo i concetti fondamentali della meccanica statistica. Inoltre sono presentate le tecniche e le strategie di parallelizzazione utilizzate descrivendo in dettaglio il codice parallelo di MD: Risultati di benchmark su diverse piattaforme MIMD (IBM SP1, SP2, Cray T3D, cluster of workstations) permettono di analizzare le performances del codice in funzione delle differenti caratteristiche delle piattaforme parallele.

  7. Green’s function molecular dynamics meets discrete dislocation plasticity

    Science.gov (United States)

    Venugopalan, Syam P.; Müser, Martin H.; Nicola, Lucia

    2017-09-01

    Metals deform plastically at the asperity level when brought in contact with a counter body even when the nominal contact pressure is small. Modeling the plasticity of solids with rough surfaces is challenging due to the multi-scale nature of surface roughness and the length-scale dependence of plasticity. While discrete-dislocation plasticity (DDP) simulations capture size-dependent plasticity by keeping track of the motion of individual dislocations, only simple two-dimensional surface geometries have so far been studied with DDP. The main computational bottleneck in contact problems modeled by DDP is the calculation of the dislocation image fields. We address this issue by combining two-dimensional DDP with Green’s function molecular dynamics. The resulting method allows for an efficient boundary-value-method based treatment of elasticity in the presence of dislocations. We demonstrate that our method captures plasticity quantitatively from single to many dislocations and that it scales more favorably with system size than conventional methods. We also derive the relevant Green’s functions for elastic slabs of finite width allowing arbitrary boundary conditions on top and bottom surface to be simulated.

  8. Cluster beam steering onto silicon surfaces studied by molecular dynamics

    CERN Document Server

    Mazzone, A M

    2002-01-01

    The purpose of this study is to investigate the effects of the impact conditions on cluster deposition in silicon and is motivated by recent results obtained using a variable incidence angle during deposition of metallic clusters and atoms. Therefore deposition of silicon clusters with a kinetic energy in the range from 0.5 to 10 eV/atom directed at normal and grazing incidence onto crystalline silicon has been studied using a molecular dynamics simulation method. The influence of other relevant parameters, such as the interatomic forces and the cluster size and shape, has also been investigated. This study shows that the physics of deposition is almost entirely dictated by the nature of the interatomic forces. When using potentials with the four-fold coordination typical of bulk a clear dependence on the size N is observed and the spreading index eta decreases with the increase of N for all incidence conditions. The cluster binding strength is perceptibly increased when using a potential accounting for the c...

  9. Molecular Dynamics Simulations of Slip on Curved Surfaces

    Directory of Open Access Journals (Sweden)

    Ross D.A.

    2016-07-01

    Full Text Available We present Molecular Dynamics (MD simulations of liquid water confined within nanoscale geometries, including slit-like and cylindrical graphitic pores. These equilibrium results are used for calculating friction coefficients, which in turn can be used to calculate slip lengths. The slip length is a material property independent of the fluid flow rate. It is therefore a better quantity for study than the fluid velocity at the wall, also known as the slip velocity. Once the slip length has been found as a function of surface curvature, it can be used to parameterise Lattice Boltzmann (LB simulations. These larger scale simulations are able to tell us about how fluid transport is affected by slip in complex geometries; not just limited to single pores. Applications include flow and transport in nano-porous engine valve deposits and gas shales. The friction coefficient is found to be a function of curvature and is higher for fluid on convex surfaces and lower for concave surfaces. Both concave and convex surfaces approach the same value of the friction coefficient, which is constant above some critical radius of curvature, here found to be 7.4 ± 2.9 nm. The constant value of the friction coefficient is 10,000 ± 600 kg m−2 s−1, which is equivalent to a slip length of approximately 67 ± 4 nm.

  10. Workflow Management Systems for Molecular Dynamics on Leadership Computers

    Science.gov (United States)

    Wells, Jack; Panitkin, Sergey; Oleynik, Danila; Jha, Shantenu

    Molecular Dynamics (MD) simulations play an important role in a range of disciplines from Material Science to Biophysical systems and account for a large fraction of cycles consumed on computing resources. Increasingly science problems require the successful execution of ''many'' MD simulations as opposed to a single MD simulation. There is a need to provide scalable and flexible approaches to the execution of the workload. We present preliminary results on the Titan computer at the Oak Ridge Leadership Computing Facility that demonstrate a general capability to manage workload execution agnostic of a specific MD simulation kernel or execution pattern, and in a manner that integrates disparate grid-based and supercomputing resources. Our results build upon our extensive experience of distributed workload management in the high-energy physics ATLAS project using PanDA (Production and Distributed Analysis System), coupled with recent conceptual advances in our understanding of workload management on heterogeneous resources. We will discuss how we will generalize these initial capabilities towards a more production level service on DOE leadership resources. This research is sponsored by US DOE/ASCR and used resources of the OLCF computing facility.

  11. Hypervelocity impact properties of graphene armor via molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Wang W.

    2012-08-01

    Full Text Available Hypervelocity impact properties of two different graphene armor systems are investigated using molecular dynamics simulations. One system is the so-called spaced armor which consists of a number of graphene plates spaced certain distance apart. Its response under normal impact of a spherical projectile is studied, focusing on the effect of the number of graphene monolayers per plate (denoted by n on the penetration resistance of the armor. We find that under normal impact by a spherical projectile the penetration resistance increases with decreasing number of monolayers per plate (n, and the best penetration resistance is achieved in the system with one graphene layer for each plate. Note that the monolayers in all the simulated multilayer graphene plates were AB-stacked. The second system being studied is the laminated copper/graphene composites with the graphene layers inside copper, on impact or back surface, or on both the impact and back surfaces. The simulation results show that under normal impact by a spherical projectile the laminated copper/graphene composite has much higher penetration resistance than the monolithic copper plate. The best efficiency is achieved when the graphene layers are on both the impact and back surfaces.

  12. Stresses and elastic constants of crystalline sodium, from molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schiferl, S.K.

    1985-02-01

    The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the results to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs.

  13. Behavior of sodium borosilicate glasses under compression using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Kilymis, D. A.; Ispas, S., E-mail: simona.ispas@univ-montp2.fr [Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Université de Montpellier, F-34095 Montpellier (France); Delaye, J.-M. [CEA, DEN, DTCD, SECM, F-30207 Bagnols-sur-Cèze (France)

    2015-09-07

    We have performed classical molecular dynamics simulations in order to study the changes under compression in the local and medium range structural properties of three sodium borosilicate glasses with varying sodium content. These glasses have been isostatically compressed up to 20 GPa and then decompressed in order to analyze the different mechanisms that affect densification, alongside with the permanent modifications of the structure after a full compression/decompression cycle. The results show that the atomic packing is the prominent characteristic that governs the amount of densification in the glass, as well as the setup of the permanent densification. During compression, the bulk modulus increases linearly up to approximately 15 GPa and more rapidly for higher pressures, a behavior which is reflected on the rate of increase of the average coordination for B and Na. Radial distribution functions at different pressures during the cycle help to quantify the amount of distortions in the elementary structural units, with a pronounced shortening of the Na–Na and Na–O bond lengths during compression. A subsequent decomposition of the glassy matrix into elementary Voronoi volumes verifies the high compressibility of Na-rich regions.

  14. Post-processing interstitialcy diffusion from molecular dynamics simulations

    Science.gov (United States)

    Bhardwaj, U.; Bukkuru, S.; Warrier, M.

    2016-01-01

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms.

  15. Post-processing interstitialcy diffusion from molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India); Bukkuru, S. [Nuclear Physics Dept., Andhra University, Visakhapatnam, 530003 (India); Warrier, M. [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India)

    2016-01-15

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.

  16. Numerical Simulations for Large Deformation of Geomaterials Using Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Ziyang Zhao

    2018-01-01

    Full Text Available From the microperspective, this paper presents a model based on a new type of noncontinuous theoretical mechanical method, molecular dynamics (MD, to simulate the typical soil granular flow. The Hertzian friction formula and viscous damping force are introduced in the MD governing equations to model the granular flow. To show the validity of the proposed approach, a benchmark problem of 2D viscous material flow is simulated. The calculated final flow runout distance of the viscous material agrees well with the result of constrained interpolated profile (CIP method as reported in the literature. Numerical modeling of the propagation of the collapse of three-dimensional axisymmetric sand columns is performed by the application of MD models. Comparison of the MD computational runout distance and the obtained distance by experiment shows a high degree of similarity. This indicates that the proposed MD model can accurately represent the evolution of the granular flow. The model developed may thus find applications in various problems involving dense granular flow and large deformations, such as landslides and debris flow. It provides a means for predicting fluidization characteristics of soil large deformation flow disasters and for identification and design of appropriate protective measures.

  17. Ethane clathrates using different water-ethane models: Molecular dynamics

    Science.gov (United States)

    Torres-García, G.; Luis, D. P.; Odriozola, G.; López-Lemus, J.

    2018-02-01

    Ethane clathrates are studied in a temperature window where the stable-unstable transition takes place by means of molecular dynamics simulations in an isothermal-isobaric ensemble. For this purpose a temperature range [200-440] K and a pressure of 2 MPa are considered. Firstly, structural analysis of the ethane clathrates is carried out at a fixed temperature of 200 K, where clathrates are stable for all considered water models. Here, it is found that structural properties of all stable clathrates do not strongly depend on the water model. As a next step, temperature is increased upon the clathrate turns unstable. This decomposition temperature is found by monitoring coordination numbers, total number of hydrogen-bonds, potential energy, potential of mean force and mean-square displacements. All properties consistently point out to the same temperature at which the stable-unstable transition takes place for each water model. As a part of our results, we notice that by using the standard Lorentz-Berthelot combining rules, the obtained temperature at which the clathrate becomes unstable is higher than the experimental reference value for all used water models. However, we have found that a reasonable way to approach the experimental-decomposition temperature is by including a re-scaling factor in the combining rules in such a way that both methyl-oxygen size and interaction energy turned out decreased. Our data indicates that the decomposition temperature is sensitive to both parameters.

  18. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

    Science.gov (United States)

    Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

    2017-06-20

    With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. Mechanical properties of borophene films: a reactive molecular dynamics investigation

    Science.gov (United States)

    Quy Le, Minh; Mortazavi, Bohayra; Rabczuk, Timon

    2016-11-01

    The most recent experimental advances could provide ways for the fabrication of several atomic thick and planar forms of boron atoms. For the first time, we explore the mechanical properties of five types of boron films with various vacancy ratios ranging from 0.1-0.15, using molecular dynamics simulations with ReaxFF force field. It is found that the Young’s modulus and tensile strength decrease with increasing the temperature. We found that boron sheets exhibit an anisotropic mechanical response due to the different arrangement of atoms along the armchair and zigzag directions. At room temperature, 2D Young’s modulus and fracture stress of these five sheets appear in the range 63-136 N m-1 and 12-19 N m-1, respectively. In addition, the strains at tensile strength are in the ranges of 9%-14%, 11%-19%, and 10%-16% at 1, 300, and 600 K, respectively. This investigation not only reveals the remarkable stiffness of 2D boron, but establishes relations between the mechanical properties of the boron sheets to the loading direction, temperature and atomic structures.

  20. Can molecular dynamics help in understanding dielectric phenomena?

    Science.gov (United States)

    Olmi, Roberto; Bittelli, Marco

    2017-01-01

    Molecular dynamics (MD) is a modeling technique widely used in material science as well as in chemical physics, biochemistry and biophysics. MD is based on ‘first principles’, allowing one to compute the physical characteristics of a material, such as density, heat capacity, isothermal compressibility and also the dielectric constant and relaxation, mixing a classical physics approach and statistical mechanics. Although a number of papers exist in the literature concerning the study of the dielectric properties of liquid and solid materials, the MD approach appears to be almost ignored in the electromagnetic aquametry community. We use a rather simple example, a mixture of ethanol and water at various concentrations, to introduce MD as a theoretical tool for investigating the dielectric behavior of more complex moist substances. We show that MD simulations suggest a time-domain model for alcohol-water solutions, consisting in a mixture of a KWW stretched-exponential and a simple exponential, whose validity could be subjected to an experimental verification.

