WorldWideScience

Sample records for based molecular dynamics

  1. Orthonormal Wavelet Bases for Quantum Molecular Dynamics

    International Nuclear Information System (INIS)

    Tymczak, C.; Wang, X.

    1997-01-01

    We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

  2. Towards the molecular bases of polymerase dynamics

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1991-03-01

    One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

  3. 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

  4. 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...

  5. Nonequilibrium molecular dynamics

    OpenAIRE

    Wm.G.Hoover; C.G.Hoover

    2005-01-01

    Nonequilibrium Molecular Dynamics is a powerful simulation tool. Like its equilibrium cousin, nonequilibrium molecular dynamics is based on time-reversible equations of motion. But unlike conventional mechanics, nonequilibrium molecular dynamics provides a consistent microscopic basis for the irreversible macroscopic Second Law of Thermodynamics. We recall here how fast computers led to the development of nonequilibrium molecular dynamics from the statistical mechanics of the 1950s. Computer-...

  6. Acidity constants from DFT-based molecular dynamics simulations

    International Nuclear Information System (INIS)

    Sulpizi, Marialore; Sprik, Michiel

    2010-01-01

    In this contribution we review our recently developed method for the calculation of acidity constants from density functional theory based molecular dynamics simulations. The method is based on a half reaction scheme in which protons are formally transferred from solution to the gas phase. The corresponding deprotonation free energies are computed from the vertical energy gaps for insertion or removal of protons. Combined to full proton transfer reactions, the deprotonation energies can be used to estimate relative acidity constants and also the Broensted pK a when the deprotonation free energy of a hydronium ion is used as a reference. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pK a values (20 units). The thermochemical corrections for the biasing potentials assisting and directing the insertion are discussed in some detail.

  7. Nonequilibrium molecular dynamics

    Directory of Open Access Journals (Sweden)

    Wm.G.Hoover

    2005-01-01

    Full Text Available Nonequilibrium Molecular Dynamics is a powerful simulation tool. Like its equilibrium cousin, nonequilibrium molecular dynamics is based on time-reversible equations of motion. But unlike conventional mechanics, nonequilibrium molecular dynamics provides a consistent microscopic basis for the irreversible macroscopic Second Law of Thermodynamics. We recall here how fast computers led to the development of nonequilibrium molecular dynamics from the statistical mechanics of the 1950s. Computer-based theories facilitated revolutionary breakthroughs in understanding during the 1970s and 1980s. The new idea key to the nonequilibrium development was the replacement of the external thermodynamic environment by internal control variables. The new variables can control temperature, or pressure, or energy, or stress, or heat flux. These thermostat, barostat, ergostat, ... variables can control and maintain nonequilibrium states. We illustrate the methods with a simple example well-suited to student exploration, a thermostatted harmonic oscillator exposed to a temperature gradient.

  8. MOLECULAR-DYNAMICS SIMULATIONS OF CARBOHYDRATE-BASED SURFACTANTS IN SURFACTANT WATER OIL SYSTEMS

    NARCIS (Netherlands)

    VANBUUREN, AR; BERENDSEN, HJC

    Molecular dynamics simulations of two monolayers of carbohydrate-based surfactants (decyl alpha-glucoside and decyl beta-glucoside) at the interface between liquid decane and liquid water have been performed with the purpose to study the properties of these monolayers on a molecular and atomic

  9. Molecular diagnostics based on clustering dynamics of magnetic nanobeads

    DEFF Research Database (Denmark)

    Donolato, Marco; Bejhed, Rebecca S.; de la Torre, Teresa Zardán Gómez

    2014-01-01

    or on the polymerase chain reaction (PCR) [1]. In this work we demonstrate detection of DNA coils formed from a Vibrio Cholerae DNA target at pM concentrations using a novel opto-magnetic approach exploiting the dynamic collective behavior of magnetic nanobeads. The technique relies on measurements of the light...... and isothermal rolling circle amplification from Vibrio cholerae DNA. The detection method is shown in Figure 1. MNBs which specifically bind to the micrometric sized DNA coil cannot rotate under the field action as free beads and form chains; this results in a strongly modified opto-magnetic signal. As a core...

  10. 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.

  11. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    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...... an MD trajectory, as another route for final phase acceleration. Our suggestions may be implemented within most MD quench implementations with a few, straightforward lines of code, thus maintaining the appealing simplicity of the MD quench algorithms. In this paper, we also bridge the conceptual gap...

  12. Molecular diagnostics based on clustering dynamics of magnetic nanobeads

    DEFF Research Database (Denmark)

    Donolato, Marco; Bejhed, Rebecca S.; de la Torre, Teresa Zardán Gómez

    2014-01-01

    or on the polymerase chain reaction (PCR) [1]. In this work we demonstrate detection of DNA coils formed from a Vibrio Cholerae DNA target at pM concentrations using a novel opto-magnetic approach exploiting the dynamic collective behavior of magnetic nanobeads. The technique relies on measurements of the light...... transmission modulation caused by the AC magnetic field-stimulated reversible formation and disruption of elongated MNB supra-structures during a cycle of the uniaxial applied magnetic field. As a specific clinically relevant diagnostic case, we detect DNA coils formed via padlock probe recognition...... and isothermal rolling circle amplification from Vibrio cholerae DNA. The detection method is shown in Figure 1. MNBs which specifically bind to the micrometric sized DNA coil cannot rotate under the field action as free beads and form chains; this results in a strongly modified opto-magnetic signal. As a core...

  13. A novel energy conversion based method for velocity correction in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Jin, Hanhui; Liu, Ningning; Ku, Xiaoke; Fan, Jianren

    2017-01-01

    Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

  14. Molecular dynamics based simulations to study the fracture strength of monolayer graphene oxide

    Science.gov (United States)

    Verma, Akarsh; Parashar, Avinash

    2018-03-01

    The aim of this article is to study the effects of functional groups such as hydroxyl, epoxide and carboxyl on the fracture toughness of graphene. These functional groups form the backbone of the intrinsic atomic structure of graphene oxide (GO). Molecular dynamics based simulations were performed in conjunction with reactive force field parameters to capture the Mode-I fracture toughness of functionalised graphene. Simulations were performed in stages, to study the effect of these functional groups, individually as well as all together on the fracture toughness of GO nanosheets. The molecular dynamics based simulations performed in this article helps us to conclude that the spatial distribution and concentration of functional groups significantly affects the fracture behavior of GO nanosheets.

  15. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  16. Nonequilibrium molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  17. Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation.

    Science.gov (United States)

    Komeiji, Yuto; Ishikawa, Takeshi; Mochizuki, Yuji; Yamataka, Hiroshi; Nakano, Tatsuya

    2009-01-15

    Fragment Molecular Orbital based-Molecular Dynamics (FMO-MD, Komeiji et al., Chem Phys Lett 2003, 372, 342) is an ab initio MD method suitable for large molecular systems. Here, FMO-MD was implemented to conduct full quantum simulations of chemical reactions in explicit solvation. Several FMO-MD simulations were performed for a sphere of water to find a suitable simulation protocol. It was found that annealing of the initial configuration by a classical MD brought the subsequent FMO-MD trajectory to faster stabilization, and also that use of bond constraint in the FMO-MD heating stage effectively reduced the computation time. Then, the blue moon ensemble method (Sprik and Ciccotti, J Chem Phys 1998, 109, 7737) was implemented and was tested by calculating free energy profiles of the Menschutkin reaction (H3N + CH3Cl --> +H3NCH3 + Cl-) in the presence and absence of the solvent water via FMO-MD. The obtained free energy profiles were consistent with the Hammond postulate in that stabilization of the product by the solvent, namely hydration of Cl-, shifted the transition state to the reactant-side. Based on these FMO-MD results, plans for further improvement of the method are discussed. Copyright 2008 Wiley Periodicals, Inc.

  18. Molecular property investigations of an ortho-hydroxy Schiff base type compound with the first-principle molecular dynamics approach.

    Science.gov (United States)

    Jezierska-Mazzarello, Aneta; Vuilleumier, Rodolphe; Panek, Jarosław J; Ciccotti, Giovanni

    2010-01-14

    The structure, proton transfer, and vibrational dynamics under ambient conditions of a selected ortho-hydroxy Schiff base type compound, 2-(N-methyl-alpha-iminoethyl)-4-chlorophenol, containing a very short intramolecular hydrogen bond, were investigated computationally in the gas phase and in the crystal by density functional theory (DFT) based first-principle molecular dynamics (FPMD). It is found that the proton is well localized on the nitrogen side of the O...H...N bridge in the crystal phase, in agreement with X-ray diffraction experiments, while a more labile proton is located most of the time on the oxygen side in a vacuum. Environmental effects on this very strong hydrogen bond thus appear crucial and lead to drastic changes of the infrared (IR) spectrum: The computed gas-phase IR spectrum shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1) assigned to the labile proton. In mere contrast, a much more localized absorption band around 2600-2700 cm(-1) is predicted in the crystal phase. Finally, effects of the quantization of the proton motion on the hydrogen bond structure were estimated in two ways. First, we constructed the one-dimensional (1D) potential energy surface (PES) for the proton along the O...H...N bridge in a vacuum. The 1D Schrodinger equation was then solved. Next, path integral molecular dynamics (PIMD) was performed in the solid state. Inclusion of quantum effects does not affect the observed change of the most probable tautomer, upon going from the gas phase to the crystal.

  19. 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....

  20. Molecular interactions of nucleic acid bases. From ab initio calculations to molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří

    2002-01-01

    Roč. 223, - (2002), s. 212 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : quantum chemistry * base pairing * base stacking Subject RIV: BO - Biophysics

  1. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    Energy Technology Data Exchange (ETDEWEB)

    Naritomi, Yusuke [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan); Fuchigami, Sotaro, E-mail: sotaro@tsurumi.yokohama-cu.ac.jp [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)

    2013-12-07

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of C{sub α} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  2. 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.

  3. Friction in Carborane-Based Molecular Rotors Driven by Gas Flow or Electric Field: Classical Molecular Dynamics

    Czech Academy of Sciences Publication Activity Database

    Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

    2012-01-01

    Roč. 6, č. 3 (2012), s. 1901-1914 ISSN 1936-0851 R&D Projects: GA ČR GA203/09/1802; GA MŠk ME09020 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular rotors * molecular dynamics * potential energy barriers * friction * intramolecular vibrational redistribution Subject RIV: CC - Organic Chemistry Impact factor: 12.062, year: 2012

  4. Facilitating in vivo tumor localization by principal component analysis based on dynamic fluorescence molecular imaging

    Science.gov (United States)

    Gao, Yang; Chen, Maomao; Wu, Junyu; Zhou, Yuan; Cai, Chuangjian; Wang, Daliang; Luo, Jianwen

    2017-09-01

    Fluorescence molecular imaging has been used to target tumors in mice with xenograft tumors. However, tumor imaging is largely distorted by the aggregation of fluorescent probes in the liver. A principal component analysis (PCA)-based strategy was applied on the in vivo dynamic fluorescence imaging results of three mice with xenograft tumors to facilitate tumor imaging, with the help of a tumor-specific fluorescent probe. Tumor-relevant features were extracted from the original images by PCA and represented by the principal component (PC) maps. The second principal component (PC2) map represented the tumor-related features, and the first principal component (PC1) map retained the original pharmacokinetic profiles, especially of the liver. The distribution patterns of the PC2 map of the tumor-bearing mice were in good agreement with the actual tumor location. The tumor-to-liver ratio and contrast-to-noise ratio were significantly higher on the PC2 map than on the original images, thus distinguishing the tumor from its nearby fluorescence noise of liver. The results suggest that the PC2 map could serve as a bioimaging marker to facilitate in vivo tumor localization, and dynamic fluorescence molecular imaging with PCA could be a valuable tool for future studies of in vivo tumor metabolism and progression.

  5. Nonequilibrium molecular dynamics simulation of coupling between nanoparticles and base-fluid in a nanofluid

    International Nuclear Information System (INIS)

    Kang, Hongbo; Zhang, Yuwen; Yang, Mo; Li, Ling

    2012-01-01

    The intent of this study is to examine nonequilibrium heat transfer in a copper–argon nanofluid by molecular dynamics simulation. Two different methods, the physical definition method and the curve fitting method, are introduced to calculate the coupling factor between nanoparticles and base fluid. The results show that the coupling factors obtained by these two methods are consistent. The coupling factor is proportional to the volume fraction of the nanoparticle and inversely proportional to nanoparticle diameter. In the temperature range of 90–200 K, the coupling factor is not affected by temperature. The nanoparticle aggregation results in a decrease of the coupling factor. -- Highlights: ► Nonequilibrium heat transfer in a copper–argon nanofluid is investigated by molecular dynamics simulation. ► The coupling factor is proportion to the volume fraction of the nanoparticle and inverse proportion to nanoparticle diameter. ► In the temperature range of 90–200 K, there is no temperature effect on the coupling factor. ► The nanoparticle aggregation results in a decrease of the coupling factor.

  6. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

    Science.gov (United States)

    Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

    2012-05-01

    MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

  7. Morphology, molecular dynamics and electric conductivity of carbohydrate polymer films based on alginic acid and benzimidazole.

    Science.gov (United States)

    Rachocki, Adam; Pogorzelec-Glaser, Katarzyna; Pawlaczyk, Czesław; Tritt-Goc, Jadwiga

    2011-12-13

    The present paper describes a preparation method and molecular investigations of new biodegradable proton-conducting carbohydrate polymer films based on alginic acid and benzimidazole. Electric conductivity was studied in a wide temperature range in order to check the potential application of these compounds as membranes for electrochemical devices. Compared to pure alginic acid powder or its film, the biodegradable film of alginic acid with an addition of benzimidazole exhibits considerably higher conductivity in the range above water boiling temperature (up to approximately 10(-3) S/cm at 473 K). Due to this important feature the obtained films can be considered as candidates for application in high-temperature electrochemical devices. The microscopic nature and mechanism of the conduction in alginate based materials were studied by proton nuclear magnetic resonance (NMR). The results show specific changes in morphology and molecular dynamics between pure alginate powders and the films obtained without and with the addition of benzimidazole molecules. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Molecular dynamics simulations.

    Science.gov (United States)

    Lindahl, Erik

    2015-01-01

    Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.

  9. Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Kai Wang

    Full Text Available Hierarchical organization of free energy landscape (FEL for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL, and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF. Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100 ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.

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

    Directory of Open Access Journals (Sweden)

    Matthew W. Thompson

    2017-10-01

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

  11. 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

  12. A sampling of molecular dynamics

    Science.gov (United States)

    Sindhikara, Daniel Jon

    The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel

  13. On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Lankaš, Filip; Gonzalez, O.; Heffler, L. M.; Stoll, G.; Moakher, M.; Maddocks, J. H.

    2009-01-01

    Roč. 11, č. 45 (2009), s. 10565-10588 ISSN 1463-9076 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular dynamics * coarse-grained models * DNA mechanical properties Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.116, year: 2009

  14. Interactive molecular dynamics

    Science.gov (United States)

    Schroeder, Daniel V.

    2015-03-01

    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.

  15. The nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-03-01

    MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

  16. Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.

    Science.gov (United States)

    Ludwiczak, Jan; Jarmula, Adam; Dunin-Horkawicz, Stanislaw

    2018-02-14

    Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. A concurrent multiscale micromorphic molecular dynamics

    International Nuclear Information System (INIS)

    Li, Shaofan; Tong, Qi

    2015-01-01

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

  18. Facilitating Students' Interaction with Real Gas Properties Using a Discovery-Based Approach and Molecular Dynamics Simulations

    Science.gov (United States)

    Sweet, Chelsea; Akinfenwa, Oyewumi; Foley, Jonathan J., IV

    2018-01-01

    We present an interactive discovery-based approach to studying the properties of real gases using simple, yet realistic, molecular dynamics software. Use of this approach opens up a variety of opportunities for students to interact with the behaviors and underlying theories of real gases. Students can visualize gas behavior under a variety of…

  19. Molecular dynamics simulation based on the multi-component molecular orbital method: Application to H5O2+,D5O2+,andT5O2+

    International Nuclear Information System (INIS)

    Ishimoto, Takayoshi; Koyama, Michihisa

    2012-01-01

    Graphical abstract: Molecular dynamics method based on multi-component molecular orbital method was applied to basic hydrogen bonding systems, H 5 O 2 + , and its isotopomers (D 5 O 2 + andT 5 O 2 + ). Highlights: ► Molecular dynamics method with nuclear quantum effect was developed. ► Multi-component molecular orbital method was used as ab initio MO calculation. ► Developed method applied to basic hydrogen bonding system, H 5 O 2 + , and isotopomers. ► O ⋯ O vibrational stretching reflected to the distribution of protonic wavefunctions. ► H/D/T isotope effect was also analyzed. - Abstract: We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MC M O) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MC M O based MD (MC M O-MD) method is applied to the basic structures, H 5 O 2 + (called “Zundel ion”), and its isotopomers (D 5 O 2 + andT 5 O 2 + ). We clearly demonstrate the geometrical difference of hydrogen bonded O ⋯ O distance induced by H/D/T isotope effect because the O ⋯ O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O ⋯ O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O ⋯ O distance becomes short during the dynamics. Our proposed MC M O-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.

  20. Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

    OpenAIRE

    Pande, Vineet; Nilsson, Lennart

    2008-01-01

    Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3′-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA–DNA, LNA–LNA, LNA–RNA, RNA–DNA and RNA–RNA) in order to characterize their structure, dynamics and hydration. Structurally, the LNA–DNA and LNA–RNA duplexes are found to be similar to regular RNA–D...

  1. Elastic properties of amorphous boron suboxide based solids studied using ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Music, Denis; Schneider, Jochen M

    2008-01-01

    We have studied the correlation between chemical composition, structure, chemical bonding and elastic properties of amorphous B 6 O based solids using ab initio molecular dynamics. These solids are of different chemical compositions, but the elasticity data appear to be a function of density. This is in agreement with previous experimental observations. As the density increases from 1.64 to 2.38 g cm -3 , the elastic modulus increases from 74 to 253 GPa. This may be understood by analyzing the cohesive energy and the chemical bonding of these compounds. The cohesive energy decreases from -7.051 to -7.584 eV/atom in the elastic modulus range studied. On the basis of the electron density distributions, Mulliken analysis and radial distribution functions, icosahedral bonding is the dominating bonding type. C and N promote cross-linking of icosahedra and thus increase the density, while H hinders the cross-linking by forming OH groups. The presence of icosahedral bonding is independent of the density

  2. A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.

    Science.gov (United States)

    Chu, Huiying; Peng, Xiangda; Li, Yan; Zhang, Yuebin; Li, Guohui

    2017-12-31

    In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.

  3. An Evaluation of Neutron Energy Spectrum Effects in Iron Based on Molecular Dynamics Displacement Cascade Simulations

    International Nuclear Information System (INIS)

    Greenwood, L.R.; Stoller, R.E.

    1998-01-01

    The results of molecular dynamics (MD) displacement cascade simulations in bcc iron have been used to obtain effective cross sections for two measures of primary damage production: (1) the number of surviving point defects expressed as a fraction of the displacements calculated using the standard secondary displacement model of Norgett, Robinson, and Torrens (NRT), and (2) the fraction of the surviving interstitials contained in clusters that formed during the cascade event. Primary knockon atom spectra for iron obtained from the SPECTER code have been used to weight these MD-based damage production cross sections in order to obtain spectrally-averaged values for several locations in commercial fission reactors and materials test reactors. An evaluation of these results indicates that neutron energy spectrum differences between the various enviromnents do not lead to significant differences between the average primary damage formation parameters. In particular, the defect production cross sections obtained for PWR and BWR neutron spectra were not significantly different. The variation of the defect production cross sections as a function of depth into the reactor pressure vessel wall is used as a sample application of the cross sections. A slight difference between the attenuation behavior of the PWR and BWR was noted; this difference could be explained by a subtle difference in the energy dependence of the neutron spectra. Overall, the simulations support the continued use of dpa as a damage correlation parameter

  4. Drug design based on x-ray diffraction and steered molecular dynamics

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Skálová, Tereza; Dohnálek, Jan; Dušková, Jarmila; Petroková, Hana; Vondráčková, Eva; Zimmermann, K.

    2005-01-01

    Roč. 12, č. 3 (2005), s. 208-210 ISSN 1211-5894. [VUFB Conference on Modern Methods in Synthesis and Analysis of Active Pharmaceutical Substances /5./. Praha, 23.11.2005-24.11.2005] R&D Projects: GA AV ČR KJB4050312 Institutional research plan: CEZ:AV0Z40500505 Keywords : drug design * X-ray diffraction * steered molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry

  5. Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

    Science.gov (United States)

    Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

    2015-01-01

    Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.

  6. A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape

    Science.gov (United States)

    Lakshminarasimhulu, Pasupulati; Madura, Jeffry D.

    2002-04-01

    A domain decomposition algorithm for molecular dynamics simulation of atomic and molecular systems with arbitrary shape and non-periodic boundary conditions is described. The molecular dynamics program uses cell multipole method for efficient calculation of long range electrostatic interactions and a multiple time step method to facilitate bigger time steps. The system is enclosed in a cube and the cube is divided into a hierarchy of cells. The deepest level cells are assigned to processors such that each processor has contiguous cells and static load balancing is achieved by redistributing the cells so that each processor has approximately same number of atoms. The resulting domains have irregular shape and may have more than 26 neighbors. Atoms constituting bond angles and torsion angles may straddle more than two processors. An efficient strategy is devised for initial assignment and subsequent reassignment of such multiple-atom potentials to processors. At each step, computation is overlapped with communication greatly reducing the effect of communication overhead on parallel performance. The algorithm is tested on a spherical cluster of water molecules, a hexasaccharide and an enzyme both solvated by a spherical cluster of water molecules. In each case a spherical boundary containing oxygen atoms with only repulsive interactions is used to prevent evaporation of water molecules. The algorithm shows excellent parallel efficiency even for small number of cells/atoms per processor.

  7. A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

    Science.gov (United States)

    Jafari, Mohieddin; Ansari-Pour, Naser; Azimzadeh, Sadegh; Mirzaie, Mehdi

    It is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

  8. Mechanical Property and Analysis of Asphalt Components Based on Molecular Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    Rui Li

    2017-01-01

    Full Text Available The asphalt-aggregate interface interaction plays a significant role in the overall performances of asphalt mixture. In order to analyze the chemical constitution of asphalt effects on the asphalt-aggregate interaction, the average structure C64H52S2 is selected to represent the asphalt, and the colloid, saturated phenol, and asphaltene are selected to represent the major constitutions in asphalt. The molecular models are established for the three compositions, respectively, and the Molecular Dynamics (MD simulation was conducted for the three kinds of asphaltene-aggregate system at different presses. Comparing the E value of Young modulus of these three polymers, the maximum modulus value of asphaltene was 2.80 GPa, the modulus value of colloid was secondary, and the minimum modulus of saturated phenol was 0.52 GPa. This result corresponds to conventional understanding.

  9. Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

    Czech Academy of Sciences Publication Activity Database

    Réblová, Kamila; Fadrná, E.; Sarzynska, J.; Kulinski, T.; Kulhánek, P.; Ennifar, E.; Koča, J.; Šponer, Jiří

    2007-01-01

    Roč. 93, č. 11 (2007), s. 3932-3949 ISSN 0006-3495 R&D Projects: GA MŠk(CZ) LC06030; GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA203/05/0388; GA AV ČR(CZ) 1QS500040581 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : molecular dynamics * RNA * virus Subject RIV: BO - Biophysics Impact factor: 4.627, year: 2007

  10. 3D-QSAR, molecular docking, and molecular dynamic simulations for prediction of new Hsp90 inhibitors based on isoxazole scaffold.

    Science.gov (United States)

    Abbasi, Maryam; Sadeghi-Aliabadi, Hojjat; Amanlou, Massoud

    2018-05-01

    Heat shock protein 90(Hsp90), as a molecular chaperone, play a crucial role in folding and proper function of many proteins. Hsp90 inhibitors containing isoxazole scaffold are currently being used in the treatment of cancer as tumor suppressers. Here in the present studies, new compounds based on isoxazole scaffold were predicted using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamic (MD) simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were also done. The steric and electrostatic contour map of CoMFA and CoMSIA were created. Hydrophobic, hydrogen bond donor and acceptor of CoMSIA model also were generated, and new compounds were predicted by CoMFA and CoMSIA contour maps. To investigate the binding modes of the predicted compounds in the active site of Hsp90, a molecular docking simulation was carried out. MD simulations were also conducted to evaluate the obtained results on the best predicted compound and the best reported Hsp90 inhibitors in the 3D-QSAR model. Findings indicate that the predicted ligands were stable in the active site of Hsp90.

  11. Raman Optical Activity Spectra from Density Functional Perturbation Theory and Density-Functional-Theory-Based Molecular Dynamics.

    Science.gov (United States)

    Luber, Sandra

    2017-03-14

    We describe the calculation of Raman optical activity (ROA) tensors from density functional perturbation theory, which has been implemented into the CP2K software package. Using the mixed Gaussian and plane waves method, ROA spectra are evaluated in the double-harmonic approximation. Moreover, an approach for the calculation of ROA spectra by means of density functional theory-based molecular dynamics is derived and used to obtain an ROA spectrum via time correlation functions, which paves the way for the calculation of ROA spectra taking into account anharmonicities and dynamic effects at ambient conditions.

  12. Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    2017-01-01

    Full Text Available The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR, are the main endocrine therapies for prostate cancer (PCa. But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

  13. Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists.

    Science.gov (United States)

    Wang, Yuwei; Han, Rui; Zhang, Huimin; Liu, Hongli; Li, Jiazhong; Liu, Huanxiang; Gramatica, Paola

    2017-01-01

    The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR), are the main endocrine therapies for prostate cancer (PCa). But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7 α -substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD) simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

  14. Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

    Science.gov (United States)

    Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

    2018-04-01

    We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

  15. Nonlocal strain gradient theory calibration using molecular dynamics simulation based on small scale vibration of nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Mehralian, Fahimeh [Mechanical Engineering Department, Shahrekord University, Shahrekord (Iran, Islamic Republic of); Tadi Beni, Yaghoub, E-mail: tadi@eng.sku.ac.ir [Faculty of Engineering, Shahrekord University, Shahrekord (Iran, Islamic Republic of); Karimi Zeverdejani, Mehran [Mechanical Engineering Department, Shahrekord University, Shahrekord (Iran, Islamic Republic of)

    2017-06-01

    Featured by two small length scale parameters, nonlocal strain gradient theory is utilized to investigate the free vibration of nanotubes. A new size-dependent shell model formulation is developed by using the first order shear deformation theory. The governing equations and boundary conditions are obtained using Hamilton's principle and solved for simply supported boundary condition. As main purpose of this study, since the values of two small length scale parameters are still unknown, they are calibrated by the means of molecular dynamics simulations (MDs). Then, the influences of different parameters such as nonlocal parameter, scale factor, length and thickness on vibration characteristics of nanotubes are studied. It is also shown that increase in thickness and decrease in length parameters intensify the effect of nonlocal parameter and scale factor.

  16. Multi-scale calculation based on dual domain material point method combined with molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Dhakal, Tilak Raj [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-02-27

    This dissertation combines the dual domain material point method (DDMP) with molecular dynamics (MD) in an attempt to create a multi-scale numerical method to simulate materials undergoing large deformations with high strain rates. In these types of problems, the material is often in a thermodynamically non-equilibrium state, and conventional constitutive relations are often not available. In this method, the closure quantities, such as stress, at each material point are calculated from a MD simulation of a group of atoms surrounding the material point. Rather than restricting the multi-scale simulation in a small spatial region, such as phase interfaces, or crack tips, this multi-scale method can be used to consider non-equilibrium thermodynamic e ects in a macroscopic domain. This method takes advantage that the material points only communicate with mesh nodes, not among themselves; therefore MD simulations for material points can be performed independently in parallel. First, using a one-dimensional shock problem as an example, the numerical properties of the original material point method (MPM), the generalized interpolation material point (GIMP) method, the convected particle domain interpolation (CPDI) method, and the DDMP method are investigated. Among these methods, only the DDMP method converges as the number of particles increases, but the large number of particles needed for convergence makes the method very expensive especially in our multi-scale method where we calculate stress in each material point using MD simulation. To improve DDMP, the sub-point method is introduced in this dissertation, which provides high quality numerical solutions with a very small number of particles. The multi-scale method based on DDMP with sub-points is successfully implemented for a one dimensional problem of shock wave propagation in a cerium crystal. The MD simulation to calculate stress in each material point is performed in GPU using CUDA to accelerate the

  17. Physical adsorption and molecular dynamics

    International Nuclear Information System (INIS)

    Cohan, N.V.

    1981-01-01

    Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

  18. A study of internal energy relaxation in shocks using molecular dynamics based models

    International Nuclear Information System (INIS)

    Li, Zheng; Parsons, Neal; Levin, Deborah A.

    2015-01-01

    Recent potential energy surfaces (PESs) for the N 2 + N and N 2 + N 2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N 2 + N 2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N 2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available

  19. Comprehensive representation of the Lennard-Jones equation of state based on molecular dynamics simulation data

    Science.gov (United States)

    Pieprzyk, S.; Brańka, A. C.; Maćkowiak, Sz.; Heyes, D. M.

    2018-03-01

    The equation of state (EoS) of the Lennard-Jones fluid is calculated using a new set of molecular dynamics data which extends to higher temperature than in previous studies. The modified Benedict-Webb-Rubin (MBWR) equation, which goes up to ca. T ˜ 6, is reparametrized with new simulation data. A new analytic form for the EoS, which breaks the fluid range into two regions with different analytic forms and goes up to ca. T ≃ 35, is also proposed. The accuracy of the new formulas is at least as good as the MBWR fit and goes to much higher temperature allowing it to now encompass the Amagat line. The fitted formula extends into the high temperature range where the system can be well represented by inverse power potential scaling, which means that our specification of the equation of state covers the entire (ρ, T) plane. Accurate analytic fit formulas for the Boyle, Amagat, and inversion curves are presented. Parametrizations of the extrema loci of the isochoric, CV, and isobaric, CP, heat capacities are given. As found by others, a line maxima of CP terminates in the critical point region, and a line of minima of CP terminates on the freezing line. The line of maxima of CV terminates close to or at the critical point, and a line of minima of CV terminates to the right of the critical point. No evidence for a divergence in CV in the critical region is found.

  20. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

    Science.gov (United States)

    Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

  1. Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases--a comparative molecular dynamics study.

    Science.gov (United States)

    Jezierska-Mazzarello, Aneta; Panek, Jarosław J; Vuilleumier, Rodolphe; Koll, Aleksander; Ciccotti, Giovanni

    2011-01-21

    We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r((O⋅⋅⋅N)) ≤ 2.6 Å), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects.

  2. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

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

    2016-01-01

    that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package......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...... capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern...

  3. Revisiting imidazolium based ionic liquids: Effect of the conformation bias of the [NTf2] anion studied by molecular dynamics simulations

    Science.gov (United States)

    Neumann, Jan; Golub, Benjamin; Odebrecht, Lisa-Marie; Ludwig, Ralf; Paschek, Dietmar

    2018-05-01

    We study ionic liquids composed of 1-alkyl-3-methylimidazolium cations and bis(trifluoromethyl-sulfonyl)imide anions ([CnMIm][NTf2]) with varying chain-length n = 2, 4, 6, 8 by using molecular dynamics simulations. We show that a reparametrization of the dihedral potentials as well as charges of the [NTf2] anion leads to an improvement of the force field model introduced by Köddermann, Paschek, and Ludwig [ChemPhysChem 8, 2464 (2007)] (KPL-force field). A crucial advantage of the new parameter set is that the minimum energy conformations of the anion (trans and gauche), as deduced from ab initio calculations and Raman experiments, are now both well represented by our model. In addition, the results for [CnMIm][NTf2] show that this modification leads to an even better agreement between experiment and molecular dynamics simulation as demonstrated for densities, diffusion coefficients, vaporization enthalpies, reorientational correlation times, and viscosities. Even though we focused on a better representation of the anion conformation, also the alkyl chain-length dependence of the cation behaves closer to the experiment. We strongly encourage to use the new NGOLP (Neumann, Golub, Odebrecht, Ludwig, Paschek) force field for the [NTf2] anion instead of the earlier KPL parameter set for computer simulations aiming to describe the thermodynamics, dynamics, and also structure of imidazolium-based ionic liquids.

  4. Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement.

    Science.gov (United States)

    Baleja, J D; Germann, M W; van de Sande, J H; Sykes, B D

    1990-10-05

    The solution structures of two alternating purine-pyrimidine octamers, [d(G-T-A-C-G-T-A-C)]2 and the reverse sequence [d(C-A-T-G-C-A-T-G)]2, are investigated by using nuclear magnetic resonance spectroscopy and restrained molecular dynamics calculations. Chemical shift assignments are obtained for non-exchangeable protons by a combination of two-dimensional correlation and nuclear Overhauser enhancement (NOE) spectroscopy experiments. Distances between protons are estimated by extrapolating distances derived from time-dependent NOE measurements to zero mixing time. Approximate dihedral angles are determined within the deoxyribose ring from coupling constants observed in one and two-dimensional spectra. Sets of distance and dihedral determinations for each of the duplexes form the bases for structure determination. Molecular dynamics is then used to generate structures that satisfy the experimental restraints incorporated as effective potentials into the total energy. Separate runs start from classical A and B-form DNA and converge to essentially identical structures. To circumvent the problems of spin diffusion and differential motion associated with distance measurements within molecules, models are improved by NOE-based refinement in which observed NOE intensities are compared to those calculated using a full matrix analysis procedure. The refined structures generally have the global features of B-type DNA. Some, but not all, variations in dihedral angles and in the spatial relationships of adjacent base-pairs are observed to be in synchrony with the alternating purine-pyrimidine sequence.

  5. A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

    Directory of Open Access Journals (Sweden)

    Mohieddin Jafari

    Full Text Available It is nearly half a century past the age of the introduction of the Central Dogma (CD of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

  6. Multiple grid methods for classical molecular dynamics.

    Science.gov (United States)

    Skeel, Robert D; Tezcan, Ismail; Hardy, David J

    2002-04-30

    Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, which are based on the hierarchical interpolation of interaction potentials on multiple grids. The concepts and details underlying multigrid interpolation are described. For integration of molecular dynamics the use of different time steps for different interactions allows longer time steps for many of the interactions, and this can be combined with multiple grids in space. Comparison is made to the fast multipole method, and evidence is presented suggesting that for molecular simulations multigrid methods may be superior to the fast multipole method and other tree methods.

  7. Multiscale Reactive Molecular Dynamics

    Science.gov (United States)

    2012-08-15

    as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP

  8. 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.

  9. 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.

  10. Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics.

    Science.gov (United States)

    Yeager, Andrew; Humphries, Kathryn; Farmer, Ellen; Cline, Gene; Miller, Bill R

    2018-02-26

    Optimizing DNA polymerases for a broad range of tasks requires an understanding of the factors influencing polymerase fidelity, but many details of polymerase behavior remain unknown, especially in the presence of mismatched nascent base pairs. Using molecular dynamics, the large fragment of Bacillus stearothermophilus DNA polymerase I is simulated in the presence of all 16 possible standard nucleoside triphosphate-template (dNTP-dN) pairs, including four Watson-Crick pairs and 12 mismatches. The precatalytic steps of nucleotide addition from nucleotide insertion to immediately preceding catalysis are explored using three starting structures representing different stages of nucleotide addition. From these simulations, interactions between dNTPs and the DNA-protein complex formed by the polymerase are elucidated. Patterns of large-scale conformational shifts, classification of nucleotide pairs based on composition, and investigation of the roles of residues interacting with dNTPs are completed on 50+ μs of simulation. The role of molecular dynamics in studies of polymerase behavior is discussed.

  11. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. I. Homogeneous fluids

    Energy Technology Data Exchange (ETDEWEB)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard, E-mail: elliot1@uakron.edu [Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325 (United States)

    2013-12-21

    In this work, we aim to develop a version of the Statistical Associating Fluid Theory (SAFT)-γ equation of state (EOS) that is compatible with united-atom force fields, rather than experimental data. We rely on the accuracy of the force fields to provide the relation to experimental data. Although, our objective is a transferable theory of interfacial properties for soft and fused heteronuclear chains, we first clarify the details of the SAFT-γ approach in terms of site-based simulations for homogeneous fluids. We show that a direct comparison of Helmholtz free energy to molecular simulation, in the framework of a third order Weeks-Chandler-Andersen perturbation theory, leads to an EOS that takes force field parameters as input and reproduces simulation results for Vapor-Liquid Equilibria (VLE) calculations. For example, saturated liquid density and vapor pressure of n-alkanes ranging from methane to dodecane deviate from those of the Transferable Potential for Phase Equilibria (TraPPE) force field by about 0.8% and 4%, respectively. Similar agreement between simulation and theory is obtained for critical properties and second virial coefficient. The EOS also reproduces simulation data of mixtures with about 5% deviation in bubble point pressure. Extension to inhomogeneous systems and united-atom site types beyond those used in description of n-alkanes will be addressed in succeeding papers.

  12. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. I. Homogeneous fluids.

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Elliott, J Richard

    2013-12-21

    In this work, we aim to develop a version of the Statistical Associating Fluid Theory (SAFT)-γ equation of state (EOS) that is compatible with united-atom force fields, rather than experimental data. We rely on the accuracy of the force fields to provide the relation to experimental data. Although, our objective is a transferable theory of interfacial properties for soft and fused heteronuclear chains, we first clarify the details of the SAFT-γ approach in terms of site-based simulations for homogeneous fluids. We show that a direct comparison of Helmholtz free energy to molecular simulation, in the framework of a third order Weeks-Chandler-Andersen perturbation theory, leads to an EOS that takes force field parameters as input and reproduces simulation results for Vapor-Liquid Equilibria (VLE) calculations. For example, saturated liquid density and vapor pressure of n-alkanes ranging from methane to dodecane deviate from those of the Transferable Potential for Phase Equilibria (TraPPE) force field by about 0.8% and 4%, respectively. Similar agreement between simulation and theory is obtained for critical properties and second virial coefficient. The EOS also reproduces simulation data of mixtures with about 5% deviation in bubble point pressure. Extension to inhomogeneous systems and united-atom site types beyond those used in description of n-alkanes will be addressed in succeeding papers.

  13. 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.

  14. Improving the Performance of Hybrid Functional-Based Molecular Dynamics Simulation through Screening of Hartree-Fock Exchange Forces.

    Science.gov (United States)

    von Rudorff, Guido Falk; Jakobsen, Rasmus; Rosso, Kevin M; Blumberger, Jochen

    2017-05-09

    Density functional theory-based molecular dynamics calculations of condensed phase systems often benefit from the use of hybrid functionals. However, their use is computationally very demanding and severely limits the system size and time scale that can be simulated. Several methods have been introduced to accelerate hybrid functional molecular dynamics including Schwarz screening and the auxiliary density matrix method (ADMM). Here we present a simple screening scheme that can be applied in addition to these methods. It works by examining Hartree-Fock exchange (HFX) integrals and subsequently excluding those that contribute very little to any nuclear force component. The resultant force error is corrected by a history-dependent extrapolation scheme. We find that for systems where the calculation of HFX forces is a major bottleneck, a large fraction of the integrals can be neglected without introducing significant errors in the nuclear forces. For instance, for a 2 × 2 × 2 unit cell of CoO, 92% of the HFX integrals that have passed Schwarz screening within the ADMM approach can be neglected leading to a performance gain of a factor of 3 at a negligible error in nuclear forces (≤5 × 10 -4 H bohr -1 ). We also show that total energy conservation and solvation structures are not adversely affected by the screening method.

  15. Novel Readout Method for Molecular Diagnostic Assays Based on Optical Measurements of Magnetic Nanobead Dynamics

    DEFF Research Database (Denmark)

    Donolato, Marco; Antunes, Paula Soares Martins; Bejhed, Rebecca S.

    2015-01-01

    transmission spectra of MNB suspensions measured upon application of a weak uniaxial AC magnetic field correlate well with the rotation dynamics of the individual MNBs. Adding a target analyte to the solution leads to the formation of permanent MNB clusters, namely, to the suppression of the dynamic MNB......We demonstrate detection of DNA coils formed from a Vibrio cholerae DNA target at picomolar concentrations using a novel optomagnetic approach exploiting the dynamic behavior and optical anisotropy of magnetic nanobead (MNB) assemblies. We establish that the complex second harmonic optical...

  16. Molecular dynamics algorithms for quantum Monte Carlo methods

    Science.gov (United States)

    Miura, Shinichi

    2009-11-01

    In the present Letter, novel molecular dynamics methods compatible with corresponding quantum Monte Carlo methods are developed. One is a variational molecular dynamics method that is a molecular dynamics analog of quantum variational Monte Carlo method. The other is a variational path integral molecular dynamics method, which is based on the path integral molecular dynamics method for finite temperature systems by Tuckerman et al. [M. Tuckerman, B.J. Berne, G.J. Martyna, M.L. Klein, J. Chem. Phys. 99 (1993) 2796]. These methods are applied to model systems including the liquid helium-4, demonstrated to work satisfactorily for the tested ground state calculations.

  17. Molecular dynamics with phase-shift-based electronic stopping for calibration of ion implantation profiles in crystalline silicon

    International Nuclear Information System (INIS)

    Chan, H.Y.; Nordlund, K.; Gossmann, H.-J.L.; Harris, M.; Montgomery, N.J.; Mulcahy, C.P.A.; Biswas, S.; Srinivasan, M.P.; Benistant, F.; Ng, C.M.; Chan, Lap

    2006-01-01

    Prediction of the final dopant positions after ion implantation has always been strongly influenced by the choice of stopping models. A molecular dynamics (MD) method is used in this work; the nuclear stopping is treated by accurate pair potentials calculated by density functional theory (DFT). The slowing down due to collisions with electrons will be described by both a non-local semi-empirical model and a local model based on Fermi level phase shift factors. Comparisons with experimental data using both models show that a local pair-specific electronic stopping model is essential in accurately predicting range profiles for any element even at low implant energies where nuclear effects are dominant

  18. Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine

    Directory of Open Access Journals (Sweden)

    Mahdi Bagherpoor Helabad

    2014-07-01

    Full Text Available Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.

  19. Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations in Molecular Dynamics Simulations *†

    Science.gov (United States)

    Gu, Yongfeng; VanCourt, Tom; Herbordt, Martin C.

    2008-01-01

    FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code. PMID:19412319

  20. Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations in Molecular Dynamics Simulations.

    Science.gov (United States)

    Gu, Yongfeng; Vancourt, Tom; Herbordt, Martin C

    2008-05-01

    FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.

  1. Eutectic-based wafer-level-packaging technique for piezoresistive MEMS accelerometers and bond characterization using molecular dynamics simulations

    Science.gov (United States)

    Aono, T.; Kazama, A.; Okada, R.; Iwasaki, T.; Isono, Y.

    2018-03-01

    We developed a eutectic-based wafer-level-packaging (WLP) technique for piezoresistive micro-electromechanical systems (MEMS) accelerometers on the basis of molecular dynamics analyses and shear tests of WLP accelerometers. The bonding conditions were experimentally and analytically determined to realize a high shear strength without solder material atoms diffusing to adhesion layers. Molecular dynamics (MD) simulations and energy dispersive x-ray (EDX) spectrometry done after the shear tests clarified the eutectic reaction of the solder materials used in this research. Energy relaxation calculations in MD showed that the diffusion of solder material atoms into the adhesive layer was promoted at a higher temperature. Tensile creep MD simulations also suggested that the local potential energy in a solder material model determined the fracture points of the model. These numerical results were supported by the shear tests and EDX analyses for WLP accelerometers. Consequently, a bonding load of 9.8 kN and temperature of 300 °C were found to be rational conditions because the shear strength was sufficient to endure the polishing process after the WLP process and there was little diffusion of solder material atoms to the adhesion layer. Also, eutectic-bonding-based WLP was effective for controlling the attenuation of the accelerometers by determining the thickness of electroplated solder materials that played the role of a cavity between the accelerometers and lids. If the gap distance between the two was less than 6.2 µm, the signal gains for x- and z-axis acceleration were less than 20 dB even at the resonance frequency due to air-damping.

  2. Prediction of the Chapman-Jouguet chemical equilibrium state in a detonation wave from first principles based reactive molecular dynamics.

    Science.gov (United States)

    Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei

    2016-01-21

    The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman-Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation.

  3. Molecular dynamics modeling of structural battery components

    NARCIS (Netherlands)

    Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.

    2015-01-01

    A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion

  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. Synthesis, crystal and molecular structure and dynamic behaviour of new dimethyldioxanedione based inherently dissymmetric overcrowded alkenes.