  1. Microstructure evolution of polycrystalline silicon by molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Xiao Chen

    2017-06-01

    Full Text Available Polycrystalline silicon is the dominant material in solar cells and plays an important role in photovoltaic industry. It is important for not only the conventional production of silicon ingots but also the direct growth of silicon wafers to control crystallization for obtaining the desired polycrystalline silicon. To the best of our knowledge, few studies have systematically reported about the effects of crystalline planes on the solidification behavior of liquid silicon and the analysis of the microstructural features of the polysilicon structure. In this study, molecular dynamics simulations were employed to investigate the solidification and microstructure evolution of polysilicon, with focus on the effects of the seed distribution and cooling rate on the growth of polycrystalline silicon. The (110, (111, and (112 planes were extruded by the (100 plane and formed the inclusion shape. The crystallization of silicon consisted of diamond-type structures is relatively high at a low cooling rate. The simulations provide substantial information regarding microstructures and serve as guidance for the growth of polycrystalline silicon.

  2. Molecular dynamics study of the thermal expansion coefficient of silicon

    Energy Technology Data Exchange (ETDEWEB)

    Nejat Pishkenari, Hossein, E-mail: nejat@sharif.edu; Mohagheghian, Erfan; Rasouli, Ali

    2016-12-16

    Due to the growing applications of silicon in nano-scale systems, a molecular dynamics approach is employed to investigate thermal properties of silicon. Since simulation results rely upon interatomic potentials, thermal expansion coefficient (TEC) and lattice constant of bulk silicon have been obtained using different potentials (SW, Tersoff, MEAM, and EDIP) and results indicate that SW has a better agreement with the experimental observations. To investigate effect of size on TEC of silicon nanowires, further simulations are performed using SW potential. To this end, silicon nanowires of different sizes are examined and their TEC is calculated by averaging in different directions ([100], [110], [111], and [112]) and various temperatures. Results show that as the size increases, due to the decrease of the surface effects, TEC approaches its bulk value. - Highlights: • MD simulations of TEC and lattice constant of bulk silicon. • Effects of four potentials on the results. • Comparison to experimental data. • Investigating size effect on TEC of silicon nanowires.

  3. Molecular dynamics study on friction of multigrain graphene

    Science.gov (United States)

    Kavalur, Aditya; Kim, Woo Kyun

    In addition to its extraordinary mechanical, electronic, and chemical properties, graphene is also a promising material for solid lubrication, which can be used for both macroscopic and small-length scale devices such as MEMS/NEMS. Although a significant number of research efforts have been devoted to unveiling the physical origin of its tribological properties from both experimental and theoretical standpoints, there are still many phenomena which remain far from completely understood. Graphene synthesized by CVD (chemical vapor deposition) is featured with the multi-grain structure, which may have detrimental effects on its mechanical and tribological properties. However, the friction of polycrystalline graphene has rarely been studied. In this study, we investigate the tribological properties of polycrystalline graphene using molecular dynamics methodology. Multigrain structures are created using a novel method and tested against pristine substrates (P-M), these results are compared with pristine-pristine (P-P) interactions. The P-M models exhibit a lower and wider range of friction forces, which may be explained through their individual configurations and a novel orientation-dependent mechanism of friction.

  4. Towards realistic molecular dynamics simulations of grain boundary mobility

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, J., E-mail: zhou@imm.rwth-aachen.de [Institut fuer Metallkunde und Metallphysik, Rheinisch-Westfaelische Technische Hochschule (RWTH), Aachen (Germany); Mohles, V. [Institut fuer Metallkunde und Metallphysik, Rheinisch-Westfaelische Technische Hochschule (RWTH), Aachen (Germany)

    2011-09-15

    In order to investigate grain boundary migration by molecular dynamics (MD) simulations a new approach involving a crystal orientation-dependent driving force has been developed by imposing an appropriate driving force on grain boundary atoms and enlarging the effective range of driving force. The new approach has been validated by the work of the driving force associated with the motion of grain boundaries. With the new approach the relation between boundary migration velocity and driving force is found to be nonlinear, as was expected from rate theory for large driving forces applied in MD simulations. By evaluating grain boundary mobility nonlinearly for a set of symmetrical <1 1 1> tilt boundaries in aluminum at high temperature, high-angle grain boundaries were shown to move much faster than low-angle grain boundaries. This agrees well with experimental findings for recrystallization and grain growth. In comparison with the available data the simulated mobility of a 38.21{sup o{Sigma}}7 boundary was found to be significantly lower than other MD simulation results and comparable with the experimental values. Furthermore, the average volume involved during atomic jumps for boundary migration is determined in MD simulations for the first time. The large magnitude of the volume indicates that grain boundary migration is accomplished by the correlated motion of atom groups.

  5. Hydration of amino acids: FTIR spectra and molecular dynamics studies.

    Science.gov (United States)

    Panuszko, Aneta; Adamczak, Beata; Czub, Jacek; Gojło, Emilia; Stangret, Janusz

    2015-11-01

    The hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results, molecular dynamics simulations of amino acids were performed. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by amino acids forms stronger and shorter H-bonds than those in pure water. Differences in the influence of amino acids on water structure have been noticed. The effect of the hydrophobic side chain of an amino acid on the solvent interactions seems to be enhanced because of the specific cooperative coupling of water strong H-bond chain, connecting the carboxyl and amino groups, with the clathrate-like H-bond network surrounding the hydrocarbon side chain. The parameter derived from the spectral data, which corresponds to the contributions of the population of weak hydrogen bonds of water molecules which have been substituted by the stronger ones in the hydration sphere of amino acids, correlated well with the amino acid hydrophobicity indexes.

  6. Unraveling Mg2+-RNA binding with atomistic molecular dynamics.

    Science.gov (United States)

    Cunha, Richard A; Bussi, Giovanni

    2017-05-01

    Interaction with divalent cations is of paramount importance for RNA structural stability and function. We report here a detailed molecular dynamics study of all the possible binding sites for Mg2+ on an 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 Mg2+ affinity due to ion competition and hybridization, respectively, and predict that RNA flexibility has a site-dependent effect. This suggests a nontrivial interplay between RNA conformational entropy and divalent cation binding. © 2017 Cunha and Bussi; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  7. Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A

    Energy Technology Data Exchange (ETDEWEB)

    Tara, Sylvia; Helms, Volkhard H.; Straatsma, TP; Mccammon, J Andrew A.

    1999-03-16

    Two molecular dynamics simulations were performed for a modeled complex of mouse acetylcholinesterase liganded with huperzine A (HupA). Analysis of these simulations shows that HupA shifts in the active site toward Tyr 337 and Phe 338, and that several residues in the active site area reach out to make hydrogen bonds with the inhibitor. Rapid fluctuations of the gorge width are observed, ranging from widths that allow substrate access to the active site, to pinched structures that do not allow access of molecules as small as water. Additional openings or channels to the active site are found. One opening is formed in the side wall of the active site gorge by residues Val 73, Asp 74, Thr 83, Glu 84, and Asn 87. Another opening is formed at the base of the gorge by residues Trp 86, Val 132, Glu 202, Gly 448, and Ile 451. Both of these openings have been observed separately in the Torpedo californica form of the enzyme. These channels could allow transport of waters and ions to and from the bulk solution.

  8. Molecular Dynamics Study of Hydrogen in α-Zirconium

    Directory of Open Access Journals (Sweden)

    Ravi Kiran Siripurapu

    2014-01-01

    Full Text Available Molecular dynamics approach is used to simulate hydrogen (H diffusion in zirconium. Zirconium alloys are used in fuel channels of many nuclear reactors. Previously developed embedded atom method (EAM and modified embedded atom method (MEAM are tested and a good agreement with experimental data for lattice parameters, cohesive energy, and mechanical properties is obtained. Both EAM and MEAM are used to calculate hydrogen diffusion in zirconium. At higher temperatures and in the presence of hydrogen, MEAM calculation predicts an unstable zirconium structure and low diffusion coefficients. Mean square displacement (MSD of hydrogen in bulk zirconium is calculated at a temperature range of 500–1200 K with diffusion coefficient at 500 K equals 1.92 * 10−7 cm2/sec and at 1200 K has a value 1.47 * 10−4 cm2/sec. Activation energy of hydrogen diffusion calculated using Arrhenius plot was found to be 11.3 kcal/mol which is in agreement with published experimental results. Hydrogen diffusion is the highest along basal planes of hexagonal close packed zirconium.

  9. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

    Science.gov (United States)

    Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

    2011-07-30

    MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

  10. Nanojoining of crossed Ag nanowires: a molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Jianlei, E-mail: cjlxjtu@mail.xjtu.edu.cn; Wang, Xuewen; Barayavuga, Theogene; Mei, Xuesong; Wang, Wenjun [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); He, Xiaoqiao, E-mail: bcxqhe@cityu.edu.hk [City University of Hong Kong, Department of Architecture and Civil Engineering (Hong Kong)

    2016-07-15

    Ag nanowires are considered to be the promising candidates for future electronic circuit owing to the excellent electrical and thermal properties, with the miniaturization of electronics devices into nanometer scale. Though interconnect technology between Ag nanowires (Ag NWs) is essential for nanofunctional devices, it lacks sufficient experimental data. Besides, the determination of Ag NW interconnection configuration is experimentally difficult to do for lacking the sufficient investigation of atomic configuration evolution during nanojoining process. So the nanojoining between the crossed Ag NWs with the same diameter of 2 nm and different lengths was performed by molecular dynamics simulation to explain the unclear nanojoining mechanism based on thermal effect. As the simulation results present, when the nanojoining temperature is relatively high, though the Ag NWs are connected with the interpenetration effect of Ag atoms at the crossed nanojunction area, the nanostructures of Ag NWs have been seriously deformed with shorter length and larger diameter, showing relatively more obvious melting characteristics based on the chaotic atomic structures. If the temperature is reduced to 300 K as cold welding, the crossed Ag NWs can be partially contacted with the partial mixture of Ag atoms, and the interstices always exist between the Si surface and the upper Ag nanowire. In addition, the obvious dislocation phenomenon will appear and evolve as time goes on. Consequently, the dominant mechanism was revealed for providing a fundamental understanding of how ‘hot’ and ‘cold’ welding technology affects the atomic contact configuration, respectively.

  11. PSExplorer: whole parameter space exploration for molecular signaling pathway dynamics.

    Science.gov (United States)

    Tung, Thai Quang; Lee, Doheon

    2010-10-01

    Mathematical models of biological systems often have a large number of parameters whose combinational variations can yield distinct qualitative behaviors. Since it is intractable to examine all possible combinations of parameters for non-trivial biological pathways, it is required to have a systematic strategy to explore the parameter space in a computational way so that dynamic behaviors of a given pathway are estimated. We present PSExplorer, a computational tool for exploring qualitative behaviors and key parameters of molecular signaling pathways. Utilizing the Latin hypercube sampling and a clustering technique in a recursive paradigm, the software enables users to explore the whole parameter space of the models to search for robust qualitative behaviors. The parameter space is partitioned into sub-regions according to behavioral differences. Sub-regions showing robust behaviors can be identified for further analyses. The partitioning result presents a tree structure from which individual and combinational effects of parameters on model behaviors can be assessed and key factors of the models are readily identified. The software, tutorial manual and test models are available for download at the following address: http://gto.kaist.ac.kr/∼psexplorer.

  12. Carbon nanotubes as nanodelivery systems an insight through molecular dynamics simulations

    CERN Document Server

    Lim, Melvin Choon Giap

    2013-01-01

    This book showcases the application of carbon nanotubes as nanodelivery systems for copper atoms, using molecular dynamics simulations as a means of investigation. The nanodelivery system of the carbon nanotube presents the possible usage of the carbon structure in many areas in the future. This book is comprehensive and informative, and serves as a guide for any reader who wishes to perform a molecular dynamics simulation of his own and to conduct an analytical study of a molecular system.