    NARCIS (Netherlands)

    Huck, NPM; Meetsma, A; Zijlstra, R; Feringa, BL; Huck, Nina P.M.; Feringa, Bernard

    1995-01-01

    Two representatives of new chiral sterically overcrowded ethylenes, 2-methyl(9-thioxanthylidene)-2,2-dimethyl- 1,3-dioxane-4,6-dione (3) and 12H-benzo[a]thioxanthylidene-2,2-dimethyl-1,3-dioxane-4,6-dione (5), have been prepared and dynamic H-1 NMR studies revealed 1 racemization barriers of 10.3

  6. Thomas-Fermi molecular dynamics

    International Nuclear Information System (INIS)

    Clerouin, J.; Pollock, E.L.; Zerah, G.

    1992-01-01

    A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

  7. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  8. The melting points of MgO up to 4 TPa predicted based on ab initio thermodynamic integration molecular dynamics.

    Science.gov (United States)

    Taniuchi, Takashi; Tsuchiya, Taku

    2018-03-21

    The melting curve of MgO is extended up to 4 TPa, corresponding to the Jovian core pressure, based on the one-step thermodynamic integration method implemented on ab initio molecular dynamics. The calculated melting temperatures are 3100 and 16 000 K at 0 and 500 GPa, respectively, which are consistent with previous experimental results, and 20 600 K at 3900 GPa, which is inconsistent with a recent experimental extrapolation, which implies the molten Jovian core. A quite small Clapeyron slope ([Formula: see text]) of [Formula: see text] is found at 3900 GPa due to comparable densities of the liquid and B2 phases under extreme compression. The Mg-O coordination number in the liquid phase is saturated at around 7.5 above 1 TPa and remains smaller than that in the B2 phase (8) even at 4 TPa, suggesting no density crossover between liquid and crystal and thus no further denser crystalline phases. Dynamical properties (atomic diffusivity and viscosity) are also investigated along the melting curve to understand these behaviors in greater detail.

  9. The melting points of MgO up to 4 TPa predicted based on ab initio thermodynamic integration molecular dynamics

    Science.gov (United States)

    Taniuchi, Takashi; Tsuchiya, Taku

    2018-03-01

    The melting curve of MgO is extended up to 4 TPa, corresponding to the Jovian core pressure, based on the one-step thermodynamic integration method implemented on ab initio molecular dynamics. The calculated melting temperatures are 3100 and 16 000 K at 0 and 500 GPa, respectively, which are consistent with previous experimental results, and 20 600 K at 3900 GPa, which is inconsistent with a recent experimental extrapolation, which implies the molten Jovian core. A quite small Clapeyron slope (dT/dP ) of 0.0+/- 0.5 is found at 3900 GPa due to comparable densities of the liquid and B2 phases under extreme compression. The Mg–O coordination number in the liquid phase is saturated at around 7.5 above 1 TPa and remains smaller than that in the B2 phase (8) even at 4 TPa, suggesting no density crossover between liquid and crystal and thus no further denser crystalline phases. Dynamical properties (atomic diffusivity and viscosity) are also investigated along the melting curve to understand these behaviors in greater detail.

  10. Molecular dynamics study of binding energies, mechanical properties, and detonation performances of bicyclo-HMX-based PBXs.

    Science.gov (United States)

    Qiu, Ling; Xiao, Heming

    2009-05-15

    To investigate the effect of polymer binders on the monoexplosive, molecular dynamics simulations were performed to study the binding energies, mechanical properties, and detonation performances of the bicyclo-HMX-based polymer-bonded explosives (PBXs). The results show that the binding energies on different crystalline surfaces of bicyclo-HMX decrease in the order of (010)>(100)>(001). On each crystalline surface, binding properties of different polymers with the same chain segment are different from each other, while those of the polymers in the same content decrease in the sequence of PVDF>F(2311)>F(2314) approximately PCTFE. The mechanical properties of a dozen of model systems (elastic coefficients, various moduli, Cauchy pressure, and Poisson's ratio) have been obtained. It is found that mechanical properties are effectively improved by adding small amounts of fluorine polymers, and the overall effect of fluorine polymers on three crystalline surfaces of bicyclo-HMX changes in the order of (010)>(001) approximately (100). In comparison with the base explosive, detonation performances of the PBXs decrease slightly, but they are still superior to TNT. These suggestions may be useful for the formulation design of bicyclo-HMX-based PBXs.

  11. A comprehensive molecular dynamics study on the self-assembly and properties of SiC based cage structures

    Science.gov (United States)

    Zhang, Congyan; Xin, Zihua; Yu, Ming; Jayanthi, C. S.; Wu, S. Y.; Shanghai University Collaboration

    2014-03-01

    A molecular dynamics study to investigate a plausible way of fabricating SiC based cage structures has been performed. In this work, the existence of the stable SiC based cage nanostructures SimCn with the size up to about 2.05nm in diameter and the compositions n/(n +m) from 0.4 to 0.6 has been demonstrated using an efficient semi-empirical Hamiltonian method (SCED-LCAO) [PRB 74, 15540 (2006)]. The structural properties are analyzed in terms of the composition, the bonding nature, the surface environment, the local strain, and types of ring structures. It is found that the sp2 bonding nature between Si and C atoms and the environmental mediation are two key factors for the self-assembly of the stable SiC based cage structures. In particular, the transition from one stable cage structure to another of similar composition might occur due to the mending process in the self-assembly. The first and second authors acknowledge the support from the NSFC (grant No.: 61176118) and 085 project of Shanghai University (China) for this work.

  12. A molecular dynamics study on the structural and electronic properties of two-dimensional icosahedral B12 cluster based structures

    Science.gov (United States)

    Kah, Cherno Baba; Yu, M.; Jayanthi, C. S.; Wu, S. Y.

    2014-03-01

    Our previous study on one-dimensional icosahedral B12 cluster (α-B12) based chain [Bulletin of APS Annual Meeting, p265 (2013)] and ring structures has prompted us to study the two-dimensional (2D) α-B12 based structures. Recently, we have carried out a systematic molecular dynamics study on the structural stabilities and electronic properties of the 2D α-B12 based structures using the SCED-LCAO method [PRB 74, 15540 (2006)]. We have considered several types of symmetry for these 2D structures such as δ3, δ4, δ6 (flat triangular), and α' types. We have found that the optimized structures are energetically in the order of δ6 < α' < δ3 < δ4 which is different from the energy order of α'< δ6 < δ4 < δ3 found in the 2D boron monolayer sheets [ACS Nano 6, 7443 (2012)]. A detailed discussion of this study will be presented. The first author acknowledges the McSweeny Fellowship for supporting his research in this work.

  13. Molecular dynamics study on the evolution of interfacial dislocation network and mechanical properties of Ni-based single crystal superalloys

    Science.gov (United States)

    Li, Nan-Lin; Wu, Wen-Ping; Nie, Kai

    2018-05-01

    The evolution of misfit dislocation network at γ /γ‧ phase interface and tensile mechanical properties of Ni-based single crystal superalloys at various temperatures and strain rates are studied by using molecular dynamics (MD) simulations. From the simulations, it is found that with the increase of loading, the dislocation network effectively inhibits dislocations emitted in the γ matrix cutting into the γ‧ phase and absorbs the matrix dislocations to strengthen itself which increases the stability of structure. Under the influence of the temperature, the initial mosaic structure of dislocation network gradually becomes irregular, and the initial misfit stress and the elastic modulus slowly decline as temperature increasing. On the other hand, with the increase of the strain rate, it almost has no effect on the elastic modulus and the way of evolution of dislocation network, but contributes to the increases of the yield stress and tensile strength. Moreover, tension-compression asymmetry of Ni-based single crystal superalloys is also presented based on MD simulations.

  14. Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling

    NARCIS (Netherlands)

    Wolthers, M.; Di Tommaso, D.; Du, Zhimei; de Leeuw, Nora H.

    2013-01-01

    It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two

  15. Ab-Initio Molecular Dynamics Simulations of Molten Ni-Based Superalloys

    National Research Council Canada - National Science Library

    Asta, Mark; Trinkle, Dallas; Woodward, Christopher

    2007-01-01

    In casting of single-crystal turbine blades for jet engines, the formation of solidification defects has become an increasingly important problem due to the rising levels of refractory elements in Ni-based superalloys...

  16. Ab-Initio Molecular Dynamics Simulations of Molten Ni-Based Superalloys (Preprint)

    National Research Council Canada - National Science Library

    Woodward, Christopher; Asta, Mark; Trinkle, Dallas R; Lill, James; Angioletti-Uberti, Stefano

    2008-01-01

    In casting of single-crystal turbine blades for jet engines, the formation of solidification defects has become an increasingly important problem due to the rising levels of refractory elements in Ni-based superalloys...

  17. Rheology via nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1982-10-01

    The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

  18. Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study.

    Science.gov (United States)

    Peón, Antonio; Robles, Adrián; Blanco, Beatriz; Convertino, Marino; Thompson, Paul; Hawkins, Alastair R; Caflisch, Amedeo; González-Bello, Concepción

    2017-09-21

    A multidisciplinary approach was used to identify and optimize a quinazolinedione-based ligand that would decrease the flexibility of the substrate-covering loop (catalytic loop) of the type II dehydroquinase from Helicobacter pylori. This enzyme, which is essential for the survival of this bacterium, is involved in the biosynthesis of aromatic amino acids. A computer-aided fragment-based protocol (ALTA) was first used to identify the aromatic fragments able to block the interface pocket that separates two neighboring enzyme subunits and is located at the active site entrance. Chemical modification of its non-aromatic moiety through an olefin cross-metathesis and Seebach's self-reproduction of chirality synthetic principle allowed the development of a quinazolinedione derivative that disables the catalytic loop plasticity, which is essential for the enzyme's catalytic cycle. Molecular dynamics simulations revealed that the ligand would force the catalytic loop into an inappropriate arrangement for catalysis by strong interactions with the catalytic tyrosine and by expelling the essential arginine out of the active site. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Molecular dynamics study of silver

    International Nuclear Information System (INIS)

    Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

    1995-03-01

    We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

  20. Adaptive Green-Kubo estimates of transport coefficients from molecular dynamics based on robust error analysis

    Science.gov (United States)

    Jones, Reese E.; Mandadapu, Kranthi K.

    2012-04-01

    We present a rigorous Green-Kubo methodology for calculating transport coefficients based on on-the-fly estimates of: (a) statistical stationarity of the relevant process, and (b) error in the resulting coefficient. The methodology uses time samples efficiently across an ensemble of parallel replicas to yield accurate estimates, which is particularly useful for estimating the thermal conductivity of semi-conductors near their Debye temperatures where the characteristic decay times of the heat flux correlation functions are large. Employing and extending the error analysis of Zwanzig and Ailawadi [Phys. Rev. 182, 280 (1969)], 10.1103/PhysRev.182.280 and Frenkel [in Proceedings of the International School of Physics "Enrico Fermi", Course LXXV (North-Holland Publishing Company, Amsterdam, 1980)] to the integral of correlation, we are able to provide tight theoretical bounds for the error in the estimate of the transport coefficient. To demonstrate the performance of the method, four test cases of increasing computational cost and complexity are presented: the viscosity of Ar and water, and the thermal conductivity of Si and GaN. In addition to producing accurate estimates of the transport coefficients for these materials, this work demonstrates precise agreement of the computed variances in the estimates of the correlation and the transport coefficient with the extended theory based on the assumption that fluctuations follow a Gaussian process. The proposed algorithm in conjunction with the extended theory enables the calculation of transport coefficients with the Green-Kubo method accurately and efficiently.

  1. Dynamical quenching of tunneling in molecular magnets

    International Nuclear Information System (INIS)

    José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

    2015-01-01

    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

  2. Molecular Dynamics-based Simulations of Bulk/Interfacial Structures and Diffusion Behaviors in Nuclear Waste Glasses

    Energy Technology Data Exchange (ETDEWEB)

    Du, Jincheng

    2018-03-16

    This NEUP Project aimed to generate accurate atomic structural models of nuclear waste glasses by using large-scale molecular dynamics-based computer simulations and to use these models to investigate self-diffusion behaviors, interfacial structures, and hydrated gel structures formed during dissolution of these glasses. The goal was to obtain realistic and accurate short and medium range structures of these complex oxide glasses, to provide a mechanistic understanding of the dissolution behaviors, and to generate reliable information with predictive power in designing nuclear waste glasses for long-term geological storage. Looking back of the research accomplishments of this project, most of the scientific goals initially proposed have been achieved through intensive research in the three and a half year period of the project. This project has also generated a wealth of scientific data and vibrant discussions with various groups through collaborations within and outside of this project. Throughout the project one book chapter and 14 peer reviewed journal publications have been generated (including one under review) and 16 presentations (including 8 invited talks) have been made to disseminate the results of this project in national and international conference. Furthermore, this project has trained several outstanding graduate students and young researchers for future workforce in nuclear related field, especially on nuclear waste immobilization. One postdoc and four PhD students have been fully or partially supported through the project with intensive training in the field material science and engineering with expertise on glass science and nuclear waste disposal

  3. Effect of lattice relaxation on thermal conductivity of fcc-based structures: an efficient procedure of molecular dynamics simulation

    Science.gov (United States)

    Ha, Min Young; Choi, Garam; Kim, Dong Hyun; Kim, Hyo Seok; Park, Sang Hyun; Lee, Won Bo

    2017-07-01

    This work studied the computational details of the Green-Kubo method with molecular dynamics (MD) simulation for thermal conductivity prediction. In MD thermal conductivity calculation, little consensus has been made about the inclusion of zero-pressure volume relaxation in the isobaric-isothermal (NpT) ensemble, which determines the simulation lattice parameters. Simulations of fcc-based structures with different lattice parameters were performed to calculate lattice thermal conductivities and phonon density of states, and the results were compared to experimental reports and ab initio results to conclude that NpT volume relaxation is crucial for accurate prediction of thermal conductivity. In addition, the relation between thermal conductivity and interatomic potential cutoff distance was also analysed in the context of lattice relaxation. The results suggested that calculated thermal conductivity is strictly dependent on the lattice parameter and essentially independent of the cutoff distance. It was also shown that reducing the cutoff distance can greatly accelerate the thermal conductivity calculation, even without sacrificing the accuracy of thermal conductivity.

  4. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

  5. Investigate the complex process in particle-fluid based surface generation technology using reactive molecular dynamics method

    Science.gov (United States)

    Han, Xuesong; Li, Haiyan; Zhao, Fu

    2017-07-01

    Particle-fluid based surface generation process has already become one of the most important materials processing technology for many advanced materials such as optical crystal, ceramics and so on. Most of the particle-fluid based surface generation technology involves two key process: chemical reaction which is responsible for surface softening; physical behavior which is responsible for materials removal/deformation. Presently, researchers cannot give a reasonable explanation about the complex process in the particle-fluid based surface generation technology because of the small temporal-spatial scale and the concurrent influence of physical-chemical process. Molecular dynamics (MD) method has already been proved to be a promising approach for constructing effective model of atomic scale phenomenon and can serve as a predicting simulation tool in analyzing the complex surface generation mechanism and is employed in this research to study the essence of surface generation. The deformation and piles of water molecule is induced with the feeding of abrasive particle which justifies the property mutation of water at nanometer scale. There are little silica molecule aggregation or materials removal because the water-layer greatly reduce the strength of mechanical interaction between particle and materials surface and minimize the stress concentration. Furthermore, chemical effect is also observed at the interface: stable chemical bond is generated between water and silica which lead to the formation of silconl and the reaction rate changes with the amount of water molecules in the local environment. Novel ring structure is observed in the silica surface and it is justified to be favored of chemical reaction with water molecule. The siloxane bond formation process quickly strengthened across the interface with the feeding of abrasive particle because of the compressive stress resulted by the impacting behavior.

  6. Investigate the complex process in particle-fluid based surface generation technology using reactive molecular dynamics method

    Directory of Open Access Journals (Sweden)

    Xuesong Han

    2017-07-01

    Full Text Available Particle-fluid based surface generation process has already become one of the most important materials processing technology for many advanced materials such as optical crystal, ceramics and so on. Most of the particle-fluid based surface generation technology involves two key process: chemical reaction which is responsible for surface softening; physical behavior which is responsible for materials removal/deformation. Presently, researchers cannot give a reasonable explanation about the complex process in the particle-fluid based surface generation technology because of the small temporal-spatial scale and the concurrent influence of physical-chemical process. Molecular dynamics (MD method has already been proved to be a promising approach for constructing effective model of atomic scale phenomenon and can serve as a predicting simulation tool in analyzing the complex surface generation mechanism and is employed in this research to study the essence of surface generation. The deformation and piles of water molecule is induced with the feeding of abrasive particle which justifies the property mutation of water at nanometer scale. There are little silica molecule aggregation or materials removal because the water-layer greatly reduce the strength of mechanical interaction between particle and materials surface and minimize the stress concentration. Furthermore, chemical effect is also observed at the interface: stable chemical bond is generated between water and silica which lead to the formation of silconl and the reaction rate changes with the amount of water molecules in the local environment. Novel ring structure is observed in the silica surface and it is justified to be favored of chemical reaction with water molecule. The siloxane bond formation process quickly strengthened across the interface with the feeding of abrasive particle because of the compressive stress resulted by the impacting behavior.

  7. Coulomb interactions via local dynamics: a molecular-dynamics algorithm

    International Nuclear Information System (INIS)

    Pasichnyk, Igor; Duenweg, Burkhard

    2004-01-01

    We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

  8. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.; Vashishta, P.

    1983-01-01

    Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

  9. Theoretical Concepts in Molecular Photodissociation Dynamics

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1995-01-01

    This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

  10. Following the molecular motion of near-resonant excited CO on Pt(111: A simulated x-ray photoelectron diffraction study based on molecular dynamics calculations

    Directory of Open Access Journals (Sweden)

    Michael Greif

    2015-05-01

    Full Text Available A THz-pump and x-ray-probe experiment is simulated where x-ray photoelectron diffraction (XPD patterns record the coherent vibrational motion of carbon monoxide molecules adsorbed on a Pt(111 surface. Using molecular dynamics simulations, the excitation of frustrated wagging-type motion of the CO molecules by a few-cycle pulse of 2 THz radiation is calculated. From the atomic coordinates, the time-resolved XPD patterns of the C 1s core level photoelectrons are generated. Due to the direct structural information in these data provided by the forward scattering maximum along the carbon-oxygen direction, the sequence of these patterns represents the equivalent of a molecular movie.

  11. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

    Science.gov (United States)

    Grimme, Stefan; Bauer, Christopher Alexander

    2015-01-01

    The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

  12. Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations.

    Science.gov (United States)

    Kumar, Sonu; Frank, Martin; Schwartz-Albiez, Reinhard

    2013-01-01

    Human Galectin-8 (Gal-8) is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD) joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD) simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose) and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB) as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose) are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76). Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.

  13. Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Sonu Kumar

    Full Text Available Human Galectin-8 (Gal-8 is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76. Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.

  14. Nanoplatform-based molecular imaging

    National Research Council Canada - National Science Library

    Chen, Xiaoyuan

    2011-01-01

    "Nanoplathform-Based Molecular Imaging provides rationale for using nanoparticle-based probes for molecular imaging, then discusses general strategies for this underutilized, yet promising, technology...

  15. An integrated approach of network-based systems biology, molecular docking, and molecular dynamics approach to unravel the role of existing antiviral molecules against AIDS-associated cancer.

    Science.gov (United States)

    Omer, Ankur; Singh, Poonam

    2017-05-01

    A serious challenge in cancer treatment is to reposition the activity of various already known drug candidates against cancer. There is a need to rewrite and systematically analyze the detailed mechanistic aspect of cellular networks to gain insight into the novel role played by various molecules. Most Human Immunodeficiency Virus infection-associated cancers are caused by oncogenic viruses like Human Papilloma Viruses and Epstein-Bar Virus. As the onset of AIDS-associated cancers marks the severity of AIDS, there might be possible interconnections between the targets and mechanism of both the diseases. We have explored the possibility of certain antiviral compounds to act against major AIDS-associated cancers: Kaposi's Sarcoma, Non-Hodgkin Lymphoma, and Cervical Cancer with the help of systems pharmacology approach that includes screening for targets and molecules through the construction of a series of drug-target and drug-target-diseases network. Two molecules (Calanolide A and Chaetochromin B) and the target "HRAS" were finally screened with the help of molecular docking and molecular dynamics simulation. The results provide novel antiviral molecules against HRAS target to treat AIDS defining cancers and an insight for understanding the pharmacological, therapeutic aspects of similar unexplored molecules against various cancers.

  16. Artificial surface-mounted molecular rotors: Molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Vacek, Jaroslav; Michl, Josef

    2007-01-01

    Roč. 17, č. 5 (2007), s. 730-739 ISSN 1616-301X R&D Projects: GA AV ČR IAA400550616; GA MŠk ME 857 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular dynamics * molecular machines * nanomaterials Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.496, year: 2007

  17. 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...

  18. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    Science.gov (United States)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  19. Exploring a model of human chemokine receptor CCR2 in presence of TAK779: A membrane based molecular dynamics study

    Science.gov (United States)

    Balupuri, Anand; Sobhia, M. Elizabeth

    2014-04-01

    Chemokine receptor 2 (CCR2) is a G-protein coupled receptor (GPCR) and a crucial target for various inflammation-driven diseases. In the present study, molecular docking and molecular dynamics simulations were performed on a CCR2 homology model. This work includes the comparative MD simulations of uncomplexed and ‘antagonist-complexed’ CCR2 models. These simulations yield insights into the binding mechanism of antagonist TAK779 and improve the understanding of various structural changes induced by the ligand in the CCR2 protein. Here, one 20 ns MD simulation was carried out on the uncomplexed CCR2 model in lipid bilayer to explore the effects of lipid membrane on the protein. Another 20 ns MD simulation was performed under the similar conditions on the docked CCR2-TAK779 complex. An alteration in the position and orientation of the ligand in binding site was observed after the simulation. Examination of protein-ligand complex suggested that TAK779 produced a greater structural change on the TM-III, TM-IV, TM-V and TM-VI than TM-I, TM-II and TM-VII. Interaction networks involving the conserved residues of uncomplexed and ‘antagonist-complexed’ CCR2 models were also examined. The major difference was observed to be the role of conserved residues of the DRY motif of TM-III and the NPxxY motif of TM-VII of CCR2.

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

    Science.gov (United States)

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

    2011-06-14

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

  1. Insight into interaction mechanism of the inhibitor pDI5W with MDM2 based on molecular dynamics

    International Nuclear Information System (INIS)

    Chen Jianzhong; Liang Zhiqiang; Wang Wei; Liu Jinqing; Zhang Qinggang; Liu Xiaoyang

    2012-01-01

    The p53-MDM2 interaction has been an important target of drug design curing cancers. In this work, molecular dynamics (MD) simulation coupled with molecular mechanics/Poisson Boltzmann surface area method (MM-PBSA) was performed to calculate the binding free energy of peptide inhibitor pDI6W to MDM2. The results show that van der Waals energy is the dominant factor of the pDI6W— MDM2 interaction. Cross-correlation matrix calculated suggests that the main motion of the residues in MMDM2 induced by the inhibitor binding is anti-correlation motion. The calculations of residue-residue interactions between pDI6W and MDM2 not only prove that five residues Phe19', Trp22', Trp23', Leu26' and Thr27' from pDI6W can produce strong interaction with MDM2, but also show that CH-π, CH-CH and π-π interactions drive the binding of pDI6W in the hydrophobic cleft of MDM2. This study can provide theoretical helps for anti-cancer drug designs. (authors)

  2. Understanding the interface between silicon-based materials and water: Molecular-dynamics exploration of infrared spectra

    Directory of Open Access Journals (Sweden)

    José A. Martinez-Gonzalez

    2017-11-01

    Full Text Available Molecular-dynamics simulations for silicon, hydrogen- and hydroxyl-terminated silicon in contact with liquid water, at 220 and 300 K, display water-density ‘ordering’ along the laboratory z-axis, emphasising the hydrophobicity of the different systems and the position of this first adsorbed layer. Density of states (DOS of the oxygen and proton velocity correlation functions (VACFs and infrared (IR spectra of the first monolayer of adsorbed water, calculated via Fourier transformation, indicate similarities to more confined, ice-like dynamical behaviour (redolent of ice. It was observed that good qualitative agreement is obtained between the DOS for this first layer in all systems. The DOS for the lower-frequency zone indicates that for the interface studied (i.e., the first layer near the surface, the water molecules try to organise in a similar form, and that this form is intermediate between liquid water and ice. For IR spectra, scrutiny of the position of the highest-intensity peaks for the stretching and bending bands indicate that such water molecules in the first solvating layer are organised in an intermediate fashion between ice and liquid water.

  3. Comparison of modeling a conical nanotube resting on the Winkler elastic foundation based on the modified couple stress theory and molecular dynamics simulation

    Science.gov (United States)

    Mohammadi, Kianoosh; Mahinzare, Mohammad; Rajabpour, Ali; Ghadiri, Majid

    2017-03-01

    In this article, the free vibration analysis of a thin conical nanotube resting on an elastic foundation is investigated for the first time by means of the modified couple stress theory (MCST) and molecular dynamics (MD) simulation. The proposed model in the MCST framework, its equations of motion and boundary conditions are derived by Hamilton's principle based on the thin shell model of Love. The differential quadrature method (DQM) is applied to discretize the equations of motion. Molecular dynamics (MD) simulation is performed via the AIREBO potential function, which is recommended in vibrational studies. The accuracy of the presented model is verified for previous studies with both methods. The novelty of the current study is reporting a specified length scale parameter of MCST which has a good conformity with MD results. This value is exclusively related to the proposed model of the present study. The effect of the elastic foundation stiffness is investigated with molecular dynamics for the first time as well. The results can have many applications, such as in modeling of scanning probe microscopy and biomedical microsystems.

  4. Novel serine-based gemini surfactants as chemical permeation enhancers of local anesthetics: A comprehensive study on structure-activity relationships, molecular dynamics and dermal delivery.

    Science.gov (United States)

    Teixeira, Raquel S; Cova, Tânia F G G; Silva, Sérgio M C; Oliveira, Rita; do Vale, M Luísa C; Marques, Eduardo F; Pais, Alberto A C C; Veiga, Francisco J B

    2015-06-01

    This work aims at studying the efficacy of a series of novel biocompatible, serine-based surfactants as chemical permeation enhancers for two different local anesthetics, tetracaine and ropivacaine, combining an experimental and computational approach. The surfactants consist of gemini molecules structurally related, but with variations in headgroup charge (nonionic vs. cationic) and in the hydrocarbon chain lengths (main and spacer chains). In vitro permeation and molecular dynamics studies combined with cytotoxicity profiles were performed to investigate the permeation of both drugs, probe skin integrity, and rationalize the interactions at molecular level. Results show that these enhancers do not have significant deleterious effects on the skin structure and do not cause relevant changes on cell viability. Permeation across the skin is clearly improved using some of the selected serine-based gemini surfactants, namely the cationic ones with long alkyl chains and shorter spacer. This is noteworthy in the case of ropivacaine hydrochloride, which is not easily administered through the stratum corneum. Molecular dynamics results provide a mechanistic view of the surfactant action on lipid membranes that essentially corroborate the experimental observations. Overall, this study suggests the viability of these serine-based surfactants as suitable and promising delivery agents in pharmaceutical formulations. Copyright © 2015. Published by Elsevier B.V.

  5. 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.

  6. Development of novel HER2 inhibitors against gastric cancer derived from flavonoid source of Syzygium alternifolium through molecular dynamics and pharmacophore-based screening

    Directory of Open Access Journals (Sweden)

    Babu TMC

    2016-11-01

    Full Text Available Tirumalasetty Muni Chandra Babu,1 Aluru Rammohan,2 Vijaya Bhaskar Baki,1 Savita Devi,3 Duvvuru Gunasekar,2 Wudayagiri Rajendra1 1Bioinformatics Center, Division of Molecular Biology, Department of Zoology, 2Natural Products Division, Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, 3Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India Abstract: Continuous usage of synthetic chemotherapeutic drugs causes adverse effects, which prompted for the development of alternative therapeutics for gastric cancer from natural source. This study was carried out with a specific aim to screen gastroprotective compounds from the fruits of Syzygium alternifolium (Myrtaceae. Three flavonoids, namely, 1 5-hydroxy-7,4'-dimethoxy-6,8-di-C-methylflavone, 2 kaempferol-3-O-β-D-glucopyranoside, and 3 kaempferol-3-O-α-L-rhamnopyranoside were isolated from the above medicinal plant by employing silica gel column chromatography and are characterized by NMR techniques. Antigastric cancer activity of these flavonoids was examined on AGS cell lines followed by cell cycle progression assay. In addition, pharmacophore-based screening and molecular dynamics of protein–ligand complex were carried out to identify potent scaffolds. The results showed that compounds 2 and 3 exhibited significant cytotoxic effect, whereas compound 1 showed moderate effect on AGS cells by inhibiting G2/M phase of cell cycle. Molecular docking analysis revealed that compound 2 has higher binding energies on human growth factor receptor-2 (HER2. The constructed pharmacophore models reveal that the compounds have more number of H-bond Acc/Don features which contribute to the inhibition of HER2 activity. By selecting these features, 34 hits were retrieved using the query compound 2. Molecular dynamic simulations (MDS of protein–ligand complexes demonstrated conspicuous

  7. Quantum master equation method based on the broken-symmetry time-dependent density functional theory: application to dynamic polarizability of open-shell molecular systems.

    Science.gov (United States)

    Kishi, Ryohei; Nakano, Masayoshi

    2011-04-21

    A novel method for the calculation of the dynamic polarizability (α) of open-shell molecular systems is developed based on the quantum master equation combined with the broken-symmetry (BS) time-dependent density functional theory within the Tamm-Dancoff approximation, referred to as the BS-DFTQME method. We investigate the dynamic α density distribution obtained from BS-DFTQME calculations in order to analyze the spatial contributions of electrons to the field-induced polarization and clarify the contributions of the frontier orbital pair to α and its density. To demonstrate the performance of this method, we examine the real part of dynamic α of singlet 1,3-dipole systems having a variety of diradical characters (y). The frequency dispersion of α, in particular in the resonant region, is shown to strongly depend on the exchange-correlation functional as well as on the diradical character. Under sufficiently off-resonant condition, the dynamic α is found to decrease with increasing y and/or the fraction of Hartree-Fock exchange in the exchange-correlation functional, which enhances the spin polarization, due to the decrease in the delocalization effects of π-diradical electrons in the frontier orbital pair. The BS-DFTQME method with the BHandHLYP exchange-correlation functional also turns out to semiquantitatively reproduce the α spectra calculated by a strongly correlated ab initio molecular orbital method, i.e., the spin-unrestricted coupled-cluster singles and doubles.

  8. Dynamic control of function by light-driven molecular motors

    NARCIS (Netherlands)

    van Leeuwen, Thomas; Lubbe, Anouk S.; Stacko, Peter; Wezenberg, Sander J.; Feringa, Ben L.

    2017-01-01

    The field of dynamic functional molecular systems has progressed enormously over the past few decades. By coupling the mechanical properties of molecular switches and motors to chemical and biological processes, exceptional control of function has been attained. Overcrowded alkene-based light-driven

  9. 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

  10. Molecular docking and molecular dynamics simulation study of inositol phosphorylceramide synthase – inhibitor complex in leishmaniasis: Insight into the structure based drug design [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Vineetha Mandlik

    2016-09-01

    Full Text Available Inositol phosphorylceramide synthase (IPCS has emerged as an important, interesting and attractive target in the sphingolipid metabolism of Leishmania. IPCS catalyzes the conversion of ceramide to IPC which forms the most predominant sphingolipid in Leishmania. IPCS has no mammalian equivalent and also plays an important role in maintaining the infectivity and viability of the parasite. The present study explores the possibility of targeting IPCS; development of suitable inhibitors for the same would serve as a treatment strategy for the infectious disease leishmaniasis. Five coumarin derivatives were developed as inhibitors of IPCS protein. Molecular dynamics simulations of the complexes of IPCS with these inhibitors were performed which provided insights into the binding modes of the inhibitors. In vitro screening of the top three compounds has resulted in the identification of one of the compounds (compound 3 which shows little cytotoxic effects. This compound therefore represents a good starting point for further in vivo experimentation and could possibly serve as an important drug candidate for the treatment of leishmaniasis.

  11. Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

    Science.gov (United States)

    Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

    2018-05-01

    One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

  12. Molecular dynamics of a proguanil derivative

    African Journals Online (AJOL)

    pc

    ABSTRACT. Proguanil is a prophylactic antimalarial drug t stopping the malaria parasites from reprod molecular dynamics of a derivative of Progua benzene ring of the molecule of Proguanil derivative. The molecular geometries of chemical calculations at the Restricted Hatre. 31G(d,p) and 6-31++G. Also, Density Func.

  13. Molecular ions, Rydberg spectroscopy and dynamics

    International Nuclear Information System (INIS)

    Jungen, Ch.

    2015-01-01

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

  14. Molecular ions, Rydberg spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  15. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

    Czech Academy of Sciences Publication Activity Database

    Lavery, R.; Zakrzewska, K.; Beveridge, D.; Bishop, T. C.; Case, D. A.; Cheatham III, T. E.; Dixit, S.; Jayaram, B.; Lankaš, Filip; Laughton, Ch.; Maddocks, J. H.; Michon, A.; Osman, R.; Orozco, M.; Pérez, A.; Singh, T.; Špačková, Naďa; Šponer, Jiří

    2010-01-01

    Roč. 38, č. 1 (2010), s. 299-313 ISSN 0305-1048 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA ČR GA203/09/1476; GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : B-DNA * molecular dynamics * sequence dependet structure and dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.836, year: 2010

  16. On the parallelization of molecular dynamics codes

    Science.gov (United States)

    Trabado, G. P.; Plata, O.; Zapata, E. L.

    2002-08-01

    Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code with message passing routines or using specific libraries intended for writing new MD programs. In this paper we propose a new library-based approach (DDLY) which supports parallelization of existing short-range MD sequential codes. The novelty of this approach is that it can directly handle the distribution of common data structures used in MD codes to represent data (arrays, Verlet lists, link cells), using domain decomposition. Thus, the insertion of run-time support for distribution and communication in a MD program does not imply significant changes to its structure. The method is simple, efficient and portable. It may be also used to extend existing parallel programming languages, such as HPF.

  17. Detecting Molecular Rotational Dynamics Complementing the Low-Frequency Terahertz Vibrations in a Zirconium-Based Metal-Organic Framework

    Science.gov (United States)

    Ryder, Matthew R.; Van de Voorde, Ben; Civalleri, Bartolomeo; Bennett, Thomas D.; Mukhopadhyay, Sanghamitra; Cinque, Gianfelice; Fernandez-Alonso, Felix; De Vos, Dirk; Rudić, Svemir; Tan, Jin-Chong

    2017-06-01

    We show clear experimental evidence of cooperative terahertz (THz) dynamics observed below 3 THz (˜100 cm-1 ), for a low-symmetry Zr-based metal-organic framework structure, termed MIL-140A [ZrO (O2C-C 6H4-CO2) ]. Utilizing a combination of high-resolution inelastic neutron scattering and synchrotron radiation far-infrared spectroscopy, we measured low-energy vibrations originating from the hindered rotations of organic linkers, whose energy barriers and detailed dynamics have been elucidated via ab initio density functional theory calculations. The complex pore architecture caused by the THz rotations has been characterized. We discovered an array of soft modes with trampolinelike motions, which could potentially be the source of anomalous mechanical phenomena such as negative thermal expansion. Our results demonstrate coordinated shear dynamics (2.47 THz), a mechanism which we have shown to destabilize the framework structure, in the exact crystallographic direction of the minimum shear modulus (Gmin ).

  18. Temperature effects on the capacitance of an imidazolium-based ionic liquid on a graphite electrode: a molecular dynamics simulation.

    Science.gov (United States)

    Liu, Xiaohong; Han, Yining; Yan, Tianying

    2014-08-25

    Temperature-dependent electric double layer (EDL) and differential capacitance-potential (C(d)-U) curves of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate (BMIM(+)/PF6(-)) were studied on a graphite electrode by molecular dynamics simulations. It was found that all C(d)-U curves were asymmetric camel-shaped with higher C(d) at negative polarization, attributed to the specific adsorption of BMIM(+). In addition, the maxima of Cd at the negative polarization decrease monotonically with temperature due to the thicker EDL, whereas at the positive polarization they gradually increase from 450 to 550 K and decrease at 600 K. Such temperature effects at positive polarization may be understood in terms of the competition between two aspects: the weakening specific adsorption of BMIM(+) allows more effective screening to the positive charge and overall increasing EDL thickness. Although the former dominates from 450 to 550 K, the latter becomes dominant at 600 K. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

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

    2015-09-15

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

  20. Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations.

    Science.gov (United States)

    Sun, Dong-Ru; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2017-03-01

    Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation and binding free energy studies were performed to investigate the biochemistry behaviors of two class inhibitors binding to matriptase. The binding free energies predicted by MM/GBSA methods are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. The key residues responsible for achieving strong binding have been identified by the MM/GBSA free energy decomposition analysis. Especially, Trp215 and Phe99 had an important impact on active site architecture and ligand binding. The results clearly identify the two class inhibitors exist different binding modes. Through summarizing the two different modes, we have mastered some important and favorable interaction patterns between matriptase and inhibitors. Our findings would be helpful for understanding the interaction mechanism between the inhibitor and matriptase and afford important guidance for the rational design of potent matriptase inhibitors.

  1. Mechanistic model of sodium/proton antiport based on X-ray crystal structures and molecular dynamics simulations

    Science.gov (United States)

    Beckstein, Oliver; Dotson, David L.; Lee, Chiara; Yashiro, Shoko; Uzdavinys, Povilas; von Ballmoos, Christoph; Drew, David; Cameron, Alexander D.

    2015-03-01

    Na+/H+ antiporters are membrane proteins that are vital for cell homeostasis but the mechanistic details of their transport mechanism remain unclear, in particular, how Na+ and protons bind to the transporter. We recently solved X-ray crystal structures for two such antiporters (NhaA and NapA) in two different conformations of the transport cycle. All-atom molecular dynamics (MD) simulations (for a total simulated time > 10 μ s), indicate that sodium binding is dependent on the charge states of two conserved aspartate residues. A conserved lysine forms a previously unidentified salt bridge with one of the asparates. Under simulated physiological pH the presence of a Na+ ion disrupts and breaks the salt bridge in NhaA. To quantify proton binding, we then performed heuristic pKa calculations on our ensemble of simulations. The calculations support our novel hypothesis that the conserved lysine in these antiporter binds protons in a sodium-dependent manner and thus acts as part of the transport machinery. In conjunction with simulations of the conformational transition we propose a new mechanistic model of ion binding for the CPA2 class of antiporters within the larger framework of the alternating access mechanism of transmembrane transport.

  2. Thermal transport of III-V semiconductor materials and superlattices based on molecular dynamics with optimized Tersoff potentials

    Science.gov (United States)

    Mei, Song; Knezevic, Irena

    III-V compound semiconductor materials are widely used in optoelectronics devices. III-V superlattices (SLs) make the active core of quantum cascade lasers (QCLs). Achieving room-temperature (RT), high-power, and continuous-wave (CW) operation in QCLs hinges on the understanding and engineering of thermal transport in the layers and across the interfaces. Cations in III-V ternary alloys differ a lot in mass and this effect on thermal transport is hard to capture using the scattering rates deduced from common perturbation theories. Molecular dynamics (MD) simulations can explicitly take the mass difference into consideration and are suitable for calculating the bulk thermal conductivity of III-V ternary alloys. Furthermore, the morphology and anharmonic interactions at an interface are naturally captured in MD, leading to an accurate description of interfacial transport. We adopt the Tersoff-type potentials for III-V binaries and optimize them according to acoustic phonon dispersions in order to capture thermal properties. The optimized potential is then used to directly compute the thermal boundary resistance at a heterojunction interface, as well as the thermal conductivity in the SL as a whole. US Department of Energy Award No. DE-SC0008712.

  3. 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

  4. Carbonic anhydrase inhibition of Schiff base derivative of imino-methyl-naphthalen-2-ol: Synthesis, structure elucidation, molecular docking, dynamic simulation and density functional theory calculations

    Science.gov (United States)

    Abbas, Saghir; Nasir, Hafiza Huma; Zaib, Sumera; Ali, Saqib; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz; Iqbal, Jamshed

    2018-03-01

    In the present study, we have designed and synthesized a Schiff base derivative 3 and characterized by FT-IR, 1H and 13C NMR spectroscopy. Single crystal X-ray diffraction and NMR studies were also performed. The synthetic compound was screened for its inhibitory potential against carbonic anhydrase II. The experimental results were validated by molecular docking and dynamic simulations of compound 3 in the active pocket of enzyme. Important binding interactions with the key residues in the active site of the carbonic anhydrase enzyme were revealed. Moreover, supramolecular assembly of the title compound was analyzed by density functional theory (DFT) calculations. These studies rendered a more clear understanding for the demonstration of novel molecular mechanism involved in CA II inhibition by the synthesized compound.

  5. Molecular Dynamics of Hexamethylbenzene at Low Temperatures: Evidence of Unconventional Magnetism Based on Rotational Motion of Protons.

    Science.gov (United States)

    Yen, Fei; Zhao, Zhenzheng; Hu, Sixia; Chen, Lang

    2017-10-23

    The types of magnetism known to date are all mainly based on contributions from electron motion. We show how rotational motion of protons (H + ) within the methyl groups in hexamethylbenzene (C 6 (CH 3 ) 6 ) also contribute significantly to the magnetic susceptibility. Starting from below 118 K, as the rotational motion of the methyl groups set in, an associated magnetic moment positive in nature due to charge of the protons renders the susceptibility to become anomalously dependent on temperature. Starting from 20 K, the susceptibility diverges with decreasing temperature indicative of spin-spin interactions between methyl groups aligned in a previously unclassified type of anti-ferromagnetic configuration. Complementary dielectric constant measurements also show the existence of magneto-dielectric coupling. Our findings allow for the study of strongly correlated systems that are based on a species that possesses much slower dynamics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Modulation of a Molecular π-Electron System in a Purely Organic Conductor that Shows Hydrogen-Bond-Dynamics-Based Switching of Conductivity and Magnetism.

    Science.gov (United States)

    Ueda, Akira; Hatakeyama, Akari; Enomoto, Masaya; Kumai, Reiji; Murakami, Youichi; Mori, Hatsumi

    2015-10-12

    New important aspects of the hydrogen-bond (H-bond)-dynamics-based switching of electrical conductivity and magnetism in an H-bonded, purely organic conductor crystal have been discovered by modulating its tetrathiafulvalene (TTF)-based molecular π-electron system by means of partial sulfur/selenium substitution. The prepared selenium analogue also showed a similar type of phase transition, induced by H-bonded deuterium transfer followed by electron transfer between the H-bonded TTF skeletons, and the resulting switching of the physical properties; however, subtle but critical differences due to sulfur/selenium substitution were detected in the electronic structure, phase transition nature, and switching function. A molecular-level discussion based on the crystal structures shows that this chemical modification of the TTF skeleton influences not only its own π-electronic structure and π-π interactions within the conducting layer, but also the H-bond dynamics between the TTF π skeletons in the neighboring layers, which enables modulation of the interplay between the H-bond and π electrons to cause such differences. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... 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...

  8. 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...

  9. 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

  10. First-principles molecular dynamics for metals

    International Nuclear Information System (INIS)

    Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

    1989-01-01

    A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

  11. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. I. Homogeneous fluids

    Science.gov (United States)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2013-12-01

    In this work, we aim to develop a version of the Statistical Associating Fluid Theory (SAFT)-γ equation of state (EOS) that is compatible with united-atom force fields, rather than experimental data. We rely on the accuracy of the force fields to provide the relation to experimental data. Although, our objective is a transferable theory of interfacial properties for soft and fused heteronuclear chains, we first clarify the details of the SAFT-γ approach in terms of site-based simulations for homogeneous fluids. We show that a direct comparison of Helmholtz free energy to molecular simulation, in the framework of a third order Weeks-Chandler-Andersen perturbation theory, leads to an EOS that takes force field parameters as input and reproduces simulation results for Vapor-Liquid Equilibria (VLE) calculations. For example, saturated liquid density and vapor pressure of n-alkanes ranging from methane to dodecane deviate from those of the Transferable Potential for Phase Equilibria (TraPPE) force field by about 0.8% and 4%, respectively. Similar agreement between simulation and theory is obtained for critical properties and second virial coefficient. The EOS also reproduces simulation data of mixtures with about 5% deviation in bubble point pressure. Extension to inhomogeneous systems and united-atom site types beyond those used in description of n-alkanes will be addressed in succeeding papers.