  13. CONDORR--CONstrained Dynamics of Rigid Residues: a molecular dynamics program for constrained molecules.

    Science.gov (United States)

    York, William S; Yi, Xiaobing

    2004-08-01

    A computer program CONDORR (CONstrained Dynamics of Rigid Residues) was developed for molecular dynamics simulations of large and/or constrained molecular systems, particularly carbohydrates. CONDORR efficiently calculates molecular trajectories on the basis of 2D or 3D potential energy maps, and can generate such maps based on a simple force field. The simulations involve three translational and three rotational degrees of freedom for each rigid, asymmetrical residue in the model. Total energy and angular momentum are conserved when no stochastic or external forces are applied to the model, if the time step is kept sufficiently short. Application of Langevin dynamics allows longer time steps, providing efficient exploration of conformational space. The utility of CONDORR was demonstrated by application to a constrained polysaccharide model and to the calculation of residual dipolar couplings for a disaccharide. [Figure: see text]. Molecular models (bottom) are created by cloning rigid residue archetypes (top) and joining them together. As defined here, the archetypes AX, HM and BG respectively correspond to an alpha-D-Xyl p residue, a hydroxymethyl group, and a beta-D-Glc p residue lacking O6, H6a and H6b. Each archetype contains atoms (indicated by boxes) that can be shared with other archetypes to form a linked structure. For example, the glycosidic link between the two D-Glc p residues is established by specifying that O1 of the nonreducing beta-D-Glc p (BG) residue (2) is identical to O4 of the reducing Glc p (BG) residue (1). The coordinates of the two residues are adjusted so as to superimpose these two (nominally distinct) atoms. Flexible hydroxymethyl (HM) groups (3 and 4) are treated as separate residues, and the torsional angles (normally indicated by the symbol omega) that define their geometric relationships to the pyranosyl rings of the BG residues are specified as psi3 and psi4, respectively. The torsional angles phi3 and phi4, defined solely to

  14. Molecular Dynamics Simulations with Quantum Mechanics / Molecular Mechanics and Adaptive Neural Networks.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2018-02-13

    Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in complex environment but very time consuming. The computational cost on QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive way. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

  15. DynamO: a free O(N) general event-driven molecular dynamics simulator.

    Science.gov (United States)

    Bannerman, M N; Sargant, R; Lue, L

    2011-11-30

    Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo. Copyright © 2011 Wiley Periodicals, Inc.

  16. Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method

    Energy Technology Data Exchange (ETDEWEB)

    Gao, N.; Yang, L.; Gao, F.; Kurtz, R. J.; West, D.; Zhang, S.

    2017-02-27

    A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic- scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state con guration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly different time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial- assisted mechanism is rst explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.

  17. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    Directory of Open Access Journals (Sweden)

    Ratna Juwita

    2013-04-01

    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  18. Mechanical properties of nano and bulk Fe pillars using molecular dynamics and dislocation dynamics simulation

    Directory of Open Access Journals (Sweden)

    S. K. Deb Nath

    2017-10-01

    Full Text Available Using molecular dynamics simulation, tension and bending tests of a Fe nanopillar are carried out to obtain its Young’s modulus and yield strength. Then the comparative study of Young’s modulus and yield strength of a Fe nanopillar under bending and tension are carried out varying its diameter in the range of diameter 1-15nm. We find out the reasons why bending Young’s modulus and yield strength of a Fe nanopillar are higher than those of tension Young’s modulus and yield strength of a Fe nanopillar. Using the mobility parameters of bulk Fe from the experimental study [N. Urabe and J. Weertman, Materials Science and Engineering 18, 41 (1975], its temperature dependent stress-strain relationship, yield strength and strain hardening modulus are obtained from the dislocation dynamics simulations. Strain rate dependent yield strength and strain hardening modulus of bulk Fe pillars under tension are studied. Temperature dependent creep behaviors of bulk Fe pillars under tension are also studied. To verify the soundness of the present dislocation dynamics studies of the mechanical properties of bulk Fe pillars under tension, the stress vs. strain relationship and dislocation density vs. strain of bulk Fe pillars obtained by us are compared with the published results obtained by S. Queyreau, G. Monnet, and B. Devincre, International Journal of Plasticity 25, 361 (2009.

  19. Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method

    Science.gov (United States)

    Gao, N.; Yang, L.; Gao, F.; Kurtz, R. J.; West, D.; Zhang, S.

    2017-04-01

    A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic-scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state configuration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly different time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial-assisted mechanism is first explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.

  20. Mechanical properties of nano and bulk Fe pillars using molecular dynamics and dislocation dynamics simulation

    Science.gov (United States)

    Nath, S. K. Deb

    2017-10-01

    Using molecular dynamics simulation, tension and bending tests of a Fe nanopillar are carried out to obtain its Young's modulus and yield strength. Then the comparative study of Young's modulus and yield strength of a Fe nanopillar under bending and tension are carried out varying its diameter in the range of diameter 1-15nm. We find out the reasons why bending Young's modulus and yield strength of a Fe nanopillar are higher than those of tension Young's modulus and yield strength of a Fe nanopillar. Using the mobility parameters of bulk Fe from the experimental study [N. Urabe and J. Weertman, Materials Science and Engineering 18, 41 (1975)], its temperature dependent stress-strain relationship, yield strength and strain hardening modulus are obtained from the dislocation dynamics simulations. Strain rate dependent yield strength and strain hardening modulus of bulk Fe pillars under tension are studied. Temperature dependent creep behaviors of bulk Fe pillars under tension are also studied. To verify the soundness of the present dislocation dynamics studies of the mechanical properties of bulk Fe pillars under tension, the stress vs. strain relationship and dislocation density vs. strain of bulk Fe pillars obtained by us are compared with the published results obtained by S. Queyreau, G. Monnet, and B. Devincre, International Journal of Plasticity 25, 361 (2009).

  1. Molecular-dynamics simulations of the dynamical excitations in commensurate submonolayer films of nitrogen molecules on graphite

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Bruch, Ludwig Walter; Taub, H.

    1996-01-01

    The dynamics of commensurate submonolayer solids of N-2 molecules adsorbed on the basal planes of graphite have been studied using molecular-dynamics simulations. The calculations yielded the temperature dependence of the Brillouin-zone-center gap in the acoustic-phonon branches, for comparison...

  2. Deep molecular characterization of HIV-1 dynamics under suppressive HAART.

    Directory of Open Access Journals (Sweden)

    Maria J Buzón

    2011-10-01

    Full Text Available In order to design strategies for eradication of HIV-1 from infected individuals, detailed insight into the HIV-1 reservoirs that persist in patients on suppressive antiretroviral therapy (ART is required. In this regard, most studies have focused on integrated (proviral HIV-1 DNA forms in cells circulating in blood. However, the majority of proviral DNA is replication-defective and archival, and as such, has limited ability to reveal the dynamics of the viral population that persists in patients on suppressive ART. In contrast, extrachromosomal (episomal viral DNA is labile and as a consequence is a better surrogate for recent infection events and is able to inform on the extent to which residual replication contributes to viral reservoir maintenance. To gain insight into the diversity and compartmentalization of HIV-1 under suppressive ART, we extensively analyzed longitudinal peripheral blood mononuclear cells (PBMC samples by deep sequencing of episomal and integrated HIV-1 DNA from patients undergoing raltegravir intensification. Reverse-transcriptase genes selectively amplified from episomal and proviral HIV-1 DNA were analyzed by deep sequencing 0, 2, 4, 12, 24 and 48 weeks after raltegravir intensification. We used maximum likelihood phylogenies and statistical tests (AMOVA and Slatkin-Maddison (SM in order to determine molecular compartmentalization. We observed low molecular variance (mean variability ≤0.042. Although phylogenies showed that both DNA forms were intermingled within the phylogenetic tree, we found a statistically significant compartmentalization between episomal and proviral DNA samples (P<10(-6 AMOVA test; P = 0.001 SM test, suggesting that they belong to different viral populations. In addition, longitudinal analysis of episomal and proviral DNA by phylogeny and AMOVA showed signs of non-chronological temporal compartmentalization (all comparisons P<10(-6 suggesting that episomal and proviral DNA forms originated

  3. Structure, dynamics, and reactivity of hydrated electrons by ab initio molecular dynamics.

    Science.gov (United States)

    Marsalek, Ondrej; Uhlig, Frank; VandeVondele, Joost; Jungwirth, Pavel

    2012-01-17

    Understanding the properties of hydrated electrons, which were first observed using pulse radiolysis of water in 1962, is crucial because they are key species in many radiation chemistry processes. Although time-resolved spectroscopic studies and molecular simulations have shown that an electron in water (prepared, for example, by water photoionization) relaxes quickly to a localized, cavity-like structure ∼2.5 Å in radius, this picture has recently been questioned. In another experimental approach, negatively charged water clusters of increasing size were studied with photoelectron and IR spectroscopies. Although small water clusters can bind an excess electron, their character is very different from bulk hydrated species. As data on electron binding in liquid water have become directly accessible experimentally, the cluster-to-bulk extrapolations have become a topic of lively debate. Quantum electronic structure calculations addressing experimental measurables have, until recently, been largely limited to small clusters; extended systems were approached mainly with pseudopotential calculations combining a classical description of water with a quantum mechanical treatment of the excess electron. In this Account, we discuss our investigations of electrons solvated in water by means of ab initio molecular dynamics simulations. This approach, applied to a model system of a negatively charged cluster of 32 water molecules, allows us to characterize structural, dynamical, and reactive aspects of the hydrated electron using all of the system's valence electrons. We show that under ambient conditions, the electron localizes into a cavity close to the surface of the liquid cluster. This cavity is, however, more flexible and accessible to water molecules than an analogous area around negatively charged ions. The dynamical process of electron attachment to a neutral water cluster is strongly temperature dependent. Under ambient conditions, the electron relaxes in the

  4. Molecular dynamics simulation studies of tailored nanostructured polymers

    Science.gov (United States)

    Liu, Lixin

    With recent advancements in the synthesis and characterization of polymeric materials, scientists are able to create multi-scale novel polymers with various cases of chemical functionalities, diversified topologies, as well as cross-linking networks. Due to those remarkable achievements, there are a broad range of possible applications of smart polymers in catalysis, in environmental remediation, and especially in drug-delivery. Because of rising interest in developing therapeutic drug binding to specific treating target, polymer chemists are in particular interests in design and engineering the drug delivery materials to be not only bio-compatible, but also to be capable of self-assembly at various in-vivo physiological stimulus. Both experimental and theoretical work indicate that the thermodynamic properties relating to the hydrophobic effect play an important role in determining self-assembly process. At the same time, computational simulation and modeling are powerful instruments to contribute to microscopic thermodynamics' understanding toward self-assembly phenomenon. Along with statistical approaches, constructing empirical model based on simulation results would also help predict for further development of tailored nano-structured materials. My Research mainly focused on investigating physical and chemical characteristics of polymer materials through molecular dynamics simulation and probing the fundamental thermodynamic driving force of self-assembly behavior. We tried to surmount technological obstacles in computational chemistry and build an efficient scheme to identify the physical and chemical Feature of molecules, to reproduce underlying properties, to understand the origin of thermodynamic signatures, and to speed up current trial and error process in screening new materials.

  5. Molecular dynamics simulations for human CAR inverse agonists.

    Science.gov (United States)

    Jyrkkärinne, Johanna; Küblbeck, Jenni; Pulkkinen, Juha; Honkakoski, Paavo; Laatikainen, Reino; Poso, Antti; Laitinen, Tuomo

    2012-02-27

    Constitutive androstane receptor (CAR), along with pregnane x receptor (PXR), is an important metabolic sensor in the hepatocytes. Like all other nuclear receptors (NRs), CAR works in concert with coregulator proteins, coactivators, and corepressors which bind to the NRs. The main basis for the receptor to distinguish between coactivators and corepressors is the position of the C-terminal helix 12 (H12), which is determined by the bound NR ligand. CAR, having constitutive activity, can be repressed or further activated by its ligands. Crystal structure of human CAR bound to an agonist and a coactivator peptide is available, but no structural information on an inverse agonist-bound human CAR and a corepressor exists. In our previous molecular dynamics (MD) studies, no corepressor peptide was included. Therefore, probably due to the strong interactions which keep the relatively short H12 of CAR in the active position, the structural changes elicited by inverse agonists were very subtle, and H12 of CAR seemed to more or less retain its active conformation. Here, we have run a series of MD simulations to study the movement of H12 in the presence of both activating and repressing ligands as well as a corepressor peptide. The presence of the corepressor on the coregulator surface of CAR induced a clear shift of H12 of the inverse agonists-bound CAR. In general, H12 moved toward H10 and not away from the ligand binding domain, as seen in some other NRs. However, H12 of CAR is short enough that this movement seems to be adequate to accommodate the binding of the corepressor.

  6. Stability mechanisms of a thermophilic laccase probed by molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Niels J Christensen

    Full Text Available Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K, probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K from 300 K, this change correlated with a beginning "unzipping" of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive at 400 K, suggesting a general salt stabilization effect. In contrast, F(- (but not Cl(- specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(- intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes.

  7. Surface Structure of Hydroxyapatite from Simulated Annealing Molecular Dynamics Simulations.

    Science.gov (United States)

    Wu, Hong; Xu, Dingguo; Yang, Mingli; Zhang, Xingdong

    2016-05-10

    The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca(2+) ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules.

  8. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  9. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  10. Structure of beryllium isotopes in fermionic molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Torabi, Bahram Ramin

    2009-02-16

    Modern theoretical nuclear physics faces two major challenges. The first is finding a suitable interaction, which describes the forces between nucleons. The second challenge is the solution of the nuclear many-body problem for a given nucleus while applying a realistic potential. The potential used in the framework of this thesis is based on the Argonne AV18 potential. It was transformed by means of the Unitary Correlation Operator Method (UCOM) to optimize convergence. The usual phenomenological corrections were applied to improve the potential for the Hilbert space used in Fermionic Molecular Dynamics (FMD). FMD is an approach to solve the nuclear many-body problem. It uses a single-particle basis which is a superposition of Gaussian distributions in phase-space. The most simple many-body state is the antisymmetric product of the singleparticle states: a Slater determinant, the so called intrinsic state. This intrinsic state is projected on parity, total angular momentum and a center of mass momentum zero. The Hilbert space is spanned by several of these projected states. The states are obtained by minimizing their energy while demanding certain constraints. The expectation values of Slater determinants, parity projected and additionally total angular momentum projected Slater determinants are used. The states that are relevant in the low energy regime are obtained by diagonalization. The lowest moments of the mass-, proton- or neutron-distribution and the excitation in proton- and neutron-shells of a harmonic oscillator are some of the used constraints. The low energy regime of the Beryllium isotopes with masses 7 to 14 is calculated by using these states. Energies, radii, electromagnetic transitions, magnetic moments and point density distributions of the low lying states are calculated and are presented in this thesis. (orig.)

  11. Contact angles from Young's equation in molecular dynamics simulations

    Science.gov (United States)

    Jiang, Hao; Müller-Plathe, Florian; Panagiotopoulos, Athanassios Z.

    2017-08-01

    We propose a method to calculate the equilibrium contact angle of heterogeneous 3-phase solid/fluid/fluid systems using molecular dynamics simulations. The proposed method, which combines the phantom-wall method [F. Leroy and F. Müller-Plathe, J. Chem. Phys. 133, 044110 (2010)] and Bennett's acceptance ratio approach [C. H. Bennett, J. Comput. Phys. 22, 245 (1976)], is able to calculate the solid/fluid surface tension relative to the solid surface energy. The calculated relative surface tensions can then be used in Young's equation to estimate the equilibrium contact angle. A fluid droplet is not needed for the proposed method, in contrast to the situation for direct simulations of contact angles. In addition, while prior free-energy based methods for contact angles mainly focused on the wetting of fluids in coexistence with their vapor on solid surfaces, the proposed approach was designed to study the contact angles of fluid mixtures on solid surfaces above the fluid saturation pressures. Using the proposed approach, the contact angles of binary Lennard-Jones fluid mixtures on a non-polar solid substrate were calculated at various interaction parameters and the contact angle of water in equilibrium with CO2 on a hydrophilic polar silica surface was obtained. For both non-polar and polar systems, the calculated contact angles from the proposed method were in agreement with those obtained from the geometry of a cylindrical droplet. The computational cost of the proposed method was found to be comparable to that of simulations that use fluid droplets, but the new method provides a way to calculate the contact angle directly from Young's equation without ambiguity.

  12. Development of molecular dynamics potential for uranium silicide fuels

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Jianguo; Zhang, Yongfeng; Hales, Jason D.

    2016-09-01

    Use of uranium–silicide (U-Si) in place of uranium dioxide (UO2) is one of the promising concepts being proposed to increase the accident tolerance of nuclear fuels. This is due to a higher thermal conductivity than UO2 that results in lower centerline temperatures. U-Si also has a higher fissile density, which may enable some new cladding concepts that would otherwise require increased enrichment limits to compensate for their neutronic penalty. However, many critical material properties for U-Si have not been determined experimentally. For example, silicide compounds (U3Si2 and U3Si) are known to become amorphous under irradiation. There was clear independent experimental evidence to support a crystalline to amorphous transformation in those compounds. However, it is still not well understood how the amorphous transformation will affect on fuel behavior. It is anticipated that modeling and simulation may deliver guidance on the importance of various properties and help prioritize experimental work. In order to develop knowledge-based models for use at the engineering scale with a minimum of empirical parameters and increase the predictive capabilities of the developed model, inputs from atomistic simulations are essential. First-principles based density functional theory (DFT) calculations will provide the most reliable information. However, it is probably not possible to obtain kinetic information such as amorphization under irradiation directly from DFT simulations due to size and time limitations. Thus, a more feasible way may be to employ molecular dynamics (MD) simulation. Unfortunately, so far no MD potential is available for U-Si to discover the underlying mechanisms. Here, we will present our recent progress in developing a U-Si potential from ab initio data. This work is supported by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program funded by the U.S. Department of Energy, Office of Nuclear Energy.

  13. Molecular dynamics simulations of bubble nucleation in dark matter detectors.

    Science.gov (United States)

    Denzel, Philipp; Diemand, Jürg; Angélil, Raymond

    2016-01-01

    Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.

  14. Molecular Dynamics Simulation of Valveless Pumping in a Closed Nanofluidic Tube System

    DEFF Research Database (Denmark)

    Hansen, Jesper S.; Ottesen, Johnny T.

    2009-01-01

    In this paper we perform a realistic nonequilibrium molecular dynamics simulation of valveless pumping in a closed nanofluidic tube system. It is shown that the simple pumping mechanism can generate a uni-directional mean flow on very small length and times scales, thereby overcoming the technical...... difficulties often encountered when manufacturing more complex pumping devices. From the molecular dynamics simulation we obtain the spatio temporal dynamics of the pressure. The molecular dynamics results are substituted into the Navier-Stokes equation and we are then able to extract the local streaming...... velocity profiles sufficiently far away from the pumping device. The mean streaming velocity is compared with molecular dynamics data showing excellent agreement. Detailed knowledge about these profiles will be valuable for future investigation of this remarkable system....

  15. Medicinal plant phytochemicals and their inhibitory activities against pancreatic lipase: molecular docking combined with molecular dynamics simulation approach

    OpenAIRE

    Ahmed, Bilal; Ali Ashfaq, Usman; Mirza, Muhammad Usman

    2017-01-01

    Obesity is the worst health risk worldwide, which is linked to a number of diseases. Pancreatic lipase is considered as an affective cause of obesity and can be a major target for controlling the obesity. The present study was designed to find out best phytochemicals against pancreatic lipase through molecular docking combined with molecular dynamics (MD) simulation. For this purpose, a total of 3770 phytochemicals were docked against pancreatic lipase and ranked them on the basis of binding ...

  16. Dynamically Tunable Nanoporous Gold for Ionic and Molecular Separations

    Science.gov (United States)

    McCurry, Daniel Arthur

    , and oxide stripping voltammetry. Gateable molecular and ionic transport through NPG was obtained by dynamic electrochemical modulation of the electrical double layer (EDL) within the pores. Application of a salt gradient across bare NPG was also used to impose an asymmetrical EDL thickness, whereas NPG coated with self-assembled monolayers altered the surface charge through the oxidation or reduction of surface moieties. Initial studies regarding protein and DNA transport through NPG have been performed. Lysozyme (Lys), bovine serum albumin (BSA), and bovine hemoglobin (BHb) served as model proteins due to differences in their isoelectric points (Lys: 11.4, BHb: 6.8, BSA: 4.7). Lys was shown to have a much stronger correlation to an applied transverse migration potential through the NPG, most likely due to its small size ( 14.3 kDa) compared to that of BSA ( 66.4 kDa) and BHb ( 64.5 kDa). DNA flux through NPG was found to be entropically unfavored and therefore demonstrated much lower rates of transport. Finally, a microfabrication route is proposed in order to scale the NPG membrane to a microfluidic device.

  17. Proton transfer dynamics in the propionic acid dimer from path integral molecular dynamics calculations.

    Science.gov (United States)

    Durlak, Piotr; Latajka, Zdzisław

    2011-09-01

    The double proton transfer process in the cyclic dimer of propionic acid in the gas phase was studied using a path integral molecular dynamics method. Structures, energies and proton trajectories were determined. Very large amplitude motions of the skeleton of a propionic acid molecule were observed during the simulations, and almost free rotation of the C(2)H(5) group around the C(α)-C bond. A double-well symmetric potential with a very small energy barrier was determined from the free energy profile for the proton motions. Infrared spectra for different isotopomers were calculated, and comparative vibrational analysis was performed. The vibrational results from CPMD appear to be in qualitative agreement with the experimental ones.

  18. Dynamic Combinatorial Libraries : From Exploring Molecular Recognition to Systems Chemistry

    NARCIS (Netherlands)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-01-01

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many

  19. Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations?

    Science.gov (United States)

    Hub, Jochen S; Grubmüller, Helmut; de Groot, Bert L

    2009-01-01

    Aquaporins (AQPs) are a family of integral membrane proteins, which facilitate the rapid and yet highly selective flux of water and other small solutes across biological membranes. Molecular dynamics (MD) simulations contributed substantially to the understanding of the molecular mechanisms that underlie this remarkable efficiency and selectivity of aquaporin channels. This chapter reviews the current state of MD simulations of aquaporins and related aquaglyceroporins as well as the insights these simulations have provided. The mechanism of water permeation through AQPs and methods to determine channel permeabilities from simulations are described. Protons are strictly excluded from AQPs by a large electrostatic barrier and not by an interruption of the Grotthuss mechanism inside the pore. Both the protein's electric field and desolvation effects contribute to this barrier. Permeation of apolar gas molecules such as CO(2) through AQPs is accompanied by a large energetic barrier and thus can only be expected in membranes with a low intrinsic gas permeability. Additionally, the insights from simulations into the mechanism of glycerol permeation through the glycerol facilitator GlpF from E. coli are summarized. Finally, MD simulations are discussed that revealed that the aro-matic/arginine constriction region is generally the filter for uncharged solutes, and that AQP selectivity is controlled by a hydrophobic effect and steric restraints.

  20. Molecular dynamics simulation: at a crossroad between molecular biophysics and petascale computing

    Science.gov (United States)

    Cheng, Xiaolin

    2015-03-01

    High-performance computing (HPC) has become crucial for most advances made in chemistry and biology today. In particular, biophysical simulation is capable of helping generate critical new insights and drive the direction of experimentation. In this talk, I will discuss our work towards addressing some fundamental membrane biophysical questions using HPC capabilities at Oak Ridge National Laboratory. I will first provide a synopsis of our current progress in developing molecular dynamics (MD) techniques that make efficient use of massively parallel supercomputers. I will then discuss a few examples of large-scale MD simulations of biomembrane vesicles, an effort aimed at shedding light on the lateral organization and cross-layer coupling in biologically-relevant membranes. In conclusion, I will discuss a few scientific and technical challenges faced by MD simulation at the exascale. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

  1. Molecular Mechanisms of How Mercury Inhibits Water Permeation through Aquaporin-1: Understanding by Molecular Dynamics Simulation

    Science.gov (United States)

    Hirano, Yoshinori; Okimoto, Noriaki; Kadohira, Ikuko; Suematsu, Makoto; Yasuoka, Kenji; Yasui, Masato

    2010-01-01

    Abstract Aquaporin (AQP) functions as a water-conducting pore. Mercury inhibits the water permeation through AQP. Although site-directed mutagenesis has shown that mercury binds to Cys189 during the inhibition process, it is not fully understood how this inhibits the water permeation through AQP1. We carried out 40 ns molecular dynamics simulations of bovine AQP1 tetramer with mercury (Hg-AQP1) or without mercury (Free AQP1). In Hg-AQP1, Cys191 (Cys189 in human AQP1) is converted to Cys-SHg+ in each monomer. During each last 10 ns, we observed water permeation events occurred 23 times in Free AQP1 and never in Hg-AQP1. Mercury binding did not influence the whole structure, but did induce a collapse in the orientation of several residues at the ar/R region. In Free AQP1, backbone oxygen atoms of Gly190, Cys191, and Gly192 lined, and were oriented to, the surface of the water pore channel. In Hg-AQP1, however, the SHg+ of Cys191-SHg+ was oriented toward the outside of the water pore. As a result, the backbone oxygen atoms of Gly190, Cys191, and Gly192 became disorganized and the ar/R region collapsed, thereby obstructing the permeation of water. We suggest that mercury disrupts the water pore of AQP1 through local conformational changes in the ar/R region. PMID:20409470

  2. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    Science.gov (United States)

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

  3. The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water with the Fragment Molecular Orbital Method

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Spencer R.; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham D.; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, M

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.