  12. Control of Mechanotransduction by Molecular Clutch Dynamics.

    Science.gov (United States)

    Elosegui-Artola, Alberto; Trepat, Xavier; Roca-Cusachs, Pere

    2018-02-26

    The linkage of cells to their microenvironment is mediated by a series of bonds that dynamically engage and disengage, in what has been conceptualized as the molecular clutch model. Whereas this model has long been employed to describe actin cytoskeleton and cell migration dynamics, it has recently been proposed to also explain mechanotransduction (i.e., the process by which cells convert mechanical signals from their environment into biochemical signals). Here we review the current understanding on how cell dynamics and mechanotransduction are driven by molecular clutch dynamics and its master regulator, the force loading rate. Throughout this Review, we place a specific emphasis on the quantitative prediction of cell response enabled by combined experimental and theoretical approaches. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. First report on 3D-QSAR and molecular dynamics based docking studies of GCPII inhibitors for targeted drug delivery applications

    Science.gov (United States)

    Pandit, Amit; Sengupta, Sagnik; Krishnan, Mena Asha; Reddy, Ramesh B.; Sharma, Rajesh; Venkatesh, Chelvam

    2018-05-01

    Prostate Specific Membrane Antigen (PSMA) or Glutamate carboxypeptidase II (GCPII) has been identified as an important target in diagnosis and therapy of prostate cancer. Among several types of inhibitors, urea based inhibitors are the most common and widely employed in preclinical and clinical studies. Computational studies have been carried out to uncover active sites and interaction of PSMA inhibitors with the protein by modifying the core structure of the ligand. Analysis of the literature, however, show lack of 3-D quantitative structure activity relationship (QSAR) and molecular dynamics based molecular docking study to identify structural modifications responsible for better GCPII inhibitory activity. The present study aims to fulfil this gap by analysing well known PSMA inhibitors reported in the literature with known experimental PSMA inhibition constants. Also in order to validate the in silico study, a new GCPII inhibitor 7 was designed, synthesized and experimental PSMA enzyme inhibition was evaluated by using freshly isolated PSMA protein from human cancer cell line derived from lymph node, LNCaP. 3D-QSAR CoMFA models on 58 urea based GCPII inhibitors were generated, and the best correlation was obtained in Gast-Huck charge assigning method with q2, r2 and predictive r2 values as 0.592, 0.995 and 0.842 respectively. Moreover, steric, electrostatic, and hydrogen bond donor field contribution analysis provided best statistical values from CoMSIA model (q2, r2 and predictive r2 as 0.527, 0.981 and 0.713 respectively). Contour maps study revealed that electrostatic field contribution is the major factor for discovering better binding affinity ligands. Further molecular dynamic assisted molecular docking was also performed on GCPII receptor (PDB ID 4NGM) and most active GCPII inhibitor, DCIBzL. 4NGM co-crystallised ligand, JB7 was used to validate the docking procedure and the amino acid interactions present in JB7 are compared with DCIBzL. The results

  14. Ultrafast molecular dynamics illuminated with synchrotron radiation

    International Nuclear Information System (INIS)

    Bozek, John D.; Miron, Catalin

    2015-01-01

    Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

  15. 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.

  16. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

    International Nuclear Information System (INIS)

    Genova, Alessandro; Pavanello, Michele; Ceresoli, Davide

    2016-01-01

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH • radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH • radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

  17. Quantum spin dynamics in molecular magnets

    International Nuclear Information System (INIS)

    Leuenberger, M.N.; Meier, F.; Loss, D.

    2003-01-01

    The detailed theoretical understanding of quantum spin dynamics in various molecular magnets is an important step on the roadway to technological applications of these systems. Quantum effects in both ferromagnetic and antiferromagnetic molecular clusters are, by now, theoretically well understood. Ferromagnetic molecular clusters allow one to study the interplay of incoherent quantum tunneling and thermally activated transitions between states with different spin orientation. The Berry phase oscillations found in Fe 8 are signatures of the quantum mechanical interference of different tunneling paths. Antiferromagnetic molecular clusters are promising candidates for the observation of coherent quantum tunneling on the mesoscopic scale. Although challenging, application of molecular magnetic clusters for data storage and quantum data processing are within experimental reach already with present day technology. Refs. 77 (author)

  18. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... 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...... transport, move on crowded tracks where they can encounter other motors, a phenomenon referred to as molecular motor traffic. In the second part, traffic models of kinesin motors under an external mechanical load are considered, and the efficiency at maximum power (EMP) is calculated as a convenient measure...

  19. Folding very short peptides using molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Bosco K Ho

    2006-04-01

    Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

  20. 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 ...

  1. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  2. An ab initio molecular dynamics study

    Indian Academy of Sciences (India)

    Abstract. The hydration structure and translocation of an excess proton in hydrogen bonded water clusters of two different sizes are investigated by means of finite tempera- ture quantum simulations. The simulations are performed by employing the method of. Car–Parrinello molecular dynamics where the forces on the ...

  3. Molecular dynamics simulations of RNA motifs

    Czech Academy of Sciences Publication Activity Database

    Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

    2002-01-01

    Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

  4. 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.)

  5. Molecular dynamics simulation on the interaction mechanism ...

    Indian Academy of Sciences (India)

    Investigation on the microscopic interaction between polymer inhibitors and calcium phosphate contributes to the understanding of their scale inhibition mechanism. The results obtained may provide a theoretical guidance to developing new scale inhibitors. In this study, molecular dynamics simulations have been ...

  6. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  7. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

    Akahoshi, Y.; Schmauder, S.; Ludwig, M.

    1998-01-01

    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.)

  8. 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.

  9. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water.

    Science.gov (United States)

    Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu

    2014-08-28

    In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfer process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps(-1), which is about 2.5 times faster than that in vacuum, 0.27 ps(-1). This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.

  10. First principles molecular dynamics without self-consistent field optimization

    International Nuclear Information System (INIS)

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-01

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

  11. Molecular dynamics simulations of weak detonations.

    Science.gov (United States)

    Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie

    2011-12-01

    Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal.

  12. Bifunctional Molecular Photoswitches Based on Overcrowded Alkenes for Dynamic Control of Catalytic Activity in Michael Addition Reactions

    NARCIS (Netherlands)

    Pizzolato, Stefano F.; Collins, Beatrice S. L.; van Leeuwen, Thomas; Feringa, Ben L.

    2017-01-01

    The emerging field of artificial photoswitchable catalysis has recently shown striking examples of functional light-responsive systems allowing for dynamic control of activity and selectivity in organocatalysis and metal-catalysed transformations. While our group has already disclosed systems

  13. Identification of Potent Chloride Intracellular Channel Protein 1 Inhibitors from Traditional Chinese Medicine through Structure-Based Virtual Screening and Molecular Dynamics Analysis

    Directory of Open Access Journals (Sweden)

    Wei Wang

    2017-01-01

    Full Text Available Chloride intracellular channel 1 (CLIC1 is involved in the development of most aggressive human tumors, including gastric, colon, lung, liver, and glioblastoma cancers. It has become an attractive new therapeutic target for several types of cancer. In this work, we aim to identify natural products as potent CLIC1 inhibitors from Traditional Chinese Medicine (TCM database using structure-based virtual screening and molecular dynamics (MD simulation. First, structure-based docking was employed to screen the refined TCM database and the top 500 TCM compounds were obtained and reranked by X-Score. Then, 30 potent hits were achieved from the top 500 TCM compounds using cluster and ligand-protein interaction analysis. Finally, MD simulation was employed to validate the stability of interactions between each hit and CLIC1 protein from docking simulation, and Molecular Mechanics/Generalized Born Surface Area (MM-GBSA analysis was used to refine the virtual hits. Six TCM compounds with top MM-GBSA scores and ideal-binding models were confirmed as the final hits. Our study provides information about the interaction between TCM compounds and CLIC1 protein, which may be helpful for further experimental investigations. In addition, the top 6 natural products structural scaffolds could serve as building blocks in designing drug-like molecules for CLIC1 inhibition.

  14. Scattering of a proton with the Li{sub 4} cluster: Non-adiabatic molecular dynamics description based on time-dependent density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Castro, A., E-mail: acastro@bifi.es [Institute for Biocomputation and Physics of Complex Systems (BIFI) and Zaragoza Scientific Center for Advanced Modelling (ZCAM), University of Zaragoza, 50018 Zaragoza (Spain); Isla, M. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain); Martinez, Jose I. [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, ES-28049 Madrid (Spain); Alonso, J.A. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain)

    2012-05-03

    Graphical abstract: Two trajectories for the collision of a proton with the Lithium tetramer. On the left, the proton is scattered away, and a Li{sub 2} molecule plus two isolated Lithium atoms result. On the right, the proton is captured and a LiH molecule is created. Highlights: Black-Right-Pointing-Pointer Scattering of a proton with Lithium clusters described from first principles. Black-Right-Pointing-Pointer Description based on non-adiabatic molecular dynamics. Black-Right-Pointing-Pointer The electronic structure is described with time-dependent density-functional theory. Black-Right-Pointing-Pointer The method allows to discern reaction channels depending on initial parameters. - Abstract: We have employed non-adiabatic molecular dynamics based on time-dependent density-functional theory to characterize the scattering behavior of a proton with the Li{sub 4} cluster. This technique assumes a classical approximation for the nuclei, effectively coupled to the quantum electronic system. This time-dependent theoretical framework accounts, by construction, for possible charge transfer and ionization processes, as well as electronic excitations, which may play a role in the non-adiabatic regime. We have varied the incidence angles in order to analyze the possible reaction patterns. The initial proton kinetic energy of 10 eV is sufficiently high to induce non-adiabatic effects. For all the incidence angles considered the proton is scattered away, except in one interesting case in which one of the Lithium atoms captures it, forming a LiH molecule. This theoretical formalism proves to be a powerful, effective and predictive tool for the analysis of non-adiabatic processes at the nanoscale.

  15. Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment based mathematical model

    NARCIS (Netherlands)

    Rybakova, K.N.; Tomaszewska, A.; Mourik, van S.; Blom, Joke; Westerhoff, H.V.; Carlberg, C.; Bruggeman, F.J.

    2015-01-01

    Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in response to external signals or as a result of a

  16. 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, hi...

  17. Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics

    NARCIS (Netherlands)

    Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de

    1997-01-01

    The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.

  18. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  19. Polypeptides Based Molecular Electronics

    National Research Council Canada - National Science Library

    Lam, Yeng M; Mhaisalkar, Subodh; Li, Lain-Jong; Dravid, Vinayak P; Shekhawat, Gajendra S; Suri, Raman

    2008-01-01

    ... the formation of molecular devices such as transistors, diodes, and sensors. We have designed the peptides, arranged them on substrates using self-assembly, Dip-PEN nanolithography, and also e-beam assisted lithography...

  20. Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Yuxin Zhang

    2012-02-01

    Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.

  1. Excited-state molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Pratt, S.T.

    1995-01-01

    This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

  2. Designing topological defects in 2D materials using scanning probe microscopy and a self-healing mechanism: a density functional-based molecular dynamics study

    Science.gov (United States)

    Popov, Igor; Đurišić, Ivana; Belić, Milivoj R.

    2017-12-01

    Engineering of materials at the atomic level is one of the most important aims of nanotechnology. The unprecedented ability of scanning probe microscopy to address individual atoms opened up the possibilities for nanomanipulation and nanolitography of surfaces and later on of two-dimensional materials. While the state-of-the-art scanning probe lithographic methods include, primarily, adsorption, desorption and repositioning of adatoms and molecules on substrates or tailoring nanoribbons by etching of trenches, the precise modification of the intrinsic atomic structure of materials is yet to be advanced. Here we introduce a new concept, scanning probe microscopy with a rotating tip, for engineering of the atomic structure of membranes based on two-dimensional materials. In order to indicate the viability of the concept, we present our theoretical research, which includes atomistic modeling, molecular dynamics simulations, Fourier analysis and electronic transport calculations. While stretching can be employed for fabrication of atomic chains only, our comprehensive molecular dynamics simulations indicate that nanomanipulation by scanning probe microscopy with a rotating tip is capable of assembling a wide range of topological defects in two-dimensional materials in a rather controllable and reproducible manner. We analyze two possibilities. In the first case the probe tip is retracted from the membrane while in the second case the tip is released beneath the membrane allowing graphene to freely relax and self-heal the pore made by the tip. The former approach with the tip rotation can be achieved experimentally by rotation of the sample, which is equivalent to rotation of the tip, whereas irradiation of the membrane by nanoclusters can be utilized for the latter approach. The latter one has the potential to yield a yet richer diversity of topological defects on account of a lesser determinacy. If successfully realized experimentally the concept proposed here could

  3. Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Haiyan Qian

    2016-09-01

    Full Text Available 11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1 is a potential target for the treatment of numerous human disorders, such as diabetes, obesity, and metabolic syndrome. In this work, molecular modeling studies combining molecular docking, 3D-QSAR, MESP, MD simulations and free energy calculations were performed on pyridine amides and 1,2,4-triazolopyridines as 11β-HSD1 inhibitors to explore structure-activity relationships and structural requirement for the inhibitory activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by docking strategy. The derived pharmacophoric features were further supported by MESP and Mulliken charge analyses using density functional theory. In addition, MD simulations and free energy calculations were employed to determine the detailed binding process and to compare the binding modes of inhibitors with different bioactivities. The binding free energies calculated by MM/PBSA showed a good correlation with the experimental biological activities. Free energy analyses and per-residue energy decomposition indicated the van der Waals interaction would be the major driving force for the interactions between an inhibitor and 11β-HSD1. These unified results may provide that hydrogen bond interactions with Ser170 and Tyr183 are favorable for enhancing activity. Thr124, Ser170, Tyr177, Tyr183, Val227, and Val231 are the key amino acid residues in the binding pocket. The obtained results are expected to be valuable for the rational design of novel potent 11β-HSD1 inhibitors.

  4. Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations.

    Science.gov (United States)

    Qian, Haiyan; Chen, Jiongjiong; Pan, Youlu; Chen, Jianzhong

    2016-09-19

    11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) is a potential target for the treatment of numerous human disorders, such as diabetes, obesity, and metabolic syndrome. In this work, molecular modeling studies combining molecular docking, 3D-QSAR, MESP, MD simulations and free energy calculations were performed on pyridine amides and 1,2,4-triazolopyridines as 11β-HSD1 inhibitors to explore structure-activity relationships and structural requirement for the inhibitory activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by docking strategy. The derived pharmacophoric features were further supported by MESP and Mulliken charge analyses using density functional theory. In addition, MD simulations and free energy calculations were employed to determine the detailed binding process and to compare the binding modes of inhibitors with different bioactivities. The binding free energies calculated by MM/PBSA showed a good correlation with the experimental biological activities. Free energy analyses and per-residue energy decomposition indicated the van der Waals interaction would be the major driving force for the interactions between an inhibitor and 11β-HSD1. These unified results may provide that hydrogen bond interactions with Ser170 and Tyr183 are favorable for enhancing activity. Thr124, Ser170, Tyr177, Tyr183, Val227, and Val231 are the key amino acid residues in the binding pocket. The obtained results are expected to be valuable for the rational design of novel potent 11β-HSD1 inhibitors.

  5. Molecular quantum dynamics. From theory to applications

    International Nuclear Information System (INIS)

    Gatti, Fabien

    2014-01-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

  6. Molecular dynamics simulations of nanobubbles and nanodrops

    OpenAIRE

    Maheshwari, Shantanu

    2018-01-01

    Understanding of bubbles and drops at the nanoscale is of primary importance to many technological applications. Although lot of theoretical understanding has been developed in the last few decades for larger size bubbles and drops, fundamental understanding of nanobubbles and nanodrops in some aspects is still inadequate. In this thesis we revealed and explained a few phenomena related to the stability and growth/dissolution of nanobubbles and nanodrops with the help from molecular dynamics ...

  7. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  8. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    from the increased number of intermolecular interactions at the higher mass densities . This may also be why the size of the hot spot increases with...of energy deposition by a shocked diatomic gas into a stationary target is studied as a function of multiple variables including gas density , impact...into the vibrational channels of the gas is a function of the density . 15. SUBJECT TERMS molecular dynamics, energy deposition, rovibrational

  9. Molecular Dynamics with Helical Periodic Boundary Conditions

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Bouř, Petr

    2014-01-01

    Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  10. Multi-scale multi-physics computational chemistry simulation based on ultra-accelerated quantum chemical molecular dynamics method for structural materials in boiling water reactor

    International Nuclear Information System (INIS)

    Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu

    2014-01-01

    In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for

  11. 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...

  12. 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

  13. DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

    Science.gov (United States)

    Humeniuk, Alexander; Mitrić, Roland

    2017-12-01

    A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

  14. 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.

  15. An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

    Science.gov (United States)

    Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

    2009-10-21

    In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

  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: 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.

  18. Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics

    OpenAIRE

    Lin, Lin; Lu, Jianfeng; Shao, Sihong

    2013-01-01

    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 dynamic simulation. We connect and compare TRBOMD with the Car-Parrinello molecular...

  19. 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.

  20. Analysis of the epidemiological dynamics during the 1982-1983 epidemic of foot-and-mouth disease in Denmark based on molecular high-resolution strain identification

    DEFF Research Database (Denmark)

    Christensen, Laurids Siig; Normann, Preben; Thykier-Nielsen, Søren

    2005-01-01

    An epidemic of foot-and-mouth disease (FMD) causing a total of 23 cases in 1982-1983, primarily on the island of Funen, Denmark, was subjected to molecular epidemiological investigations. In an attempt to exploit the quasi-species nature of foot-and-mouth disease virus strains for molecular high......-resolution strain identification in order to analyse the dynamics of this epidemic, full-length VP1 coding regions were sequenced for 17 isolates collected at different farms during the epidemic. The sequence information together with epidemiological information gathered during the epidemic suggests...

  1. 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.

  2. 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.

  3. Molecular dynamics in high electric fields

    International Nuclear Information System (INIS)

    Apostol, M.; Cune, L.C.

    2016-01-01

    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. Classical molecular dynamics simulation of nuclear fuels

    International Nuclear Information System (INIS)

    Devanathan, R.; Krack, M.; Bertolus, M.

    2015-01-01

    Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

  5. Accelerated molecular dynamics simulations of protein folding.

    Science.gov (United States)

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

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

  6. Hydration structure in concentrated aqueous lithium chloride solutions: a reverse Monte Carlo based combination of molecular dynamics simulations and diffraction data.

    Science.gov (United States)

    Harsányi, I; Pusztai, L

    2012-11-28

    We report on a comparison of three interaction potential models of water (SPC/E, TIP4P-2005, and SWM4-DP) for describing the structure of concentrated aqueous lithium chloride solutions. Classical molecular dynamics simulations have been carried out and total scattering structure factors, calculated from the particle configurations, were compared with experimental diffraction data. Later, reverse Monte Carlo structural modelling was applied for refining molecular dynamics results, so that particle configurations consistent with neutron and X-ray diffraction data could be prepared that, at the same time, were as close as possible to the final stage of the molecular dynamics simulations. Partial radial distribution functions, first neighbors, and angular correlations were analysed further from the best fitting particle configurations. It was found that none of the water potential models describe the structure perfectly; overall, the SWM4-DP model seems to be the most promising. At the highest concentrations the SPC/E model appears to provide the best approximation of the water structure, whereas the TIP4P-2005 model proved to be the most successful for estimating the lithium-oxygen partial radial distribution function at each concentration.

  7. Molecular electron recollision dynamics in intense circularly polarized laser pulses

    Science.gov (United States)

    Bandrauk, André D.; Yuan, Kai-Jun

    2018-04-01

    Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.

  8. 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)

  9. Combined NMR and molecular dynamics modeling study of transport properties in sulfonamide based deep eutectic lithium electrolytes: LiTFSI based binary systems.

    Science.gov (United States)

    Pauric, Allen D; Halalay, Ion C; Goward, Gillian R

    2016-03-07

    The trend toward Li-ion batteries operating at increased (>4.3 V vs. Li/Li(+)) voltages requires the development of novel classes of lithium electrolytes with electrochemical stability windows exceeding those of LiPF6/carbonate electrolyte solutions. Several new classes of electrolytes have been synthesized and investigated over the past decade, in the search for LIB electrolytes with improved properties (increased hydrolytic stability, improved thermal abuse tolerance, higher oxidation voltages, etc.) compared with the present state-of-the-art LiPF6 and organic carbonates-based formulations. Among these are deep eutectic electrolytes (DEEs), which share many beneficial characteristics with ionic liquids, such as low vapor pressure and large electrochemical stability windows, with the added advantage of a significantly higher lithium transference number. The present work presents the pulsed field gradient NMR characterization of the transport properties (diffusion coefficients and cation transport numbers) of binary DEEs consisting of a sulfonamide solvent and lithium bis(trifluoromethanesulfonyl)imide salt. Insights into the structural and dynamical properties, which enable one to rationalize the observed ionic conductivity behavior were obtained from a combination of NMR data and MD simulations. The insights thus gained should assist the formulation of novel DEEs with improved properties for LIB applications.

  10. 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..

  11. Molecular dynamics simulation of laser shock phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).

    2001-10-01

    Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)

  12. Molecular Dynamics Simulations for Predicting Surface Wetting

    Directory of Open Access Journals (Sweden)

    Jing Chen

    2014-06-01

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

  13. Nonequilibrium molecular dynamics: The first 25 years

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-08-01

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

  14. Molecular dynamics of ultradian glucocorticoid receptor action.

    Science.gov (United States)

    Conway-Campbell, Becky L; Pooley, John R; Hager, Gordon L; Lightman, Stafford L

    2012-01-30

    In recent years it has become evident that glucocorticoid receptor (GR) action in the nucleus is highly dynamic, characterized by a rapid exchange at the chromatin template. This stochastic mode of GR action couples perfectly with a deterministic pulsatile availability of endogenous ligand in vivo. The endogenous glucocorticoid hormone (cortisol in man and corticosterone in rodent) is secreted from the adrenal gland with an ultradian rhythm made up of pulses at approximately hourly intervals. These two components - the rapidly fluctuating ligand and the rapidly exchanging receptor - appear to have evolved to establish and maintain a system that is exquisitely responsive to the physiological demands of the organism. In this review, we discuss recent and innovative work that questions the idea of steady state, static hormone receptor responses, and replaces them with new concepts of stochastic mechanisms and oscillatory activity essential for optimal function in molecular and cellular systems. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  15. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

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

  16. Fiber lubrication: A molecular dynamics simulation study

    Science.gov (United States)

    Liu, Hongyi

    Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence

  17. Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay.