  4. POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

    Science.gov (United States)

    Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

    2015-12-01

    We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

  5. Molecular dynamics study of ferroelectric domain nucleation and domain switching dynamics.

    Science.gov (United States)

    Boddu, Vishal; Endres, Florian; Steinmann, Paul

    2017-04-11

    Ferroelectric materials contain domains of ordered electric dipoles, separated by domain walls, that can undergo polarisation switching under externally applied electric fields. The domain switching dynamics in ferroelectric materials plays an essential role in their application to electronic and electro-optic de- vices. Previous studies suggest that the switching occurs largely through domain wall motion which is explained from the viewpoint of statistical physics on surface growth as the behaviour of a pinned elas- tic interface. We perform molecular dynamics simulations to investigate the domain switching process and quantitatively estimate the switching speed of anti-parallel 180° domains in ferroelectric, tetragonal BaTiO 3 perfect single crystals at room temperature using the core-shell model. We observe an unprece- dented, non-linear increase in the domain switching speed caused by the nucleation of new domains within the switching domain. We determine the strength of the electric field to evoke nucleation of new domains and show that the nucleated domains diffuse into nearby favourable domains when the electric field is removed. Furthermore, we discuss the prominence of domain nucleations during ferroelectric switching.

  6. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  7. Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations.

    Science.gov (United States)

    Posokhov, Yevgen O; Kyrychenko, Alexander

    2013-10-01

    The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ~0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of -3.6 kcal/mol, located at 15-16Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8-5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and

  8. Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study

    Science.gov (United States)

    Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

    2017-10-01

    The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.

  9. Molecular Dynamics Modeling of PPTA Crystals in Aramid Fibers

    Energy Technology Data Exchange (ETDEWEB)

    Mercer, Brian Scott [Univ. of California, Berkeley, CA (United States)

    2016-05-19

    In this work, molecular dynamics modeling is used to study the mechanical properties of PPTA crystallites, which are the fundamental microstructural building blocks of polymer aramid bers such as Kevlar. Particular focus is given to constant strain rate axial loading simulations of PPTA crystallites, which is motivated by the rate-dependent mechanical properties observed in some experiments with aramid bers. In order to accommodate the covalent bond rupture that occurs in loading a crystallite to failure, the reactive bond order force eld ReaxFF is employed to conduct the simulations. Two major topics are addressed: The rst is the general behavior of PPTA crystallites under strain rate loading. Constant strain rate loading simulations of crystalline PPTA reveal that the crystal failure strain increases with increasing strain rate, while the modulus is not a ected by the strain rate. Increasing temperature lowers both the modulus and the failure strain. The simulations also identify the C N bond connecting the aromatic rings as weakest primary bond along the backbone of the PPTA chain. The e ect of chain-end defects on PPTA micromechanics is explored, and it is found that the presence of a chain-end defect transfers load to the adjacent chains in the hydrogen-bonded sheet in which the defect resides, but does not in uence the behavior of any other chains in the crystal. Chain-end defects are found to lower the strength of the crystal when clustered together, inducing bond failure via stress concentrations arising from the load transfer to bonds in adjacent chains near the defect site. The second topic addressed is the nature of primary and secondary bond failure in crystalline PPTA. Failure of both types of bonds is found to be stochastic in nature and driven by thermal uctuations of the bonds within the crystal. A model is proposed which uses reliability theory to model bonds under constant strain rate loading as components with time-dependent failure rate

  10. Molecular dynamics simulation of a two-dimensional system

    Directory of Open Access Journals (Sweden)

    S. M. Huseini

    2001-06-01

    Full Text Available   The study of a two-dimensional (2-D system started nearly half a century ago when Peierls and Landau showed the lack of long range translational order in a two-dimensional solid. In 1968, Mermin proved that despite the absence of long range translational order. Two-dimensional solids can still exhibit a different kind of long range bond orientation. During the last decade, fascinating theories were put forward to explain the role of topological defects in the melting of two-dimensional solids, starting with Kosterlitz and Thouless. Recent surge of interest in melting is also due to the theoretical ideas of Halperin, Nelson and Young. They have suggested that the transition may be fundamentally different from that observed in ordinary three-dimensional systems. Computer simulations suggest that the transition is of the usual first-order type observed in a three-dimensional system. A large body of experimental and simulation research into the two-dimensional melting followed the announcement of the KTHNY theory. In spite of all this effort, the question as to the nature of two dimensional melting remains unresolved. Recent experimental work supporting the existence of continuous melting transitions in some two-dimentsional systems indicates the need for further theoretical and computational work to lead to an understanding of the experimental results.   In this paper we intend to summarze and clarify the current situation with regard to research in the two-dimensional melting with an emphasis on computer simulations. The paper begins with an overview of the current status of relevant theoretical, experimental and simulation research, then a two-dimensional simulation of an ionic salt system is studied in detail. This simulation has been done by using the molecular dynamics method. The most important parameters that have been determined are ,The trnsition temperature, the total energy of the system, the mean square displacement and the bond

  11. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    Directory of Open Access Journals (Sweden)

    G.M. Bhuiyan

    2012-10-01

    Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  12. Thermal Stability of Modified Insulation Paper Cellulose Based on Molecular Dynamics Simulation

    National Research Council Canada - National Science Library

    Chao Tang; Song Zhang; Qian Wang; Xiaobo Wang; Jian Hao

    2017-01-01

    In this paper, polysiloxane is used to modify insulation paper cellulose, and molecular dynamics methods are used to evaluate the glass transition temperature and mechanical properties of the paper...

  13. Impact of vacancies on the thermal conductivity of graphene nanoribbons: A molecular dynamics simulation study

    National Research Council Canada - National Science Library

    Noshin, Maliha; Khan, Asir Intisar; Navid, Ishtiaque Ahmed; Uddin, H. M. Ahsan; Subrina, Samia

    2017-01-01

    Equilibrium molecular dynamics simulation using 2nd generation Reactive Bond Order interatomic potential has been performed to model the thermal transport of nanometer sized zigzag defected graphene nanoribbons (GNRs...

  14. Introduction to the quantum trajectory method and to Fermi molecular dynamics

    CERN Document Server

    Lagattuta, K J

    2003-01-01

    The quantum trajectory method (QTM) will be introduced, and an approximation to the QTM known as Fermi molecular dynamics (FMD) will be described. Results of simulations based on FMD will be mentioned for specific nonequilibrium systems dominated by Coulomb interactions.

  15. Determining the shear viscosity of model liquids from molecular dynamics simulations

    NARCIS (Netherlands)

    Hess, B

    2002-01-01

    Several methods are available for calculating shear viscosities of liquids from molecular dynamics simulations. There are equilibrium methods based on pressure or momentum fluctuations and several nonequilibrium methods. For the nonequilibrium method using a periodic shear flow, all relevant

  16. Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

    Energy Technology Data Exchange (ETDEWEB)

    Okumura, Hisashi [Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585 (Japan); Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 (Japan)

    2015-12-31

    Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

  17. A molecular dynamics study of the effects of fast molecular motions on solid-state NMR parameters

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Hodgkinson, P.

    2013-01-01

    Roč. 15, č. 43 (2013), s. 8705-8712 ISSN 1466-8033 Grant - others:Seventh Framework Programme of the European Union(XE) FP7-299242 People Institutional support: RVO:61388963 Keywords : molecular dynamics * DFT calculations * NMR spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 3.858, year: 2013

  18. Memory effects in nonadiabatic molecular dynamics at metal surfaces

    DEFF Research Database (Denmark)

    Olsen, Thomas; Schiøtz, Jakob

    2010-01-01

    We study the effect of temporal correlation in a Langevin equation describing nonadiabatic dynamics at metal surfaces. For a harmonic oscillator, the Langevin equation preserves the quantum dynamics exactly and it is demonstrated that memory effects are needed in order to conserve the ground state...... energy of the oscillator. We then compare the result of Langevin dynamics in a harmonic potential with a perturbative master equation approach and show that the Langevin equation gives a better description in the nonperturbative range of high temperatures and large friction. Unlike the master equation...... the temporal correlation function and dynamical friction within density functional theory....

  19. An adaptive mass algorithm for Car-Parrinello and Ehrenfest ab initio molecular dynamics

    OpenAIRE

    Kadir, Ashraful; Sandberg, Mattias; Szepessy, Anders

    2014-01-01

    Ehrenfest and Car-Parrinello molecular dynamics are computational alternatives to approximate Born-Oppenheimer molecular dynamics without solving the electron eigenvalue problem at each time-step. A non-trivial issue is to choose the artificial electron mass parameter appearing in the Car-Parrinello method to achieve both good accuracy and high computational efficiency. In this paper, we propose an algorithm, motivated by the Landau-Zener probability, to systematically choose an artificial ma...

  20. 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...

  1. Dataset showing the impact of the protonation states on molecular dynamics of HIV protease

    Directory of Open Access Journals (Sweden)

    Rosemberg O. Soares

    2016-09-01

    Full Text Available The data described here supports the research article “Unraveling HIV Protease Flaps Dynamics by Constant pH Molecular Dynamics Simulations” (Soares et al., 2016 [1]. The data involves both standard Molecular Dynamics (MD and Constant pH Molecular Dynamics (CpHMD to elucidate the effect of protonation states of catalytic dyad on the HIV-PR conformation. The data obtained from MD simulation demonstrate that the protonation state of the two aspartic acids (Asp25/Asp25′ has a strong influence on the dynamics of the HIV-PR. Regarding the CpHMD simulation, we performed pka calculations for HIV-PR and the data indicate that only one catalytic aspartate should be protonated.

  2. Creating Stop-Motion Animations to Learn Molecular Biology Dynamics

    Directory of Open Access Journals (Sweden)

    Celeste N. Peterson

    2015-08-01

    Full Text Available Classes in molecular biology have historically used static diagrams to capture how molecular processes occur in space and time. Here we describe using 3D claymation as an alternative. Students choose a molecular process, plan how to represent it with physical objects, and produce a stop motion video that then is shared with other students over the internet. This process can be easily implemented in undergraduate biology classes at all levels, and requires very little resources. The exercise offers the students a multisensory learning experience and the opportunity to contribute to open education resources. 

  3. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

    NARCIS (Netherlands)

    Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

    2007-01-01

    We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated

  4. Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations

    NARCIS (Netherlands)

    Haverkort, Frank; Stradomska, Anna; de Vries, Alex H.; Knoester, Jasper

    2013-01-01

    We perform molecular dynamics (MD) simulations of the self-assembly process of pseudoisocyanine dye molecules with amphiphilic substituents (amphi-PIC). The spontaneous aggregation of cyanine molecules into large molecular J-aggregates with optical functionality has drawn attention for many decades

  5. Car-Parrinello Molecular Dynamics With A Sinusoidal Time-Dependent Potential Field

    OpenAIRE

    Alznauer, Tobias; Frank, Irmgard

    2012-01-01

    We solve the problem of applying an external field in periodic boundary conditions by choosing a sine potential. We present an implementation in the Car-Parrinello molecular dynamics code (CPMD) and discuss applications to electron and ion transfers in complex molecular systems.

  6. Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study

    DEFF Research Database (Denmark)

    Laradji, Mohamed; Mouritsen, Ole G.

    2000-01-01

    Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface, corres...

  7. Molecular Dynamics Study of Alkanethiolate Self-Assembled Monolayer Coated Gold Nanoparticle

    Science.gov (United States)

    2007-06-01

    of Organosulfur Compounds on Au( 111). Implications for Molecular Self-Assembly on Gold 21. Plimpton, S.J., "Fast Parallel Algorithms for Short-Range... Organosulfur Compounds SHAKE Algorithm for Molecular Dynamics." Journal of Adsorbed on Gold Single Crystals: Electron Diffraction Computational Physics, 52

  8. Molecular dynamic simulation of complex NS2B-NS3 DENV2 ...

    African Journals Online (AJOL)

    In many researches, several models of peptides inhibitor were generated in complexes with the NS2B-NS3 DENV2 protease by performing molecular docking. The goal of this research was to study the interaction of ligands as inhibitors for protein (enzyme) in solvent explicit condition by performing molecular dynamics ...

  9. Transport diffusion of argon in AIPO4-5 from equilibrium molecular dynamics simulations

    NARCIS (Netherlands)

    Hoogenboom, Jacob; Tepper, H.L.; van der Vegt, N.F.A.; Briels, Willem J.

    2000-01-01

    Transport diffusion of argon in the unidirectional channels of the molecular sieve AlPO4-5 has been studied using molecular dynamics simulations. Using the Green–Kubo formalism, this nonequilibrium property is, for the first time, extracted from just one equilibrium simulation. Apart from the

  10. Molecular dynamics calculations of melting rates with a novel order parameter. The diatomic Pa3 crystal.

    NARCIS (Netherlands)

    Tepper, H.L.; Scheinhardt-Engels, S.M.; Briels, Willem J.

    2003-01-01

    A method is presented to design order parameters that can be used as discriminator in two-phase crystal-liquid molecular dynamics simulations. The proposed methodology is an extension to molecular crystal structures of a previously introduced discriminator for the atomic fcc environment [Phys. Rev.

  11. Creating Stop-Motion Animations to Learn Molecular Biology Dynamics

    National Research Council Canada - National Science Library

    Peterson, Celeste N; Ngo, Pauline

    2015-01-01

    .... Here we describe using 3D claymation as an alternative. Students choose a molecular process, plan how to represent it with physical objects, and produce a stop motion video that then is shared with other students over the internet...

  12. 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.

  13. Structural and dipolar fluctuations in liquid water: a Car–Parrinello molecular dynamics study

    OpenAIRE

    Skarmoutsos, Ioannis; Masia, Marco; Guàrdia Manuel, Elvira

    2016-01-01

    A Car–Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order...

  14. Molecular music: Repurposing a mixed quantum-classical atomic dynamics model as an audiovisual instrument

    OpenAIRE

    Hyde, J. I.; Mitchell, T J; Tew, P.; Glowacki, D. R.

    2014-01-01

    Molecular Music is an offshoot of a long-term collaborative project, the multi- award winning danceroom Spectroscopy (dS)[1]. dS has its roots in computational molecular dynamics, and was originally conceived to serve as an interactive platform for molecular simulation [2,3,4]. It offers a multisensory immersive experience based on cutting-edge science facilitating an understanding of the principles of our microscopic world through direct experience rather than traditional academic learning. ...

  15. A dynamic styrofoam-ball model for simulating molecular motion

    Science.gov (United States)

    Mak, Se-yuen; Cheung, Derek

    2001-01-01

    In this paper we introduce a simple styrofoam-ball model that can be used for simulating molecular motion in all three states. As the foam balls are driven by a vibrator that is in turn driven by a signal generator, the frequency and the amplitude of vibration can be adjusted independently. Thus, the model is appropriate for simulating molecular motion in the liquid state, which is a combination of vibration and meandering motion.

  16. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

    Science.gov (United States)

    van der Vaart, Arjan

    2015-05-01

    Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

  17. Widom line, dynamical crossover, and percolation transition of supercritical oxygen via molecular dynamics simulations.

    Science.gov (United States)

    Raman, Abhinav S; Li, Huiyong; Chiew, Y C

    2018-01-07

    Supercritical oxygen, a cryogenic fluid, is widely used as an oxidizer in jet propulsion systems and is therefore of paramount importance in gaining physical insights into processes such as transcritical and supercritical vaporization. It is well established in the scientific literature that the supercritical state is not homogeneous but, in fact, can be demarcated into regions with liquid-like and vapor-like properties, separated by the "Widom line." In this study, we identified the Widom line for oxygen, constituted by the loci of the extrema of thermodynamic response functions (heat capacity, volumetric thermal expansion coefficient, and isothermal compressibility) in the supercritical region, via atomistic molecular dynamics simulations. We found that the Widom lines derived from these response functions all coincide near the critical point until about 25 bars and 15-20 K, beyond which the isothermal compressibility line begins to deviate. We also obtained the crossover from liquid-like to vapor-like behavior of the translational diffusion coefficient, shear viscosity, and rotational relaxation time of supercritical oxygen. While the crossover of the translational diffusion coefficient and shear viscosity coincided with the Widom lines, the rotational relaxation time showed a crossover that was largely independent of the Widom line. Further, we characterized the clustering behavior and percolation transition of supercritical oxygen molecules, identified the percolation threshold based on the fractal dimension of the largest cluster and the probability of finding a cluster that spans the system in all three dimensions, and found that the locus of the percolation threshold also coincided with the isothermal compressibility Widom line. It is therefore clear that supercritical oxygen is far more complex than originally perceived and that the Widom line, dynamical crossovers, and percolation transitions serve as useful routes to better our understanding of the

  18. Photoinactivation related dynamics of ctenophore photoproteins: Insights from molecular dynamics simulation under electric-field.

    Science.gov (United States)

    Pashandi, Zaiddodine; Molakarimi, Maryam; Mohseni, Ammar; Sajedi, Reza H; Taghdir, Majid; Naderi-Manesh, Hossein

    2017-08-19

    Photoinactivation is a common phenomenon in bioluminescence ctenophore photoproteins (e.g mnemiopsin, berovin and BfosPP) with still unknown mechanism. The activity of coelenterate photoproteins (e.g aequorin), which has high structural similarity with ctenophore photoproteins, is not affected by light. Recently, we have characterized the effects of light on ctenophore photoprotein mnemiopsin, in different conformations, which has demonstrated light induced structural changes, uniquely secondary structures, of both apo and holo mnemiopsin. This paper is further expansion of our previous work, by applying molecular dynamics simulations to investigate photoinactivation related dynamics of berovin at atomistic level, in comparison with aequorin, under the influence of electric component of electromagnetic field. The results have indicated that the intense electric filed could influence structure of both berovin and aequorin but in different manner, whereas moderate electric field only effects on berovin's structure remarkably. In this case, increased helicity of residues E180-M193 and decreased helical contents of L38-D46 and L125-D138 segments are considerable in berovin as well as flexibility elevation of calcium binding loops. These changes cause structural expansion of berovin, especially at N-terminal domain, in direction of electric field. In conclusion, the induced structural changes of mentioned helical parts together with elevated fluctuation of their adjacent segments, N26-D46 and M193-Y206, indicate the influence of light on substrate stabilizing residues, Arg41 and Y204. This condition could presumably leads to inactivation of bioluminescence reaction due to separation of substrate from the cavity of the protein. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Conformational and dynamical properties of disaccharides in water: a molecular dynamics study.

    Science.gov (United States)

    Pereira, Cristina S; Kony, David; Baron, Riccardo; Müller, Martin; van Gunsteren, Wilfred F; Hünenberger, Philippe H

    2006-06-15

    Explicit-solvent molecular dynamics simulations (50 ns, 300 K) of the eight reducing glucose disaccharides (kojibiose, sophorose, nigerose, laminarabiose, maltose, cellobiose, isomaltose, and gentiobiose) have been carried out using the GROMOS 45A4 force field (including a recently reoptimized carbohydrate parameter set), to investigate and compare their conformational preferences, intramolecular hydrogen-bonding patterns, torsional dynamics, and configurational entropies. The calculated average values of the glycosidic torsional angles agree well with available experimental data, providing validation for the force field and simulation methodology employed in this study. These simulations show in particular that: 1) (1-->6)-linked disaccharides are characterized by an increased flexibility, the absence of any persistent intramolecular hydrogen bond and a significantly higher configurational entropy (compared to the other disaccharides); 2) cellobiose presents a highly persistent interresidue hydrogen bond and a significantly lower configurational entropy (compared to the other disaccharides); 3) persistent hydrogen bonds are observed for all disaccharides (except (1-->6)-linked) and typically involve a hydrogen donor in the reducing residue and an acceptor in the nonreducing one; 4) the probability distributions associated with the glycosidic dihedral angles and psi are essentially unimodal for all disaccharides, and full rotation around these angles occurs at most once or twice for (never for psi) on the 50-ns timescale; and 5) the timescales associated with torsional transitions (except around and psi) range from approximately 30 ps (rotation of hydroxyl groups) to the nanosecond range (rotation of the lactol and hydroxymethyl groups, and around the omega-glycosidic dihedral angle in (1-->6)-linked disaccharides).

  20. Theory of molecular nonadiabatic electron dynamics in condensed phases

    Science.gov (United States)

    Takatsuka, Kazuo

    2017-11-01

    In light of the rapid progress of ultrafast chemical dynamics driven by the pulse lasers having width as short as several tens of attoseconds, we herein develop a theory of nonadiabatic electron wavepacket dynamics in condensed phases, with which to directly track the dynamics of electronic-state mixing such as electron transfer in liquid solvents. Toward this goal, we combine a theory of path-branching representation for nonadiabatic electron wavepacket dynamics in vacuum {a mixed quantum-classical representation, Yonehara and Takatsuka [J. Chem. Phys. 129, 134109 (2008)]} and a theory of entropy functional to treat chemical dynamics in condensed phases {a mixed dynamical-statistical representation, Takatsuka and Matsumoto [Phys. Chem. Chem. Phys. 18, 1771 (2016)]}. Difficulty and complexity in the present theoretical procedure arise in embedding the Schrödinger equation into classically treated statistical environment. Nevertheless, the resultant equations of motion for electronic-state mixing due to the intrinsic nonadiabatic interactions and solute-solvent interactions, along with the force matrix that drives nuclear branching paths, both turn out to be clear enough to make it possible to comprehend the physical meanings behind. We also discuss briefly the nonvalidness of naive application of the notion of nonadiabatic transition dynamics among free energy surfaces.

  1. Theory of molecular nonadiabatic electron dynamics in condensed phases.

    Science.gov (United States)

    Takatsuka, Kazuo

    2017-11-07

    In light of the rapid progress of ultrafast chemical dynamics driven by the pulse lasers having width as short as several tens of attoseconds, we herein develop a theory of nonadiabatic electron wavepacket dynamics in condensed phases, with which to directly track the dynamics of electronic-state mixing such as electron transfer in liquid solvents. Toward this goal, we combine a theory of path-branching representation for nonadiabatic electron wavepacket dynamics in vacuum {a mixed quantum-classical representation, Yonehara and Takatsuka [J. Chem. Phys. 129, 134109 (2008)]} and a theory of entropy functional to treat chemical dynamics in condensed phases {a mixed dynamical-statistical representation, Takatsuka and Matsumoto [Phys. Chem. Chem. Phys. 18, 1771 (2016)]}. Difficulty and complexity in the present theoretical procedure arise in embedding the Schrödinger equation into classically treated statistical environment. Nevertheless, the resultant equations of motion for electronic-state mixing due to the intrinsic nonadiabatic interactions and solute-solvent interactions, along with the force matrix that drives nuclear branching paths, both turn out to be clear enough to make it possible to comprehend the physical meanings behind. We also discuss briefly the nonvalidness of naive application of the notion of nonadiabatic transition dynamics among free energy surfaces.

  2. Molecular dynamics of liquid alkaline-earth metals near the melting ...

    Indian Academy of Sciences (India)

    using molecular dynamics (MD) simulation technique using a pseudopotential proposed by us are presented in this article. ... cular dynamics simulation technique using the pseudopotential of Baria and Jani. [13–15] in the ..... is a strong argument in favour of the transferability of the pseudopotential from the solid state to the ...

  3. Molecular Dynamics Simulation of Spinodal Decomposition in Three-Dimensional Binary Fluids

    DEFF Research Database (Denmark)

    Laradji, Mohamed; Toxvaerd, Søren; Mouritsen, Ole G.