    Science.gov (United States)

    Uba, Abdullahi Ibrahim; Yelekçi, Kemal

    2017-10-23

    Histone deacetylases (HDACs) have gained increased attention as targets for anticancer drug design and development. HDAC inhibitors have proven to be effective for reversing the malignant phenotype in HDAC-dependent cancer cases. However, lack of selectivity of the many HDAC inhibitors in clinical use and trials contributes to toxicities to healthy cells. It is believed that, the continued identification of isoform-selective inhibitors will eliminate these undesirable adverse effects - a task that remains a major challenge to HDAC inhibitor designs. Here, in an attempt to identify isoform-selective inhibitors, a large compound library containing 2,703,000 compounds retrieved from Otava database was screened against class I HDACs by exhaustive approach of structure-based virtual screening using rDOCK and Autodock Vina. A total of 41 compounds were found to show high-isoform selectivity and were further redocked into their respective targets using Autodock4. Thirty-six compounds showed remarkable isoform selectivity and passed drug-likeness and absorption, distribution, metabolism, elimination and toxicity prediction tests using ADMET Predictor™ and admetSAR. Furthermore, to study the stability of ligand binding modes, 10 ns-molecular dynamics (MD) simulations of the free HDAC isoforms and their complexes with respective best-ranked ligands were performed using nanoscale MD software. The inhibitors remained bound to their respective targets over time of the simulation and the overall potential energy, root-mean-square deviation, root-mean-square fluctuation profiles suggested that the detected compounds may be potential isoform-selective HDAC inhibitors or serve as promising scaffolds for further optimization towards the design of selective inhibitors for cancer therapy.

  18. Study of the Thermal Decomposition of PFPEs Lubricants on a Thin DLC Film Using Finitely Extensible Nonlinear Elastic Potential Based Molecular Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    S. K. Deb Nath

    2014-01-01

    Full Text Available Perfluoropolyethers (PFPEs are widely used as hard disk lubricants for protecting carbon overcoat reducing friction between the hard disk interface and the head during the movement of head during reading and writing data in the hard disk. Due to temperature rise of PFPE Zdol lubricant molecules on a DLC surface, how polar end groups are detached from lubricant molecules during coating is described considering the effect of temperatures on the bond/break density of PFPE Zdol using the coarse-grained bead spring model based on finitely extensible nonlinear elastic potential. As PFPE Z contains no polar end groups, effects of temperature on the bond/break density (number of broken bonds/total number of bonds are not so significant like PFPE Zdol. Effects of temperature on the bond/break density of PFPE Z on DLC surface are also discussed with the help of graphical results. How bond/break phenomenonaffects the end bead density of PFPE Z and PFPE Zdol on DLC surface is discussed elaborately. How the overall bond length of PFPE Zdol increases with the increase of temperature which is responsible for its decomposition is discussed with the help of graphical results. At HAMR condition, as PFPE Z and PFPE Zdol are not suitable lubricant on a hard disk surface, it needs more investigations to obtain suitable lubricant. We study the effect of breaking of bonds of nonfunctional lubricant PFPE Z, functional lubricants such as PFPE Zdol and PFPE Ztetrao, and multidented functional lubricants such as ARJ-DS, ARJ-DD, and OHJ-DS on a DLC substrate with the increase of temperature when heating of all of the lubricants on a DLC substrate is carried out isothermally using the coarse-grained bead spring model by molecular dynamics simulations and suitable lubricant is selected which is suitable on a DLC substrate at high temperature.

  19. 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...

  20. 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.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  2. 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.

  3. Molecular dynamics simulations and novel drug discovery.

    Science.gov (United States)

    Liu, Xuewei; Shi, Danfeng; Zhou, Shuangyan; Liu, Hongli; Liu, Huanxiang; Yao, Xiaojun

    2018-01-01

    Molecular dynamics (MD) simulations can provide not only plentiful dynamical structural information on biomacromolecules but also a wealth of energetic information about protein and ligand interactions. Such information is very important to understanding the structure-function relationship of the target and the essence of protein-ligand interactions and to guiding the drug discovery and design process. Thus, MD simulations have been applied widely and successfully in each step of modern drug discovery. Areas covered: In this review, the authors review the applications of MD simulations in novel drug discovery, including the pathogenic mechanisms of amyloidosis diseases, virtual screening and the interaction mechanisms between drugs and targets. Expert opinion: MD simulations have been used widely in investigating the pathogenic mechanisms of diseases caused by protein misfolding, in virtual screening, and in investigating drug resistance mechanisms caused by mutations of the target. These issues are very difficult to solve by experimental methods alone. Thus, in the future, MD simulations will have wider application with the further improvement of computational capacity and the development of better sampling methods and more accurate force fields together with more efficient analysis methods.

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

    International Nuclear Information System (INIS)

    Sanz-Navarro, Carlos F.

    2002-01-01

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

  5. Application of Connection in Molecular Dynamics

    Science.gov (United States)

    Sun, Xin

    2018-03-01

    The evolution of electronic states in molecule has two origins: dynamical one produced by Schrödinger equation and kinematical one caused by base transformation due to nuclear motion. In current theories, the former gets analytic expression; the latter depends on heavy numerical calculation, which contains uncertainty. By using connection of fiber bundles, this paper establishes an analytic formula for the latter, and the numerical work is simplified. It shows the mathematical structure of molecule is fiber bundle.

  6. 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.

  7. 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.

  8. Molecular dynamics modeling and characterization of graphene/polymer nanocomposites

    Science.gov (United States)

    Rahman, Rezwanur

    The current work focuses on the characterization of graphene based nanocomposites using molecular dynamic simulation and multiscale modeling approaches. Both graphene-epoxy and graphene-cellulose nanocomposites were considered in this study. A hierarchical multiscale modeling approach has been proposed using peridynamics and molecular dynamics simulation. Firstly, the mechanical properties of crosslinked graphene/epoxy (G-Ep) nanocomposites were investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. The influence of graphene's weight concentration, aspect ratio and dispersion on stress-strain response and elastic properties were studied. The results show significant improvement in Young's modulus and shear modulus for the G-Ep system in comparison to the neat epoxy resin. It appears that the RDF, molecular energy and aspect ratios are influenced by both graphene concentrations and aspect ratios. The graphene concentrations in the range of 1-3% are seen to improve Young's modulus and shorter graphenes are observed to be more effective than larger ones. In addition, the dispersed graphene system is more promising in enhancing in-plane elastic modulus than the agglomerated graphene system. The cohesive and pullout forces versus displacements data were plotted under normal and shear modes in order to characterize interfacial properties. The cohesive force is significantly improved by attaching the graphene with a chemical bond at the graphene-epoxy interface. In the second part of the work, cellulose was considered to study the mechanical properties of graphene-cellulose bionanocomposite. Similar to graphene-epoxy systems, the effect of graphene dispersion and agglomeration were studied in the stress-strain plots of graphene-cellulose system. A pcff forcefield was used to define intermolecular and intramolecular interactions. The effect of graphene's aspect ratio and weight concentration on the structural property of each unitcell was

  9. 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.

  10. Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions

    Science.gov (United States)

    Baltoumas, Fotis A.; Theodoropoulou, Margarita C.; Hamodrakas, Stavros J.

    2016-06-01

    A significant amount of experimental evidence suggests that G-protein coupled receptors (GPCRs) do not act exclusively as monomers but also form biologically relevant dimers and oligomers. However, the structural determinants, stoichiometry and functional importance of GPCR oligomerization remain topics of intense speculation. In this study we attempted to evaluate the nature and dynamics of GPCR oligomeric interactions. A representative set of GPCR homodimers were studied through Coarse-Grained Molecular Dynamics simulations, combined with interface analysis and concepts from network theory for the construction and analysis of dynamic structural networks. Our results highlight important structural determinants that seem to govern receptor dimer interactions. A conserved dynamic behavior was observed among different GPCRs, including receptors belonging in different GPCR classes. Specific GPCR regions were highlighted as the core of the interfaces. Finally, correlations of motion were observed between parts of the dimer interface and GPCR segments participating in ligand binding and receptor activation, suggesting the existence of mechanisms through which dimer formation may affect GPCR function. The results of this study can be used to drive experiments aimed at exploring GPCR oligomerization, as well as in the study of transmembrane protein-protein interactions in general.

  11. Molecular dynamics simulation of ion mobility in gases

    Science.gov (United States)

    Lai, Rui; Dodds, Eric D.; Li, Hui

    2018-02-01

    A force field molecular dynamics method is developed to directly simulate ion drift in buffer gases driven by an electric field. The ion mobility and collision cross sections (CCSs) with relevance to ion mobility spectrometry can be obtained from the simulated drift velocity in high-density buffer gases (pressure ˜50 bars) and high electric fields (˜107 V/m). Compared to trajectory methods, the advantage of the molecular dynamics method is that it can simultaneously sample the internal dynamic motions of the ion and the ion-gas collisions. For ions with less than 100 atoms, the simulated collision cross section values can be converged to within ±1%-2% by running a 100 ns simulation for 5-19 h using one computer core. By using a set of element-based Lennard-Jones parameters that are not tuned for different atomic types in different molecules, the simulated collision cross sections for 15 small molecular ions (number of atoms ranging from 17 to 85, mass ranging from 74.1 to 609.4 g/mol) are consistent with experimental values: the mean unsigned error is 2.6 Å2 for He buffer gas and 4.4 Å2 for N2 buffer gas. The sensitivity of the simulated CCS values to random diffusion, drift velocity, electric field strength, temperature, and buffer gas density is examined.

  12. 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.

  13. Molecular design of responsive fluids: molecular dynamics studies of viscoelastic surfactant solutions

    Science.gov (United States)

    Boek, E. S.; Jusufi, A.; Löwen, H.; Maitland, G. C.

    2002-10-01

    Understanding how macroscopic properties depend on intermolecular interactions for complex fluid systems is an enormous challenge in statistical mechanics. This issue is of particular importance for designing optimal industrial fluid formulations such as responsive oilfield fluids, based on viscoelastic surfactant solutions. We have carried out extensive molecular dynamics simulations, resolving the full chemical details in order to study how the structure of the lamellar phase of viscoelastic surfactant solutions depends on the head group (HG) chemistry of the surfactant. In particular, we consider anionic carboxylate and quaternary ammonium HGs with erucyl tails in aqueous solutions together with their sodium and chloride counterions at room temperature. We find a strong HG dependence of the lamellar structure as characterized by suitable pair correlation functions and density distributions. The depth of penetration of water into the bilayer membrane, the nature of counterion condensation on the HGs and even the order and correlation of the tails in the lamellae depend sensitively on the chemical details of the HG. We also determine the compressibility of the lamellar system as a first step to using atom-resolved molecular dynamics in order to link the molecular and macroscopic scales of length and time. The results give important insight into the links between molecular details and surfactant phase structure which is being exploited to develop more systematic procedures for the molecular design and formulation of industrial systems.

  14. Investigating Ebola virus pathogenicity using molecular dynamics.

    Science.gov (United States)

    Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

    2017-08-11

    Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

  15. Heat capacity effects associated with the hydrophobic hydration and interaction of simple solutes: a detailed structural and energetical analysis based on molecular dynamics simulations.

    Science.gov (United States)

    Paschek, Dietmar

    2004-06-08

    We examine the SPCE [H. J. C. Berendsen et al., J. Chem. Phys. 91, 6269 (1987)] and TIP5P [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys 112, 8910 (2000)] water models using a temperature series of molecular-dynamics simulations in order to study heat-capacity effects associated with the hydrophobic hydration and interaction of xenon particles. The temperature interval between 275 and 375 K along the 0.1-MPa isobar is studied. For all investigated models and state points we calculate the excess chemical potential for xenon employing the Widom particle insertion technique. The solvation enthalpy and excess heat capacity is obtained from the temperature dependence of the chemical potentials and, alternatively, directly by Ewald summation, as well as a reaction field based method. All three methods provide consistent results. In addition, the reaction field technique allows a separation of the solvation enthalpy into solute/solvent and solvent/solvent parts. We find that the solvent/solvent contribution to the excess heat capacity is dominating, being about one order of magnitude larger than the solute/solvent part. This observation is attributed to the enlarged heat capacity of the water molecules in the hydration shell. A detailed spatial analysis of the heat capacity of the water molecules around a pair of xenon particles at different separations reveals that even more enhanced heat capacity of the water located in the bisector plane between two adjacent xenon atoms is responsible for the maximum of the heat capacity found for the desolvation barrier distance, recently reported by Shimizu and Chan [J. Am. Chem. Soc. 123, 2083 (2001)]. The about 60% enlarged heat capacity of water in the concave part of the joint xenon-xenon hydration shell is the result of a counterplay of strengthened hydrogen bonds and an enhanced breaking of hydrogen bonds with increasing temperature. Differences between the two models with respect to the heat capacity in the xenon

  16. Accelerating molecular dynamics simulations by linear prediction of time series

    Science.gov (United States)

    Brutovsky, B.; Mülders, T.; Kneller, G. R.

    2003-04-01

    We present a molecular dynamics simulation scheme which allows to speed up molecular dynamics simulations by linear prediction of force time series. The explicit calculation of nonbonding forces is periodically replaced by linear prediction from past values. Applying our method to liquid oxygen consisting of flexible molecules we obtained real speedups between 5.4 and 6.5, compared to conventional molecular dynamics simulations. Here only the bond-stretching forces were calculated at each time step. We demonstrate that essential dynamical quantities, such as the mean-square displacement and the velocity autocorrelation function, are preserved.

  17. 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.

  18. First principles molecular dynamics of molten NaCl

    Science.gov (United States)

    Galamba, N.; Costa Cabral, B. J.

    2007-03-01

    First principles Hellmann-Feynman molecular dynamics (HFMD) results for molten NaCl at a single state point are reported. The effect of induction forces on the structure and dynamics of the system is studied by comparison of the partial radial distribution functions and the velocity and force autocorrelation functions with those calculated from classical MD based on rigid-ion and shell-model potentials. The first principles results reproduce the main structural features of the molten salt observed experimentally, whereas they are incorrectly described by both rigid-ion and shell-model potentials. Moreover, HFMD Green-Kubo self-diffusion coefficients are in closer agreement with experimental data than those predicted by classical MD. A comprehensive discussion of MD results for molten NaCl based on different ab initio parametrized polarizable interionic potentials is also given.

  19. Consequences of Molecular-Scale Non-Equilibrium Activity on the Dynamics and Mechanics of Self-Assembled Actin-Based Structures and Materials

    Science.gov (United States)

    Marshall Mccall, Patrick

    Living cells are hierarchically self-organized forms of active soft matter: molecules on the nanometer scale form functional structures and organelles on the micron scale, which then compose cells on the scale of 10s of microns. While the biological functions of intracellular organelles are defined by the composition and properties of the structures themselves, how those bulk properties emerge from the properties and interactions of individual molecules remains poorly understood. Actin, a globular protein which self-assembles into dynamic semi-flexible polymers, is the basic structural material of cells and the major component of many functional organelles. In this thesis, I have used purified actin as a model system to explore the interplay between molecular-scale dynamics and organelle-scale functionality, with particular focus on the role of molecular-scale non-equilibrium activity. One of the most canonical forms of molecular-scale non-equilibrium activity is that of mechanoenzymes, also called motor proteins. These proteins utilized the free energy liberated by hydrolysis of ATP to perform mechanical work, thereby introducing non-equilibrium "active" stresses on the molecular scale. Combining experiments with mathematical modeling, we demonstrate in this thesis that non-equilibrium motor activity is sufficient to drive self-organization and pattern formation of the multimeric actin-binding motor protein Myosin II on 1D reconstituted actomyosin bundles. Like myosin, actin is itself an ATPase. However, nono-equilibrium ATP hydrolysis on actin is known to regulate the stability and assembly kinetics of actin filaments rather than generate active stresses per se. At the level of single actin filaments, the inhomogeneous nucleotide composition generated along the filament length by hydrolysis directs binding of regulatory proteins like cofilin, which mediate filament disassembly and thereby accelerate actin filament turnover. The concequences of this non

  20. Emission of water clusters: molecular dynamic simulation

    International Nuclear Information System (INIS)

    Kutliev, U.O.; Kalandarov, K.S.

    2006-01-01

    Full text: Secondary ion mass spectrometry (SIMS) is a wonderful technique for providing mass spectrometric information of molecules on surfaces. Theoretical studies of the keV bombardment of organic films on metallic surfaces have contributed to our understanding of the mechanisms governing these processes. Many experiments of keV bombardment, however, are performed both thick and thin organic targets [1]. Molecular systems investigated experimentally by SIMS include adsorbed films on a metal substrate, molecular solids, polymers, or even biological cells. In this account, we focus on thin organic layers on metal substrates as they are used for analytical purposes, are intriguing from a fundamental viewpoint, and are computationally tractable [2]. There are we present molecular dynamics (MD) simulations aimed at obtaining such a microscopic picture and mass spectrum of sputtering particles. Because of the importance of H 2 O in many of the experiments, we have chosen it as our system. Water is also attractive as a system because of the extensive literature available on its physical properties. The interaction potentials available for MD simulations of H 2 O are sufficiently reliable such that a quantitative analysis of the simulation results can be directly related to the parameters of water. From the variety of substrate materials used in different experiments, we have chosen to perform our simulations using Au. This substance is chosen to match preliminary experiments with the selective killing of cells by inserted Au nanoparticles and because of the availability of good interaction potentials for gold. In the simulations, we bombarded by ions Ar the surface Au(III) covered by ice film. The interaction potential employed to describe the H 2 O-H 2 O interaction is the simple-point-charge (SPC) water potential developed by Berendsen et al. [3]. This potential has been used extensively to study the properties of H 2 O as a solid [4, 5]. It has been shown that the

  1. 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

  2. Structural, dynamical, and electronic properties of amorphous silicon: An ab initio molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Car, R.; Parrinello, M.

    1988-01-18

    An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.

  3. 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...

  4. Full quantum treatment of charge dynamics in amorphous molecular semiconductors

    Science.gov (United States)

    de Vries, Xander; Friederich, Pascal; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.

    2018-02-01

    We present a treatment of charge dynamics in amorphous molecular semiconductors that accounts for the coupling of charges to all intramolecular phonon modes in a fully quantum mechanical way. Based on ab initio calculations, we derive charge transfer rates that improve on the widely used semiclassical Marcus rate and obtain benchmark results for the mobility and energetic relaxation of electrons and holes in three semiconductors commonly applied in organic light-emitting diodes. Surprisingly, we find very similar results when using the simple Miller-Abrahams rate. We conclude that extracting the disorder strength from temperature-dependent charge transport studies is very possible but extracting the reorganization energy is not.

  5. Effects of Vacancy Concentration and Temperature on Mechanical Properties of Single-Crystal γ-TiAl Based on Molecular Dynamics Simulation

    Science.gov (United States)

    Ruicheng, Feng; Hui, Cao; Haiyan, Li; Zhiyuan, Rui; Changfeng, Yan

    2018-01-01

    Molecular dynamics simulation is used to analyze tensile strength and elastic modulus under different temperatures and vacancy concentrations. The effects of temperature and vacancy concentration on the mechanical properties of γ-TiAl alloy are investigated. The results show that the ultimate stress, ultimate strain and elastic modulus decrease nonlinearly with increasing temperature and vacancy concentration. As the temperature increases, the plastic of material is reinforced. The influence of temperature on strength and elastic modulus is larger than that of vacancy concentration. The evolution process of vacancy could be observed clearly. Furthermore, vacancies with different concentrations develop into voids first as a function of external forces or other factors, micro cracks evolve from those voids, those micro cracks then converge to a macro crack, and fracture will finally occur. The vacancy evolution process cannot be observed clearly owing to the thermal motion of atoms at high temperature. In addition, potential energy is affected by both temperature and vacancy concentration.

  6. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations.

    Science.gov (United States)

    Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad

    2015-02-15

    The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported. © 2014 Wiley Periodicals, Inc.

  7. Investigation of the dynamics of aqueous proline solutions using neutron scattering and molecular dynamics simulations.

    Science.gov (United States)

    Malo de Molina, Paula; Alvarez, Fernando; Frick, Bernhard; Wildes, Andrew; Arbe, Arantxa; Colmenero, Juan

    2017-10-18

    We applied quasielastic neutron scattering (QENS) techniques to samples with two different contrasts (deuterated solute/hydrogenated solvent and the opposite label) to selectively study the component dynamics of proline/water solutions. Results on diluted and concentrated solutions (31 and 6 water molecules/proline molecule, respectively) were analyzed in terms of the susceptibility and considering a recently proposed model for water dynamics [Arbe et al., Phys. Rev. Lett., 2016, 117, 185501] which includes vibrations and the convolution of localized motions and diffusion. We found that proline molecules not only reduce the average diffusion coefficient of water but also extend the time/frequency range of the crossover region ('cage') between the vibrations and purely diffusive behavior. For the high proline concentration we also found experimental evidence of water heterogeneous dynamics and a distribution of diffusion coefficients. Complementary molecular dynamics simulations show that water molecules start to perform rotational diffusion when they escape the cage regime but before the purely diffusive behavior is established. The rotational diffusion regime is also retarded by the presence of proline molecules. On the other hand, a strong coupling between proline and water diffusive dynamics which persists with decreasing temperature is directly observed using QENS. Not only are the temperature dependences of the diffusion coefficients of both components the same, but their absolute values also approach each other with increasing proline concentration. We compared our results with those reported using other techniques, in particular using dielectric spectroscopy (DS). A simple approach based on molecular hydrodynamics and a molecular treatment of DS allows rationalizing the a priori puzzling inconsistency between QENS and dielectric results regarding the dynamic coupling of the two components. The interpretation proposed is based on general grounds and therefore

  8. 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

  9. Molecular dynamics simulations of Pd-Ni transition metal alloys

    International Nuclear Information System (INIS)

    Kart, S. O.; Kart, H. H.; Uludogan, M.; Tomak, M.; Cagin, T.

    2002-01-01

    Molecular Dynamics simulations are performed to study bulk properties of fcc metals and metal alloys by using the quantum Sutton-Chen many-body potentials within the context of the tight-binding approach. The Molecular Dynamics algorithms we used in the simulations of Pd-Ni alloys are based on an extended Hamiltonian formalism arising from the works of Andersen (1980), Parinello and Rahman (1980), Nose (1984), Hoover (1985) and Cagin (1988). In these simulations, the effect of temperature and concentration on the solid and liquid properties are studied. Elastic constants and phonon dispersion relation are the solid properties we simulated in this work. Dynamic and static properties of liquid Pd-Ni are also computed by examining the behavior of density, enthalpy, pair distribution function and structure factor. The melting temperatures of Pd-Ni alloys are investigated. The diffusion coefficients are calculated from the mean square displacement using Einstein relation and from velocity auto-correlation function using Green-Kubo relations. The simulation results are in good agreement with the experiments

  10. 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.