    1996-01-01

    Using large-scale molecular dynamics simulations of a two-component Lennard-Jones model in three dimensions, we show that the late-time dynamics of spinodal decomposition in concentrated binary fluids reaches a viscous scaling regime with a growth exponent n = 1, in agreement with experiments...

  4. First principles molecular dynamics applied to homogeneous catalysis: on ethylene insertion mechanisms and metathesis

    NARCIS (Netherlands)

    Meier, R.J.; Aagaard, O.M.; Buda, F.

    2000-01-01

    We have summarized part of our work involving first principles molecular dynamics simulations on organometallic-based homogeneous catalysts. Explicit dynamics effects can be uniquely extracted from such simulations, and related to structure and reactivity. Examples given deal with metallocene-based

  5. Hydrogen production methods efficiency coupled to an advanced high temperature accelerator driven system

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez, Daniel González; Lira, Carlos Alberto Brayner de Oliveira [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Energia Nuclear; Fernández, Carlos García, E-mail: danielgonro@gmail.com, E-mail: mmhamada@ipen.br [Instituto Superior de Tecnologías y Ciencias aplicadas (InSTEC), La Habana (Cuba)

    2017-07-01

    The hydrogen economy is one of the most promising concepts for the energy future. In this scenario, oil is replaced by hydrogen as an energy carrier. This hydrogen, rather than oil, must be produced in volumes not provided by the currently employed methods. In this work two high temperature hydrogen production methods coupled to an advanced nuclear system are presented. A new design of a pebbled-bed accelerator nuclear driven system called TADSEA is chosen because of the advantages it has in matters of transmutation and safety. For the conceptual design of the high temperature electrolysis process a detailed computational fluid dynamics model was developed to analyze the solid oxide electrolytic cell that has a huge influence on the process efficiency. A detailed flowsheet of the high temperature electrolysis process coupled to TADSEA through a Brayton gas cycle was developed using chemical process simulation software: Aspen HYSYS®. The model with optimized operating conditions produces 0.1627 kg/s of hydrogen, resulting in an overall process efficiency of 34.51%, a value in the range of results reported by other authors. A conceptual design of the iodine-sulfur thermochemical water splitting cycle was also developed. The overall efficiency of the process was calculated performing an energy balance resulting in 22.56%. The values of efficiency, hydrogen production rate and energy consumption of the proposed models are in the values considered acceptable in the hydrogen economy concept, being also compatible with the TADSEA design parameters. (author)

  6. 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation of Pseudomonas aeruginosa LpxC Inhibitors.

    Science.gov (United States)

    Zuo, Ke; Liang, Li; Du, Wenyi; Sun, Xin; Liu, Wei; Gou, Xiaojun; Wan, Hua; Hu, Jianping

    2017-05-06

    As an important target for the development of novel antibiotics, UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) has been widely studied. Pyridone methylsulfone hydroxamate (PMH) compounds can effectively inhibit the catalytic activity of LpxC. In this work, the three-dimensional quantitative structure-activity relationships of PMH inhibitors were explored and models with good predictive ability were established using comparative molecular field analysis and comparative molecular similarity index analysis methods. The effect of PMH inhibitors' electrostatic potential on the inhibitory ability of Pseudomonas aeruginosa LpxC (PaLpxC) is revealed at the molecular level via molecular electrostatic potential analyses. Then, two molecular dynamics simulations for the PaLpxC and PaLpxC-inhibitor systems were also performed respectively to investigate the key residues of PaLpxC hydrolase binding to water molecules. The results indicate that orderly alternative water molecules can form stable hydrogen bonds with M62, E77, T190, and H264 in the catalytic center, and tetracoordinate to zinc ion along with H78, H237, and D241. It was found that the conformational transition space of PaLpxC changes after association with PMH inhibitors through free energy landscape and cluster analyses. Finally, a possible inhibitory mechanism of PMH inhibitors was proposed, based on our molecular simulation. This paper will provide a theoretical basis for the molecular design of LpxC-targeting antibiotics.

  7. Structure and Dynamics of Polymers in Cylindrical Nanoconfinement: A Molecular Dynamics Study

    Science.gov (United States)

    Pressly, James; Riggleman, Robert; Winey, Karen

    The structure and dynamics of polymers under nanoconfinement is critical for understanding how polymers behave in applications from hydraulic fracking to fabricating integrated circuits. We previously used simulations to explore the effect of the diameter of cylindrical pores (d = 10-40 σ, where σ is the unit length in reduced units) on polymer end-to-end distance (Ree,perp, Ree,par) , entanglement density, melt diffusion coefficient (D), and local relaxation time (τperp, τpar) at fixed polymer chain length (N = 350). These studies found D, Ree,par, and τperp increased with increasing confinement while entanglement density, Ree,perp, and τpar decreased. Experiments also found that D increased but to a lesser extent. Here, we examine the molecular weight dependence of these properties using N = 25, 50, 100, 200, 350, and 500 confined to pores of diameter 14 σ to examine a range of confinements. Our preliminary results show that as N increases D and Ree,par, increase as well, relative to the unconfined state, while entanglement density and Ree,perp decrease, consistent with our previous work. Interestingly, τ is shown to be independent of chain length indicating the impact of confinement imposed by reducing pore diameter is distinct from that imposed by increasing chain length.

  8. Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, William H.

    2006-04-27

    The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.

  9. Physical Properties and Hydrogen-Bonding Network of Water-Ethanol Mixtures from Molecular Dynamics Simulations.

    Science.gov (United States)

    Ghoufi, A; Artzner, F; Malfreyt, P

    2016-02-04

    While many numerical and experimental works were focused on water-ethanol mixtures at low ethanol concentration, this work reports predictions of a few physical properties (thermodynamical, interfacial, dynamical, and dielectrical properties) of water-ethanol mixture at high alcohol concentrations by means of molecular dynamics simulations. By using a standard force field a good agreement was found between experiment and molecular simulation. This was allowed us to explore the dynamics, structure, and interplay between both hydrogen-bonding networks of water and ethanol.

  10. Conformational flexibility in designing peptides for immunology: the molecular dynamics approach.

    Science.gov (United States)

    Stavrakoudis, Athanassios

    2010-09-01

    Computational modeling techniques and computer simulations have become a routine in biological sciences and have gained great attention from researchers. Molecular dynamics simulation is a valuable tool towards an understanding of the complex structure of biological systems, especially in the study of the flexibility of the biological molecules such as peptides or proteins. Peptides play a very important role in human physiology and control many of the processes involved in the immune system response. Designing new and optimal peptide vaccines is one of the hottest challenges of the 21(st) century science and it brings together researchers from different fields. Molecular dynamics simulations have proven to be a helpful tool assisting laboratory work, saving financial sources and opening possibilities for exploring properties of the molecular systems that are hardly accessible by conventional experimental methods. Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes.

  11. Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex.

    Science.gov (United States)

    Park, Kyung-Lae

    2017-01-01

    A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.

  12. Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: insights from molecular dynamics simulation.

    Science.gov (United States)

    Verdian Doghaei, A; Housaindokht, M R; Bozorgmehr, M R

    2015-01-07

    Intracellular space is highly crowded with different biomolecules such as proteins, nucleic acids and ions. Therefore molecular crowding is a crucial factor in determining the structure, stability and function of G-quadruplexs. The effect of crowding on the DNA G-quadruplexes structure and stability has been studied by experimental methods, but it hasn't been known how crowding agents stabilize the G-quadruplex structure in molecular level yet. Here, we present a molecular dynamics investigation over the effect of molecular crowding, imitated here by ethanol, on the stability of G-quadruplex structure both in presence and absence of stabilizing K(+) cations. It was demonstrated that G-quadruplex structure in the water collapses in the absence of this cation, while ethanol stabilizes the structure of G-quadruplex by the excluded volume and decreases the water activity. The presence of ethanol can increase the stability of the Hoogsteen hydrogen bonds within the G-quartet. To understand the importance of cations, simulation has been performed on the cation containing G-quadruplex in the presence of ethanol with different concentrations. Molecular dynamics simulations of the structure and stability of human telomeric G-quadruplex in ethanol containing solution has enhanced our understanding on how the parallel-stranded G-quadruplex is affected in a condition where the water content is reduced. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations.

    Science.gov (United States)

    Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka

    2011-11-15

    Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. Copyright © 2011 Wiley Periodicals, Inc.

  14. Effect of orbital and ionic dynamics coupling in barrier crossing rates for Car-Parrinello molecular dynamics

    Science.gov (United States)

    Mohanam, L. N.; Ong, S. W.; Tok, E. S.; Kang, H. C.

    2015-02-01

    Even though the Car-Parrinello molecular dynamics (CPMD) method provides excellent sampling for thermal equilibrium, coupling between ionic motion and the fictitious orbital dynamics leads to an underestimation of ionic vibration frequencies In this letter we examine how this coupling affects calculated rates of energy-barrier crossing. Simulating double-well potentials in 'toy' models based on H3O2- and H5O2+ complexes, we demonstrate that barrier crossing rates can be dramatically affected depending upon how orbitals evolve at the top of the reaction barrier. Thus, it is important that calculated dynamical quantities such as chemical reaction rates be assessed for this coupling effect.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structu...

  16. Coarse – grained molecular dynamics simulation of cross – linking ...

    African Journals Online (AJOL)

    These three superatom structures are then allowed to crosslink (based on the attainment of a minimum distance of approach) with a coarse grained crosslinker ... Our predictions of the value of the work of separation, obtained from only a description of the molecular architecture of DGEBA and the crosslinker molecule, falls ...

  17. 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…

  18. Molecular regulation of mitochondrial dynamics in cardiac disease.

    Science.gov (United States)

    Nan, Jinliang; Zhu, Wei; Rahman, M S; Liu, Mingfei; Li, Dan; Su, Shengan; Zhang, Na; Hu, Xinyang; Yu, Hong; Gupta, Mahesh P; Wang, Jian'an

    2017-07-01

    Mitochondrial homeostasis is critical for keeping functional heart in response to metabolic or environmental stresses. Mitochondrial fission and fusion (mitochondrial dynamics) play essential roles in maintaining mitochondrial homeostasis, defects in mitochondrial dynamics lead to cardiac diseases such as ischemia-reperfusion injury (IRI), heart failure and diabetic cardiomyopathy. Mitochondrial dynamics is determined by mitochondrial fission and fusion proteins, including OPA1, mitofusins and Drp1. These proteins are tightly regulated by a series of signaling pathways through different aspects such as transcription, post translation modifications (PTMs) and proteasome-dependent protein degradation. By modulating these mitochondrial fission and fusion proteins, mitochondria fine-tune their metabolic status to meet the energy demands of the heart. Moreover, these mitochondrial fission and fusion proteins are essential for mediating mitochondrial autophagy (mitophagy), leading to clearance of damaged mitochondria to maintain a healthy population of mitochondria in heart under stressed conditions. Mitochondrial dynamics dependent improvement in mitochondrial metabolism and quality could partially reverse the pathological conditions of heart. This review describes an overview of mechanisms on mitochondrial dynamics regulation and provides potential therapeutic targets for treating cardiovascular diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Nonlinear Hamiltonian mechanics applied to molecular dynamics theory and computational methods for understanding molecular spectroscopy and chemical reactions

    CERN Document Server

    Farantos, Stavros C

    2014-01-01

    This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.

  20. Coalescence of silver unidimensional structures by molecular dynamics simulation; Coalescencia de estructuras unidimensionales de plata por simulacion dinamica molecular

    Energy Technology Data Exchange (ETDEWEB)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico); Arenas, J. [IFUNAM, 04510 Mexico D.F. (Mexico)

    2007-07-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  1. Generation of Multicomponent Molecular Cages using Simultaneous Dynamic Covalent Reactions.