  11. Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers

    International Nuclear Information System (INIS)

    Vashishta, Priya; Kalia, Rajiv

    2005-01-01

    Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report

  12. 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

  13. 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)

  14. Multiscale molecular dynamics using the matched interface and boundary method

    International Nuclear Information System (INIS)

    Geng Weihua; Wei, G.W.

    2011-01-01

    The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.

  15. 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...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration...... rate, different dehydrated structures were observed. Removing all water molecules immediately and removing water relatively fast (10 water molecules/10 ps) resulted in an amorphous system, whereas relatively slow computational dehydration (3 water molecules/10 ps) resulted in a crystalline anhydrate...

  16. Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting

    National Research Council Canada - National Science Library

    Low, Tammy K

    2006-01-01

    .... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...

  17. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  18. 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.

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

    Science.gov (United States)

    Zhao, Lei; Cheng, Jiangtao

    2017-09-07

    In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

  20. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    Science.gov (United States)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  1. A ReaxFF-based molecular dynamics study of the mechanisms of interactions between reactive oxygen plasma species and the Candida albicans cell wall

    Science.gov (United States)

    Zhao, T.; Shi, L.; Zhang, Y. T.; Zou, L.; Zhang, L.

    2017-10-01

    Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.

  2. Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data

    International Nuclear Information System (INIS)

    Eichenberger, Andreas P.; Gunsteren, Wilfred F. van; Smith, Lorna J.

    2013-01-01

    Various experimental studies of hen egg white lysozyme (HEWL) in water and TFE/water clearly indicate structural differences between the native state and TFE state of HEWL, e.g. the helical content of the protein in the TFE state is much higher than in the native state. However, the available detailed NMR studies were not sufficient to determine fully a structure of HEWL in the TFE state. Different molecular dynamics (MD) simulations, i.e. at room temperature, at increased temperature and using proton–proton distance restraints derived from NMR NOE data, have been used to generate configurational ensembles corresponding to the TFE state of HEWL. The configurational ensemble obtained at room temperature using atom-atom distance restraints measured for HEWL in TFE/water solution satisfies the experimental data and has the lowest protein energy. In this ensemble residues 50–58, which are part of the β-sheet in native HEWL, adopt fluctuating α-helical secondary structure.

  3. Key amino acid associated with acephate detoxification by Cydia pomonella carboxylesterase based on molecular dynamics with alanine scanning and site-directed mutagenesis.

    Science.gov (United States)

    Yang, Xue Qing; Liu, Ji Yuan; Li, Xian Chun; Chen, Mao Hua; Zhang, Ya Lin

    2014-05-27

    Insecticide-detoxifying carboxylesterase (CE) gene CpCE-1 was cloned from Cydia pomonella. Molecular dynamics (MD) simulation and computational alanine scanning (CAS) indicate that Asn 232 in CpCE-1 constitutes an approximate binding hot-spot with a binding free energy difference (ΔΔGbind) value of 3.66 kcal/mol. The catalytic efficiency (kcat/km) of N232A declined dramatically, and the half inhibitory concentrations (IC50) value increased by more than 230-fold. Metabolism assay in vitro reveals that the acephate could be metabolized by wild CpCE-1, whereas N232A mutation is unable to metabolize the acephate, which suggests that the hot-spot Asn 232 is a crucial residue for acephate metabolism. Mutation detection suggests that low frequency of Asn 232 replacement occurred in Europe field strains. Our MD, CAS, site-directed mutagenesis, and metabolism studies introduce a new amino acid residue Asn 232 involved in the metabolism of the acephate with CpCE-1, and this method is reliable in insecticide resistance mechanism research and prediction of key amino acids in a protein which is associated with specific physiological and biochemical functions.

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

    Indian Academy of Sciences (India)

    ANIRBAN MONDAL

    TMG][L]) that absorbs an equimolar amount of SO2 through chemisorption.12 Subsequently, a sig- ...... Visual molecular dynamics J. Mol. Graphics 14 33. 83. Fiorin G, Klein M L and Hénin J 2013 Using collective variables to drive molecular ...

  5. Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

    Science.gov (United States)

    Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

    2012-01-01

    The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

  6. Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

    Directory of Open Access Journals (Sweden)

    Ji-Long Zhang

    Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

  7. 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).

  8. 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.

  9. 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

  10. 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...

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

    Indian Academy of Sciences (India)

    Abstract. We have carried out a molecular dynamics simulation of two- and three- dimensional double Yukawa fluids near the triple point. We have compared some of the static and dynamic correlation functions with those of Lennard–Jones, when parameters occurring in double Yukawa potential are chosen to fit ...

  12. Interfacial Properties of an Ionic Liquid by Molecular Dynamics

    NARCIS (Netherlands)

    Heggen, B.; Zhao, W.; Leroy, F.; Dammers, A.T.; Müller-Plathe, F.

    2010-01-01

    We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) by molecular dynamics simulations. In the interfacial region, reorientation of

  13. Dynamic imaging of molecular motion ultrashort intense laser pulses

    Science.gov (United States)

    Bandrauk, Andre D.

    2002-05-01

    The nonlinear nonperturbative response of atoms in intense laser fields has been extensively studied both experimentally and theoretically in the past twenty years leading to new unexpected effects such as Above Threshold Ionization, ATI, high order frequency generation etc. and these are documented in recent book The similar studies of molecules is a new chapter in the pursuit of laser control and manipulation of molecules. The nonlinear nonperturbative response of molecules to intense (Icm2 ) and ultrashort (V10 fs) laser pulses [2] is expected to yield new effects due to the extra degrees of freedom nuclear motion as compared to atoms [3], such as creation of Laser Induced Molecular Potentials, LIMP' s, Charge Resonance Enhanced Ionization, CREI [4] and molecular High Order Harmonic Generation [5]. These nonlinear nonperturbative in effects were seen in experiments [6] and were predicted and confirmed by high-level numerical simulations of appropriate time-dependent Schrodinger equations [3-5,7], TDSE's, of molecules in laser fields. Our recent supercomputer simulations of H2+ molecule dynamics in intense laser fields, [7-9] based on TDSE, also allowed us to propose two new molecular imaging techniques: a) LCEI, Laser Coulomb Explosion Imaging [8] and b) LPEI, Laser Photoelectron Imaging [9]. The first is based on the analysis of the kinetic energy of molecular fragments after Coulomb Explosion, CE, whereas the latter imaging uses the shape of ATI electron peaks, produced by an intense laser pulse. We describe summarily in the present communication these two imaging methods which were developed using high level supercomputer simulations

  14. 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.

  15. Optimal control of molecular motion expressed through quantum fluid dynamics

    Science.gov (United States)

    Dey, Bijoy K.; Rabitz, Herschel; Askar, Attila

    2000-04-01

    A quantum fluid-dynamic (QFD) control formulation is presented for optimally manipulating atomic and molecular systems. In QFD the control quantum system is expressed in terms of the probability density ρ and the quantum current j. This choice of variables is motivated by the generally expected slowly varying spatial-temporal dependence of the fluid-dynamical variables. The QFD approach is illustrated for manipulation of the ground electronic state dynamics of HCl induced by an external electric field.

  16. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  17. Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene.

    Science.gov (United States)

    Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M

    2015-02-14

    The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

  18. 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...

  19. Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling.

    Science.gov (United States)

    Zheng, Wenjun

    2017-01-10

    Dynactin, a large multiprotein complex, binds with the cytoplasmic dynein-1 motor and various adaptor proteins to allow recruitment and transportation of cellular cargoes toward the minus end of microtubules. The structure of the dynactin complex is built around an actin-like minifilament with a defined length, which has been visualized in a high-resolution structure of the dynactin filament determined by cryo-electron microscopy (cryo-EM). To understand the energetic basis of dynactin filament assembly, we used molecular dynamics simulation to probe the intersubunit interactions among the actin-like proteins, various capping proteins, and four extended regions of the dynactin shoulder. Our simulations revealed stronger intersubunit interactions at the barbed and pointed ends of the filament and involving the extended regions (compared with the interactions within the filament), which may energetically drive filament termination by the capping proteins and recruitment of the actin-like proteins by the extended regions, two key features of the dynactin filament assembly process. Next, we modeled the unknown binding configuration among dynactin, dynein tails, and a number of coiled-coil adaptor proteins (including several Bicaudal-D and related proteins and three HOOK proteins), and predicted a key set of charged residues involved in their electrostatic interactions. Our modeling is consistent with previous findings of conserved regions, functional sites, and disease mutations in the adaptor proteins and will provide a structural framework for future functional and mutational studies of these adaptor proteins. In sum, this study yielded rich structural and energetic information about dynactin and associated adaptor proteins that cannot be directly obtained from the cryo-EM structures with limited resolutions.

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

    Science.gov (United States)

    Arkun, Yaman; Gur, Mert

    2012-01-01

    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.

  1. 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.

  2. Dynamics of molecular superrotors in an external magnetic field

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Valery

    2015-08-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

  3. Dynamics of molecular superrotors in an external magnetic field

    International Nuclear Information System (INIS)

    Korobenko, Aleksey; Milner, Valery

    2015-01-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

  4. VUV studies of molecular photofragmentation dynamics

    Energy Technology Data Exchange (ETDEWEB)

    White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

  5. Molecular dynamics simulations of temperature equilibration in dense hydrogen

    Science.gov (United States)

    Glosli, J. N.; Graziani, F. R.; More, R. M.; Murillo, M. S.; Streitz, F. H.; Surh, M. P.; Benedict, L. X.; Hau-Riege, S.; Langdon, A. B.; London, R. A.

    2008-08-01

    The temperature equilibration rate between electrons and protons in dense hydrogen has been calculated with molecular dynamics simulations for temperatures between 10 and 600eV and densities between 1020cm-3to1024cm-3 . Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L≳1 , a model by Gericke-Murillo-Schlanges (GMS) [D. O. Gericke , Phys. Rev. E 65, 036418 (2002)] based on a T -matrix method and the approach by Brown-Preston-Singleton [L. S. Brown , Phys. Rep. 410, 237 (2005)] agrees with the simulation data to within the error bars of the simulation. For smaller Coulomb logarithms, the GMS model is consistent with the simulation results. Landau-Spitzer models are consistent with the simulation data for L>4 .

  6. First principles centroid molecular dynamics simulation of high pressure ices

    Science.gov (United States)

    Ikeda, Takashi

    2018-03-01

    The nuclear quantum effects (NQEs) on the structural, elastic, electronic, and vibrational properties of high pressure ices (HPIs) VIII, VII, and X at 270 K were investigated via first principles centroid molecular dynamics (CMD). Our simulations clearly show that even at relatively high temperature of 270 K, the NQEs play a definite role in the pressure-induced proton order (ice VIII)-disorder (ice VII) transition occurring at ˜30 GPa in our H2O ice and the subsequent transition to the symmetric phase ice X suggested to occur at ˜80 GPa. The internal pressure computed at constant NVT conditions shows that the NQEs manifest themselves in the equation of state of HPIs. Our employed approach based on first principles CMD for computing vibrational spectra is proved to be able to reproduce well the overall features of the measured infrared and Raman spectra.

  7. 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

    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......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...

  8. 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

  9. Simplistic Coulomb Forces in Molecular Dynamics

    DEFF Research Database (Denmark)

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

    2012-01-01

    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. Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

    2004-01-01

    Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches

  11. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

    Science.gov (United States)

    Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C

    2013-11-07

    Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

  12. Structure-composition trends in multicomponent borosilicate-based glasses deduced from molecular dynamics simulations with improved B-O and P-O force fields.

    Science.gov (United States)

    Stevensson, Baltzar; Yu, Yang; Edén, Mattias

    2018-03-28

    We present a comprehensive molecular dynamics (MD) simulation study of composition-structure trends in a set of 25 glasses of widely spanning compositions from the following four systems of increasing complexity: Na 2 O-B 2 O 3 , Na 2 O-B 2 O 3 -SiO 2 , Na 2 O-CaO-SiO 2 -P 2 O 5 , and Na 2 O-CaO-B 2 O 3 -SiO 2 -P 2 O 5 . The simulations involved new B-O and P-O potential parameters developed within the polarizable shell-model framework, thereby combining the beneficial features of an overall high accuracy and excellent transferability among different glass systems and compositions: this was confirmed by the good accordance with experimental data on the relative BO 3 /BO 4 populations in borate and boro(phospho)silicate networks, as well as with the orthophosphate fractions in bioactive (boro)phosphosilicate glasses, which is believed to strongly influence their bone-bonding properties. The bearing of the simulated melt-cooling rate on the borate/phosphate speciations is discussed. Each local {BO 3 , BO 4 , SiO 4 , PO 4 } coordination environment remained independent of the precise set of co-existing network formers, while all trends observed in bond-lengths/angles mainly reflected the glass-network polymerization, i.e., the relative amounts of bridging oxygen (BO) and non-bridging oxygen (NBO) species. The structural roles of the Na + /Ca 2+ cations were also probed, targeting their local coordination environments and their relative preferences to associate with the various borate, silicate, and phosphate moieties. We evaluate and discuss the common classification of alkali/alkaline-earth metal ions as charge-compensators of either BO 4 tetrahedra or NBO anions in borosilicate glasses, also encompassing the less explored NBO-rich regime: the Na + /Ca 2+ cations mainly associate with BO/NBO species of SiO 4 /BO 3 groups, with significant relative Na-BO 4 contacts only observed in B-rich glass networks devoid of NBO species, whereas NBO-rich glass networks also

  13. Base damage, local sequence context and TP53 mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability.

    Science.gov (United States)

    Menzies, Georgina E; Reed, Simon H; Brancale, Andrea; Lewis, Paul D

    2015-10-30

    The mutational pattern for the TP53 tumour suppressor gene in lung tumours differs to other cancer types by having a higher frequency of G:C>T:A transversions. The aetiology of this differing mutation pattern is still unknown. Benzo[a]pyrene,diol epoxide (BPDE) is a potent cigarette smoke carcinogen that forms guanine adducts at TP53 CpG mutation hotspot sites including codons 157, 158, 245, 248 and 273. We performed molecular modelling of BPDE-adducted TP53 duplex sequences to determine the degree of local distortion caused by adducts which could influence the ability of nucleotide excision repair. We show that BPDE adducted codon 157 has greater structural distortion than other TP53 G:C>T:A hotspot sites and that sequence context more distal to adjacent bases must influence local distortion. Using TP53 trinucleotide mutation signatures for lung cancer in smokers and non-smokers we further show that codons 157 and 273 have the highest mutation probability in smokers. Combining this information with adduct structural data we predict that G:C>T:A mutations at codon 157 in lung tumours of smokers are predominantly caused by BPDE. Our results provide insight into how different DNA sequence contexts show variability in DNA distortion at mutagen adduct sites that could compromise DNA repair at well characterized cancer related mutation hotspots. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Molecular Dynamics: from basic techniques to applications (A Molecular Dynamics Primer)

    Science.gov (United States)

    Hernández, E. R.

    2008-11-01

    It is now 50 years since the first papers describing the use of Molecular Dynamics (MD) were published by Alder and Wainright, and since then, together with Monte Carlo (MC) techniques, MD has become an essential tool in the theoretical study of materials properties at finite temperatures. In its early days, MD was used in combination with simple yet general models, such as hard spheres or Lennard-Jones models of liquids, systems which, though simple, were nevertheless not amenable to an analytical statistical mechanical treatment. Nowadays, however, MD is most frequently used in combination with rather sophisticated models, ranging all the way between empirical force fields to first-principles methods, with the aim of describing as accurately as possible any given material. From a computational aid in statistical mechanics and many-body physics, MD has evolved to become a widely used tool in physical chemistry, condensed matter physics, biology, geology and materials science. The aim of this course is to describe the basic algorithms of MD, and to provide attendees with the necessary theoretical background in order to enable them to use MD simulations in their research work. Also, examples of the use of MD in different scientific disciplines will be provided, with the aim of illustrating the the many possibilities and the wide spread use of MD simulation techniques in scientific research today.

  15. Molecular dynamics study of atomic displacements in disordered solid alloys

    Science.gov (United States)

    Puzyrev, Yevgeniy S.

    The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

  16. Forcefields based molecular modeling on the mechanical and physical properties of emeraldine base polyaniline

    NARCIS (Netherlands)

    Chen, X.; Yuan, C.A.; Wong, K.Y.; Zhang, G.Q.

    2010-01-01

    Molecular dynamics (MD) and molecular mechanical (MM) analysis are carried out to provide reliable and accurate model for emeraldine base polyaniline. This study validate the forcefields and model with the physical and mechanical properties of the polyaniline. The temperature effects on non-bond

  17. Understanding ion association states and molecular dynamics using infrared spectroscopy

    Science.gov (United States)

    Masser, Hanqing

    A molecular level understanding of the ion transport mechanism within polymer electrolytes is crucial to the further development for advanced energy storage applications. This can be achieved by the identification and quantitative measurement of different ion species in the system and further relating them to the ion conductivity. In the first part of this thesis, research is presented towards understanding the ion association states (free ions, ion pairs and ion aggregates) in ionomer systems, and the correlation of ion association states, ion conduction, polymer dynamics, and morphology. Ion conductivity in ionomers can be improved by lowering glass transition temperature, increasing polymer ion solvation ability, and adjusting ionomer structural variables such as ion content, cation type and side chain structure. These effects are studied in three ionomer systems respectively, using a combination of characterization methods. Fourier Transform Infrared Spectroscopy (FTIR) identifies and quantifies the ion association states. Dielectric Spectroscopy (DRS) characterizes ion conductivity and polymer and ion dynamics. X-ray scattering reveals changes in morphology. The influence of a cation solvating plasticizer on a polyester ionomer is systematically investigated with respect to ion association states, ion and polymer dynamics and morphology. A decrease in the number ratio of ion aggregates with increased plasticizer content and a slight increase at elevated temperature are observed in FTIR. Similar results are also detected by X-ray scattering. As determined from dielectric spectroscopy, ion conductivity increases with plasticizer content, in accordance with the decrease in glass transition temperature. Research on copolymer of poly(ethylene oxide) (PEO) and poly(tetramethylene oxide) (PTMO) based ionomers further develops an understanding of the trade-off between ion solvation and segmental dynamics. Upon the incorporation of PTMO, the majority of the PTMO

  18. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    Directory of Open Access Journals (Sweden)

    Federico Fogolari

    2012-01-01

    Full Text Available Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

  19. Structural, dynamical, electronic, and bonding properties of laser-heated silicon: An ab initio molecular-dynamics study

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1997-01-01

    The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting

  20. Driving Ordering Processes in Molecular-Dynamics Simulations

    Science.gov (United States)

    Dittmar, Harro; Kusalik, Peter G.

    2014-05-01

    Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized.

  1. Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

    Science.gov (United States)

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-07

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

  2. 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

  3. 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.

  4. 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.

  5. Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

    Science.gov (United States)

    Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

    2018-01-01

    Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

  6. Multiscale Molecular Dynamics Approach to Energy Transfer in Nanomaterials.

    Science.gov (United States)

    Espinosa-Duran, John M; Sereda, Yuriy V; Abi-Mansour, Andrew; Ortoleva, Peter

    2018-02-13

    After local transient fluctuations are dissipated, in an energy transfer process, a system evolves to a state where the energy density field varies slowly in time relative to the dynamics of atomic collisions and vibrations. Furthermore, the energy density field remains strongly coupled to the atomic scale processes (collisions and vibrations), and it can serve as the basis of a multiscale theory of energy transfer. Here, a method is introduced to capture the long scale energy density variations as they coevolve with the atomistic state in a way that yields insights into the basic physics and implies an efficient algorithm for energy transfer simulations. The approach is developed based on the N-atom Liouville equation and an interatomic force field and avoids the need for conjectured phenomenological equations for energy transfer and other processes. The theory is demonstrated for sodium chloride and silicon dioxide nanoparticles immersed in a water bath via molecular dynamics simulations of the energy transfer between a nanoparticle and its aqueous host fluid. The energy density field is computed for different sets of symmetric grid densities, and the multiscale theory holds when slowly varying energy densities at the nodes are obtained. Results strongly depend on grid density and nanoparticle constituent material. A nonuniform temperature distribution, larger thermal fluctuations in the nanoparticle than in the bath, and enhancement of fluctuations at the surface, which are expressed due to the atomic nature of the systems, are captured by this method rather than by phenomenological continuum energy transfer models.

  7. Molecular dynamics simulation of irradiation damage in tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Park, Na-Young [School of Advanced Materials Engineering, Kookmin University, Seoul 136-702 (Korea, Republic of); Kim, Yu-Chan; Seok, Hyun-Kwang; Han, Seung-Hee [Advanced Metals Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791 (Korea, Republic of); Cho, Seungyon [Reactor Engineering Team, Division of Research and Development, National Fusion Research Center, Daejeon 305-333 (Korea, Republic of); Cha, Pil-Ryung [School of Advanced Materials Engineering, Kookmin University, Seoul 136-702 (Korea, Republic of)], E-mail: cprdream@kookmin.ac.kr

    2007-12-15

    Molecular dynamics (MD) simulations have been performed for the radiation damage of tungsten using a modified Finnis-Sinclair type many-body interatomic potential. The interstitial defects and vacancies are distinguished by the Wigner-Seitz cell method and the types of the interstitial dumbbells are also identified by the azimuth and polar angles of dumbbell line vectors. It is observed that the number of interstitial defects and vacancies initially sharply increases and passing through the peak position, relaxes to the steady state for all PKA energies and that all residual interstitial dumbbells at the steady state are the <1 1 1>-oriented. Based on the variation of the orientation angles of dumbbells during the radiation damage simulation, it is found that the recombination of the <1 1 1>-oriented dumbbells with the vacancies is much faster than that of two other types of dumbbells and that the population of the <1 0 0> dumbbells is much larger than that of the <1 1 0> ones in spite of its higher formation energy, the reason of which is explained with the dynamics of the individual dumbbell.

  8. 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

  9. 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.

  10. 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.

  11. Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1.

    Directory of Open Access Journals (Sweden)

    Min-Sun Park

    Full Text Available Glucose transporters (GLUTs provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and cancer. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE, a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM domains and the intracellular helices (ICH domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states.