    Science.gov (United States)

    Drożdż, Wojciech; Bouillon, Camille; Kotras, Clément; Richeter, Sébastien; Barboiu, Mihail; Clément, Sébastien; Stefankiewicz, Artur R; Ulrich, Sébastien

    2017-12-19

    Cage compounds are very attractive structures for a wide range of applications and there is ongoing interest in finding effective ways to access such kinds of complex structures, particularly those possessing dynamic adaptive features. Here we report the accessible synthesis of new type of organic cage architectures, possessing two different dynamic bonds within one structure: hydrazones and disulfides. Implementation of three distinct functional groups (thiols, aldehydes and hydrazides) in the structure of two simple building blocks resulted in their spontaneous and selective self-assembly into aromatic cage-type architectures. These organic cages contain up to ten components linked together by twelve reversible covalent bonds. The advantage provided by the presented approach is that these cage structures can adaptively self-sort from a complex virtual mixture of polymers or macrocycles and that dynamic covalent chemistry enables their deliberate disassembly through controlled component exchange. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Dynamic Coherence in Excitonic Molecular Complexes under Various Excitation Conditions

    CERN Document Server

    Chenu, Aurélia; Mancal, Tomáš

    2013-01-01

    In this paper, we investigate the relevance of dynamic electronic coherence under conditions natural to light-harvesting systems. We formulate the results of a quantum mechanical treatment of a weak light-matter interaction in terms of experimental observable, such as the incident light spectrum and the absorption spectrum of the material, and we derive the description of the incoherent F\\"orster type energy transfer fully from the wave function formalism. We demonstrate that excitation of a coherent superposition of electronic eigenstates of natural light-harvesting complexes by sunlight or by excitation transfer from a neighboring antenna is unlikely and that dynamical coherence therefore cannot play any significant role in natural photosynthesis, regardless of their life time. Dynamical coherence as a transient phenomenon must be strictly distinguished from the effect of excited state delocalization (also termed quantum coherence in the literature) which is established by interaction between the pigments a...

  3. Molecular spectroscopy and dynamics: a polyad-based perspective.

    Science.gov (United States)

    Herman, Michel; Perry, David S

    2013-07-07

    The efficiency and insight of global, polyad-based modeling in overtone spectroscopy and dynamics is demonstrated. Both vibration and vibration-rotation polyads are considered. The spectroscopic implications of polyad Hamiltonians derive from their ability to account for the detailed line positions and intensities of spectral features and their unique predictive power. The dynamical implications of polyad Hamiltonians include classical bifurcations that lead to the birth of new vibrational modes and intramolecular vibrational-rotational energy redistribution over multiple timescales. The literature is reviewed, with emphasis on acetylene results.

  4. Resolving the anomalous infrared spectrum of the MeCN-HCl molecular cluster using ab Initio molecular dynamics

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Loukonen, Ville; Kjærgaard, Henrik Grum

    2014-01-01

    We present a molecular dynamics (MD) based study of the acetonitrile-hydrogen chloride molecular cluster in the gas phase, aimed at resolving the anomalous features often seen in infrared spectra of hydrogen bonded complexes. We find that the infrared spectrum obtained from the Fourier transform...... trajectory for a structural based analysis. We find that the most populated values of the N-H-Cl angle are around 162°. The global minimum energy conformation at 180.0° is essentially unpopulated. We re-model the spectrum by combining population data from the MD simulations with optimizations constraining...... the N-H-Cl angle. This re-modelled spectrum is in excellent accordance with the experimental spectrum and we conclude that the observed spectral anomaly is due to the dynamics of the N-H-Cl angle....

  5. Mean field ring polymer molecular dynamics for electronically nonadiabatic reaction rates.

    Science.gov (United States)

    Duke, Jessica Ryan; Ananth, Nandini

    2016-12-22

    We present a mean field ring polymer molecular dynamics method to calculate the rate of electron transfer (ET) in multi-state, multi-electron condensed-phase processes. Our approach involves calculating a transition state theory (TST) estimate to the rate using an exact path integral in discrete electronic states and continuous Cartesian nuclear coordinates. A dynamic recrossing correction to the TST rate is then obtained from real-time dynamics simulations using mean field ring polymer molecular dynamics. We employ two different reaction coordinates in our simulations and show that, despite the use of mean field dynamics, the use of an accurate dividing surface to compute TST rates allows us to achieve remarkable agreement with Fermi's golden rule rates for nonadiabatic ET in the normal regime of Marcus theory. Further, we show that using a reaction coordinate based on electronic state populations allows us to capture the turnover in rates for ET in the Marcus inverted regime.

  6. Spinodal decomposition in multicomponent fluid mixtures: A molecular dynamics study

    DEFF Research Database (Denmark)

    Laradji, Mohamed; Mouritsen, Ole G.; Toxvaerd, Søren

    1996-01-01

    parameter, leading to large growth-exponent values, the dynamics in multicomponent fluids (p = 3, 4) is found to follow a t(1/3) growth law, where t is time, which we relate to a long-wavelength evaporation-condensation process. These findings, which are proposed to be consequences of the compact domain...

  7. Dynamic Paper Constructions for Easier Visualization of Molecular Symmetry

    Science.gov (United States)

    Sein, Lawrence T., Jr.

    2010-01-01

    A system for construction of simple poster-board models is described. The models dynamically demonstrate the symmetry operations of proper rotation, improper rotation, reflection, and inversion for the chemically important point groups D[subscript 3h], D[subscript 4h], D[subscript 5h], D[subscript 6h], T[subscript d], and O[subscript h]. The…

  8. 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.

  9. From molecular systems to continuum solids: A multiscale structure and dynamics.

    Science.gov (United States)

    Tong, Qi; Li, Shaofan

    2015-08-14

    We propose a concurrent multiscale molecular dynamics for molecular systems in order to apply macroscale mechanical boundary conditions such as traction and average displacement for solid state materials, which is difficult to do in traditional molecular dynamics where boundary conditions are applied in terms of forces and displacements on selected particles. The multiscale model is systematically constructed in terms of multiscale structures of kinematics, force field, and dynamical equations. The idea is to extend the Anderson-Parrinello-Rahman molecular dynamics to the cases that have arbitrary finite domain and boundary, thus the model is capable of solving inhomogeneous, non-equilibrium problems. The macroscale stress loading on a representative volume element with periodic boundary condition is generalized to all kinds of macroscale mechanical boundary conditions. Unlike most multiscale techniques, our theory is aimed at understanding fundamental physics rather than achieving computing efficiency. Examples of problems with prescribed average displacements and surface tractions are presented to demonstrate the validity of the proposed multiscale molecular dynamics.

  10. Theoretical aspects of gas-phase molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Muckerman, J.T. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    Research in this program is focused on the development and application of time-dependent quantum mechanical and semiclassical methods for treating inelastic and reactive molecular collisions, and the photochemistry and photophysics of atoms and molecules in laser fields. Particular emphasis is placed on the development and application of grid methods based on discrete variable representations, on time-propagation methods, and, in systems with more that a few degrees of freedom, on the combined use of quantal wavepackets and classical trajectories.

  11. Molecular Dynamics Simulations of the Hydrogen Peroxyl Radical

    Science.gov (United States)

    2014-05-01

    direction of future research would focus on understanding the coupling between rotation and vibration. Frederick et al. 112 used trajectories to study...myzzxmmxy mxzmxyzym I . (44) This allows the vibrational energy to be defined as 121 106 RRVV HHH  . (45) Frederick et al.112...2352 (1982). They used a similar symmetrization strategy to correct a similar seam in an earlier HO2 PES. 88 G. Herzberg , Molecular Spectra and

  12. Probing the limits of metal plasticity with molecular dynamics simulations

    Science.gov (United States)

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

    2017-10-01

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

  13. Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

    Science.gov (United States)

    Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

    2017-01-01

    Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

  14. Friction in carborane-based molecular rotors driven by gas flow or electric field: classical molecular dynamics.

    Science.gov (United States)

    Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

    2012-03-27

    Friction in molecular rotors is examined by classical molecular dynamics simulations for grid-mounted azimuthal dipolar molecular rotors, whose rotation is either allowed to decay freely or is driven at GHz frequencies by a flow of rare gas or by a rotating electric field. The rotating parts (rotators) are propeller-shaped. Their two to six blades consist of condensed aromatic rings and are attached to a deltahedral carborane hub, whose antipodal carbons carry [n]staffane axles mounted on a square molecular grid. The dynamic friction constant η has been derived in several independent ways with similar results. Analysis of free rotation decay yields η as a continuous exponentially decreasing function of rotor frequency. The calculated dependence of friction torque on frequency resembles the classical macroscopic Stribeck curve. Its relation to rotational potential energy barriers and the key role of the rate of intramolecular vibrational redistribution (IVR) of energy and angular momentum from rotator rotation to other modes are considered in two limiting regimes. (i) In the strongly overdamped regime, rotation is much slower than IVR, and effective friction can be expressed through potential barriers to rotation. (ii) In the strongly underdamped regime, rotation is much faster than IVR, whose rate then determines friction. © 2012 American Chemical Society

  15. An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

    Science.gov (United States)

    Sahihi, M; Ghayeb, Y

    2014-08-01

    Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

    Science.gov (United States)

    Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

    2007-01-01

    The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are

  17. Dynamical localization in molecular alignment of kicked quantum rotors

    Energy Technology Data Exchange (ETDEWEB)

    Kamalov, A.; Broege, D. W.; Bucksbaum, P. H.

    2015-07-13

    The periodically δ -kicked quantum linear rotor is known to experience nonclassical bounded energy growth due to quantum dynamical localization in angular momentum space. We study the effect of random deviations of the kick period in simulations and experiments. This breaks the energy and angular momentum localization and increases the rotational alignment, which is the analog of the onset of Anderson localization in one-dimensional chains.

  18. Diverse Soil Carbon Dynamics Expressed at the Molecular Level

    Science.gov (United States)

    van der Voort, T. S.; Zell, C. I.; Hagedorn, F.; Feng, X.; McIntyre, C. P.; Haghipour, N.; Graf Pannatier, E.; Eglinton, T. I.

    2017-12-01

    The stability and potential vulnerability of soil organic matter (SOM) to global change remain incompletely understood due to the complex processes involved in its formation and turnover. Here we combine compound-specific radiocarbon analysis with fraction-specific and bulk-level radiocarbon measurements in order to further elucidate controls on SOM dynamics in a temperate and subalpine forested ecosystem. Radiocarbon contents of individual organic compounds isolated from the same soil interval generally exhibit greater variation than those among corresponding operationally defined fractions. Notably, markedly older ages of long-chain plant leaf wax lipids (n-alkanoic acids) imply that they reflect a highly stable carbon pool. Furthermore, marked 14C variations among shorter- and longer-chain n-alkanoic acid homologues suggest that they track different SOM pools. Extremes in SOM dynamics thus manifest themselves within a single compound class. This exploratory study highlights the potential of compound-specific radiocarbon analysis for understanding SOM dynamics in ecosystems potentially vulnerable to global change.

  19. Live Cell Imaging and Measurements of Molecular Dynamics

    Science.gov (United States)

    Frigault, M.; Lacoste, J.; Swift, J.; Brown, C.

    2010-01-01

    w3-2 Live cell microscopy is becoming widespread across all fields of the life sciences, as well as, many areas of the physical sciences. In order to accurately obtain live cell microscopy data, the live specimens must be properly maintained on the imaging platform. In addition, the fluorescence light path must be optimized for efficient light transmission in order to reduce the intensity of excitation light impacting the living sample. With low incident light intensities the processes under study should not be altered due to phototoxic effects from the light allowing for the long term visualization of viable living samples. Aspects for maintaining a suitable environment for the living sample, minimizing incident light and maximizing detection efficiency will be presented for various fluorescence based live cell instruments. Raster Image Correlation Spectroscopy (RICS) is a technique that uses the intensity fluctuations within laser scanning confocal images, as well as the well characterized scanning dynamics of the laser beam, to extract the dynamics, concentrations and clustering of fluorescent molecules within the cell. In addition, two color cross-correlation RICS can be used to determine protein-protein interactions in living cells without the many technical difficulties encountered in FRET based measurements. RICS is an ideal live cell technique for measuring cellular dynamics because the potentially damaging high intensity laser bursts required for photobleaching recovery measurements are not required, rather low laser powers, suitable for imaging, can be used. The RICS theory will be presented along with examples of live cell applications.

  20. Molecular excitation dynamics and relaxation quantum theory and spectroscopy

    CERN Document Server

    Valkunas, Leonas; Mancal, Tomas

    2013-01-01

    Meeting the need for a work that brings together quantum theory and spectroscopy to convey excitation processes to advanced students and specialists wishing to conduct research and understand the entire field rather than just single aspects.Written by an experienced author and recognized authority in the field, this text covers numerous applications and offers examples taken from different disciplines. As a result, spectroscopists, molecular physicists, physical chemists, and biophysicists will all find this a must-have for their research. Also suitable as supplementary reading in graduate