  12. [Molecular bases of prion diseases].

    Science.gov (United States)

    Pokrovskiĭ, V I; Kiselev, O I

    1998-01-01

    The paper briefly analyzes the origin of priones and their association with the cellular gene and homologous protein of diseases in man and animals. There is evidence for a direct relationship of the agents that cause spongious encephalitis in the cattle and a new type of Creutzfeldt-Jacob disease in man. The molecular organization of priones and the conformational cellular protein changes underlying the infectious activation of the cell homologue of priones. Emphasis is first laid on the capacity of the cell homologue of priones and their infectiously active derivative to bind to DNA or RNA. In the context of concepts of the priones yeasts an attempt was made to explain the reproduction through the altered control of translation of mRNA that encodes the cellular homologue of priones, which accounts for the duration of the incubation period of the disease. The infections caused by priones are referred to as the so-called slow infections. But in the context of the proposed hypothesis, an infective process in the tissues did not really have some typical signs of infection and resembles accumulation diseases more without the replicative burst typical of infectious processes. The paper gives data on the vital cycle of priones in infected animals and changes in the accumulation of an infective agent. This assesses the currently available diagnostic methods and gives preference to the methods which will be based on the use of monoclonal antibodies that specifically recognize the conformationally altered form of an infectious prione or on the identification of primary oligomeric forms which manifest the onset of amyloidization of the damaged tissues. The main conclusion of the paper is that protein prionization is a common biological phenomenon and the diseases caused by these processes will increase in number in the near future, which makes it necessary to develop diagnostic methods and universal treatments of diseases, such as bacterial infections by using antibiotics.

  13. 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.

  14. Bases moleculares de las leucemias agudas

    Directory of Open Access Journals (Sweden)

    G. Martínez Antuña

    2006-04-01

    Full Text Available El gran desarrollo de la biología molecular en los últimos años ha contribuido a un importante avance en los conocimientos relacionados con las bases moleculares de las leucemias agudas (LA. Ademas de profundizar en la biología de estas enfermedades y conocer las bases moleculares, ha renido también gran impacto en mejorar el resultado de los tratamientos y disminuir la toxicidad de las terapias.

  15. 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.

  16. 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

  17. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.

    1979-01-01

    Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard

  18. 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

  19. Metal cluster fission: jellium model and Molecular dynamics simulations

    DEFF Research Database (Denmark)

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

    2004-01-01

    Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...

  20. Hydration of Cd(II): molecular dynamics study | M. Mohammed ...

    African Journals Online (AJOL)

    The inclusion of the three-body correction was found to be crucial for the description of the system, and results thus obtained are in good agreement with experimental values. Radial ... KEY WORDS: Molecular dynamics, Umbrella sampling, Hydration structure, Cd(II), Water exchange, Three-body corrections. Bull. Chem.

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

    Indian Academy of Sciences (India)

    Unknown

    The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. .... In that case the muffin–tin approximation is used solely to define the basis set. ..... functions probe the local character of the auxiliary wave function in the atomic region. Examples ...

  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. CF3+ etching silicon surface: A molecular dynamics study

    NARCIS (Netherlands)

    Zhao, C.; Lu, X.; He, P.; Zhang, P.; Sun, W.; Zhang, Jingwei; Chen, F.; Gou, F.

    2012-01-01

    In this study, a molecular dynamics simulation method has been employed to investigate CF3 + ions, bombarding Si surface with the energy of 100, 200, 300 and 400 eV and an incident angle of 45 degrees with respect to the normal. The simulation results show that when CF3+ ions approach the Si surface

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

    African Journals Online (AJOL)

    version 3.5,. Accelrys Inc., San Diego, CA) was used for protein design and molecular dynamics simulation. The analysis of the MD data was made using Origin Pro (version 9.0). Mean ± standard error of mean (SEM) of the data were computed.

  5. Molecular dynamics simulations and free energy profile of ...

    Indian Academy of Sciences (India)

    Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers. YOUSEF NADEMIa, SEPIDEH AMJAD IRANAGHb, ABBAS YOUSEFPOURa,. SEYEDEH ZAHRA MOUSAVIa and HAMID MODARRESSa,∗. aDepartment of Chemical Engineering, bDepartment of Chemistry, ...

  6. 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 ...

  7. 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 ...

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

    DEFF Research Database (Denmark)

    Christensen, Niels Johan; Kepp, Kasper Planeta

    2013-01-01

    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...

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

    NARCIS (Netherlands)

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

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

  10. 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...

  11. A molecular dynamics study of SiSe2 glass

    International Nuclear Information System (INIS)

    Antonio, G.A.; Kalia, R.K.; Vashishta, P.

    1988-10-01

    We report the results of a molecular dynamics study of molten and glassy SiSe 2 using an effective interparticle interaction. Results for the partial pair-correlation functions, partial structure factors, bond-angle distributions and statistics of rings are reported. Results are in good agreement with the neutron diffraction experiments. 11 refs., 6 figs

  12. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

    1991-09-15

    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

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

    Indian Academy of Sciences (India)

    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 employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

  14. Molecular dynamics simulations of phase transformations in niti bicrystals

    NARCIS (Netherlands)

    Srinivasan, P.; Nicola, L.; Simone, A.; Floryan, J.M.; Tvergaard, V.; van Campen, D.

    2016-01-01

    The influence of grain boundaries and grain misorientation on the nucleation and growth of martensite in an equi-atomic nickeltitanium (NiTi) shape memory alloy (SMA) is investigated by performing molecular dynamics (MD) simulations on bicrystals with a modified embedded atom method (MEAM)

  15. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  16. 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 ...

  17. Coarse – grained molecular dynamics simulation of cross – linking ...

    African Journals Online (AJOL)

    Coarse – grained molecular dynamics simulation of cross – linking of DGEBA epoxy resin and estimation of the adhesive strength. ... The PDF file you selected should load here if your Web browser has a PDF reader plug-in installed (for example, a recent version of Adobe Acrobat Reader). If you would like more ...

  18. Dynamical photo-induced electronic properties of molecular junctions

    Science.gov (United States)

    Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

    2018-03-01

    Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

  19. 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.

  20. Structure and dynamics of alkali borate glasses: a molecular dynamics study

    NARCIS (Netherlands)

    Verhoef, A.H; den Hartog, H. W.

    Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at

  1. 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).

  2. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    Directory of Open Access Journals (Sweden)

    Dirk-Sören Lühmann

    2015-08-01

    Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

  3. 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.

  4. mdFoam+: Advanced molecular dynamics in OpenFOAM

    Science.gov (United States)

    Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.

    2018-03-01

    This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.

  5. Molecular dynamics in germinating, endophyte-colonized quinoa seeds

    Science.gov (United States)

    2017-01-01

    Aims The pseudo-cereal quinoa has an outstanding nutritional value. Seed germination is unusually fast, and plant tolerance to salt stress exceptionally high. Seemingly all seeds harbor bacterial endophytes. This work examines mitogen-activated protein kinase (MAPK) activities during early development. It evaluates possible contribution of endophytes to rapid germination and plant robustness. Methods MAPK activities were monitored in water- and NaCl-imbibed seeds over a 4-h-period using an immunoblot-based approach. Cellulolytic and pectinolytic abilities of bacteria were assessed biochemically, and cellular movement, biofilm, elicitor and antimicrobial compound synthesis genes sequenced. GyrA-based, cultivation-independent studies provided first insight into endophyte diversity. Results Quinoa seeds and seedlings exhibit remarkably complex and dynamic MAPK activity profiles. Depending on seed origin, variances exist in MAPK patterns and probably also in endophyte assemblages. Mucilage-degrading activities enable endophytes to colonize seed surfaces of a non-host species, chia, without apparent adverse effects. Conclusions Owing to their motility, cell wall-loosening and elicitor-generating abilities, quinoa endophytes have the potential to drive cell expansion, move across cell walls, generate damage-associated molecular patterns and activate MAPKs in their host. Bacteria may thus facilitate rapid germination and confer a primed state directly upon seed rehydration. Transfer into non-native crops appears both desirable and feasible. PMID:29416180

  6. 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

  7. Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

    Science.gov (United States)

    Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

    2018-04-24

    In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

  8. Molecular dynamics simulations of nucleation and phase transitions in molecular clusters of hexafluorides

    International Nuclear Information System (INIS)

    Xu, S.

    1993-01-01

    Molecular dynamics simulations of nucleation and phase transitions in TeF 6 and SeF 6 clusters containing 100-350 molecules were carried out. Simulations successfully reproduced the crystalline structures observed in electron diffraction studies of large clusters (containing about 10 4 molecules) of the same materials. When the clusters were cooled, they spontaneously underwent the same bcc the monoclinic phase transition in simulations as in experiment, despite the million-fold difference in the time scales involved. Other transitions observed included melting and freezing. Several new techniques based on molecular translation and orientation were introduced to identify different condensed phases, to study nucleation and phase transitions, and to define characteristic temperatures of transitions. The solid-state transition temperatures decreased with cluster size in the same way as did the melting temperature, in that the depression of transition temperature was inversely proportional to the cluster radius. Rotational melting temperatures, as inferred from the rotational diffusion of molecules, coincided with those of the solid-state transition. Nucleation in liquid-solid and bcc-monoclinic transitions started in the interior of clusters on cooling, and at the surface on heating. Transition temperatures on cooling were always lower than those on heating due to the barriers to nucleation. Linear growth rates of nuclei in freezing were an order of magnitude lower than those in the bcc-monoclinic transition. Revealing evidence about the molecular behavior associated with phase changes was found. Simulations showed the formation of the actual transition complexes along the transition pathway, i.e., the critical nuclei of the new phase. These nuclei, consisting of a few dozen molecules, were distinguishable in the midst of the surrounding matter

  9. A general-purpose coarse-grained molecular dynamics program

    Science.gov (United States)

    Aoyagi, Takeshi; Sawa, Fumio; Shoji, Tatsuya; Fukunaga, Hiroo; Takimoto, Jun-ichi; Doi, Masao

    2002-05-01

    In this article, we describe a general-purpose coarse-grained molecular dynamics program COGNAC ( COarse Grained molecular dynamics program by NAgoya Cooperation). COGNAC has been developed for general molecular dynamics simulation, especially for coarse-grained polymer chain models. COGNAC can deal with general molecular models, in which each molecule consists of coarse-grained atomic units connected by chemical bonds. The chemical bonds are specified by bonding potentials for the stretching, bending and twisting of the bonds, each of which are the functions of the position coordinates of the two, three and four atomic units. COGNAC can deal with both isotropic and anisotropic interactions between the non-bonded atomic units. As an example, the Gay-Berne potential is implemented. New potential functions can be added to the list of existing potential functions by users. COGNAC can do simulations for various situations such as under constant temperature, under constant pressure, under shear and elongational deformation, etc. Some new methods are implemented in COGNAC for modeling multiphase structures of polymer blends and block copolymers. A density biased Monte Carlo method and a density biased potential method can generate equilibrium chain configurations from the results of the self-consistent field calculations. Staggered reflective boundary conditions can generate interfacial structures with smaller system size compared with those of periodic boundary conditions.

  10. Polymerase chain reaction (PCR) based molecular characterization ...

    African Journals Online (AJOL)

    Polymerase chain reaction (PCR) based molecular characterization of popular wheat varieties of Khyber Pukhtunkhwa (KPK) region of Pakistan. ... Molecular markers used in this study show high rate of genetic diversity that can be used to assist a breeding program for the improvement of wheat in KPK-Pakistan. Key words: ...

  11. Quasi- and inelastic neutron scattering to investigate the molecular dynamics of discotic molecules in the bulk

    Directory of Open Access Journals (Sweden)

    Krause Christina

    2015-01-01

    Full Text Available In- and quasielastic neutron scattering is employed to investigate both the vibrational density of states and the molecular dynamics of two homologous discotic liquid crystals (DLC with different length of the alkyl side chain based on a triphenylene derivate. For both compounds characteristic low frequency excess contributions to the vibrational density of states are found. Therefore it is concluded that these liquid crystals show a glass-like behaviour. Elastic scans further show that in these materials a rich molecular dynamics takes place.

  12. Utilization of the molecular dynamic to study the effect of hydrogen in the stress corrosion

    International Nuclear Information System (INIS)

    Arnoux, P.

    2007-01-01

    Many microscopic and theoretical models of stress corrosion have been proposed, in particularly to explain the grain boundary cracking of stainless steels and nickel base. In this work calculus of molecular dynamic have been used to propose a mechanism of stress corrosion at the atomic scale. The author aims to reproduce, by molecular dynamic, the mechanism of an open crack in irradiated stainless steel in PWR reactor and show that the growth of the oxide at the crack back produce hydrogen. (A.L.B.)

  13. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

    Science.gov (United States)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-07-01

    In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of "statistical associating fluid theory" that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH2 and CH3 and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ˜2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ˜1% from simulation data while the theory reproduces the excess

  14. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

    International Nuclear Information System (INIS)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-01-01

    In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of “statistical associating fluid theory” that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH 2 and CH 3 and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ∼2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ∼1% from simulation data while the theory reproduces

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

    International Nuclear Information System (INIS)

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

    2010-01-01

    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.

  16. Molecular dynamics of TBP and DBP studied by neutron transmission

    International Nuclear Information System (INIS)

    Salles Filho, J.B.V.; Refinetti, M.E.; Fulfaro, R.; Vinhas, L.A.

    1984-04-01

    Differences between the properties of TBP and DBP, concerning the uranium extraction processes, may be related to certain characteristics of the molecular dynamics of each compound. In order to investigate the dynamical behaviour of hydrogen in these molecules, neutron transmission of TBP and DBP has been measured as a function of neutron wavelenght in the range 4.0 - 6.0 A, at room temperature. Scattering cross sections per hydrogen atom have been obtained. From the comparison with results previously obtained for n-butanol, similar dynamical behaviour of butyl radicals in these compounds could be observed. This similarity indicates that the presence of two or three butyl radicals in butylphosphate molecules does not exert influence in the hydrogen motion of methyl and methylene groups. This suggests that the different chemical behaviour between TBP and DBP is related to the dynamics of the hydrogen directly bound to the DBP phosphate group.(Author) [pt

  17. 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.

  18. Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

    Science.gov (United States)

    Tsukanov, A. A.; Psakhie, S. G.

    2017-12-01

    The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

  19. 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.

  20. Spectra modelling combining molecular dynamics and quantum mechanics

    Czech Academy of Sciences Publication Activity Database

    Novák, Vít; Bouř, Petr

    2015-01-01

    Roč. 22, č. 1 (2015), s. 48 ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] R&D Projects: GA ČR GAP208/11/0105; GA ČR GA15-09072S Grant - others:GA MŠk(CZ) LM2010005; GA MŠk(CZ) ED3.2.00/08.0144 Institutional support: RVO:61388963 Keywords : Raman scattering * molecular dynamics * autocorrelation function Subject RIV: CF - Physical ; Theoretical Chemistry

  1. Mg/Ca partitioning between aqueous solution and aragonite mineral: a molecular dynamics study

    NARCIS (Netherlands)

    Ruiz-Hernandez, S.E.; Grau-Crespo, R.; Almora-Barrios, N.; Wolthers, M.; Ruiz-Salvador, A.R.; Fernandez, N.; Leeuw, N.H. de

    2012-01-01

    We have calculated the concentrations of Mg in the bulk and surfaces of aragonite CaCO3 in equilibrium with aqueous solution, based on molecular dynamics simulations and grand-canonical statistical mechanics. Mg is incorporated in the surfaces, in particular in the (001) terraces,

  2. Conductance of Alkanedithiol Single-Molecule Junctions: A Molecular Dynamics Study

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Krag, Casper; Frederiksen, Thomas

    2009-01-01

    We study formation and conductance of alkanedithiol junctions using density functional based molecular dynamics. The formation involves straightening of the molecule, migration of thiol end-groups, and pulling out Au atoms. Plateaus are found in the low-bias conductance traces which decrease by 1...

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

    International Nuclear Information System (INIS)

    Bianchi, L.

    2000-05-01

    distribution functions, showing that the agreement at the rdf level does not provide a critical evaluation of appropriateness of a chosen potential model to reproduce the observed liquid structure. Both the simulations reproduce equally well the X-X partial comprising of six correlations. The ability of the 3-site model simulations to satisfactorily reproduce this function dominated by contributions from the methyl group, demonstrates that the methyl group does not participate in any bonding in the liquid. However, the main peaks of the simulated Ho-Ho pdf are found to be slightly higher and shifted to larger distances as compared to the ND results. A comparison of the simulated and ND X-Ho inter-molecular functions dominated by H-Ho correlations shows that although the 3-site model reproduces at least qualitatively the experimental features, the six-site model fails badly. The structure of liquid benzene at 298 K is investigated by performing molecular dynamics (MD) simulations in NVE ensemble using three different force field models differing both in their functional form and in the way they were devised. Surprisingly however, they lead to similar results for the pdfs. The structural results from MD simulations are compared with the neutron diffraction (ND) results where the newly C-C, C-H and H-H inter-molecular pdfs are obtained in this study by the H/D substitution on hydrogen atoms of benzene. A good agreement is found between the simulated and experimental total inter-molecular rdfs for C 6 D 6 and C 6 (H/D) 6 experimental, but not for C 6 H 6 . Most of the structural properties of benzene discussed in the past have been based on the models, which showed a reasonable agreement between the simulated and neutron inter-molecular rdf or X-ray C-C pdf The C-C pdf extracted from the present ND studies however differs from the one obtained earlier from the X-ray measurements. Apart from that, the simulated C-C pdf reproduces the corresponding ND function better than that

  4. Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.

    Science.gov (United States)

    Dixit, Anshuman; Verkhivker, Gennady M

    2012-01-01

    Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based "conformational selection" of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected residue clusters may be

  5. Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.

    Directory of Open Access Journals (Sweden)

    Anshuman Dixit

    Full Text Available Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based "conformational selection" of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  7. 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,…

  8. 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.

  9. Elucidating Cellular Population Dynamics by Molecular Density Function Perturbations

    Directory of Open Access Journals (Sweden)

    Thanneer Malai Perumal

    2018-01-01

    Full Text Available Studies performed at single-cell resolution have demonstrated the physiological significance of cell-to-cell variability. Various types of mathematical models and systems analyses of biological networks have further been used to gain a better understanding of the sources and regulatory mechanisms of such variability. In this work, we present a novel sensitivity analysis method, called molecular density function perturbation (MDFP, for the dynamical analysis of cellular heterogeneity. The proposed analysis is based on introducing perturbations to the density or distribution function of the cellular state variables at specific time points, and quantifying how such perturbations affect the state distribution at later time points. We applied the MDFP analysis to a model of a signal transduction pathway involving TRAIL (tumor necrosis factor-related apoptosis-inducing ligand-induced apoptosis in HeLa cells. The MDFP analysis shows that caspase-8 activation regulates the timing of the switch-like increase of cPARP (cleaved poly(ADP-ribose polymerase, an indicator of apoptosis. Meanwhile, the cell-to-cell variability in the commitment to apoptosis depends on mitochondrial outer membrane permeabilization (MOMP and events following MOMP, including the release of Smac (second mitochondria-derived activator of caspases and cytochrome c from mitochondria, the inhibition of XIAP (X-linked inhibitor of apoptosis by Smac, and the formation of the apoptosome.

  10. 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.

  11. Elastic constants of diamond from molecular dynamics simulations

    International Nuclear Information System (INIS)

    Gao Guangtu; Van Workum, Kevin; Schall, J David; Harrison, Judith A

    2006-01-01

    The elastic constants of diamond between 100 and 1100 K have been calculated for the first time using molecular dynamics and the second-generation, reactive empirical bond-order potential (REBO). This version of the REBO potential was used because it was redesigned to be able to model the elastic properties of diamond and graphite at 0 K while maintaining its original capabilities. The independent elastic constants of diamond, C 11 , C 12 , and C 44 , and the bulk modulus were all calculated as a function of temperature, and the results from the three different methods are in excellent agreement. By extrapolating the elastic constant data to 0 K, it is clear that the values obtained here agree with the previously calculated 0 K elastic constants. Because the second-generation REBO potential was fit to obtain better solid-state force constants for diamond and graphite, the agreement with the 0 K elastic constants is not surprising. In addition, the functional form of the second-generation REBO potential is able to qualitatively model the functional dependence of the elastic constants and bulk modulus of diamond at non-zero temperatures. In contrast, reactive potentials based on other functional forms do not reproduce the correct temperature dependence of the elastic constants. The second-generation REBO potential also correctly predicts that diamond has a negative Cauchy pressure in the temperature range examined

  12. 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.

    2018-04-01

    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.

  13. 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 Mg 2+ 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 Mg 2+ 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.

  14. 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.

  15. 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.

  16. Efficient stochastic thermostatting of path integral molecular dynamics.

    Science.gov (United States)

    Ceriotti, Michele; Parrinello, Michele; Markland, Thomas E; Manolopoulos, David E

    2010-09-28

    The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat which exploits an analytic knowledge of the free path integral normal mode frequencies. We also apply a recently developed colored noise thermostat based on a generalized Langevin equation (GLE), which automatically achieves a similar, frequency-optimized sampling. The sampling efficiencies of these thermostats are compared with that of the more conventional Nosé-Hoover chain (NHC) thermostat for a number of physically relevant properties of the liquid water and hydrogen-in-palladium systems. In nearly every case, the new PILE thermostat is found to perform just as well as the NHC thermostat while allowing for a computationally more efficient implementation. The GLE thermostat also proves to be very robust delivering a near-optimum sampling efficiency in all of the cases considered. We suspect that these simple stochastic thermostats will therefore find useful application in many future PIMD simulations.

  17. 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.

  18. Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction

    Science.gov (United States)

    Lynch, Diane L.; Hurst, Dow P.; Shore, Derek M.; Pitman, Mike C.; Reggio, Patricia H.

    2018-01-01

    The cannabinoid type 1 and 2 G-protein-coupled receptors are currently important pharmacological targets with significant drug discovery potential. These receptors have been shown to display functional selectivity or biased agonism, a property currently thought to have substantial therapeutic potential. Although recent advances in crystallization techniques have provided a wealth of structural information about this important class of membrane-embedded proteins, these structures lack dynamical information. In order to fully understand the interplay of structure and function for this important class of proteins, complementary techniques that address the dynamical aspects of their function are required such as NMR as well as a variety of other spectroscopies. Complimentary to these experimental approaches is molecular dynamics, which has been effectively used to help unravel, at the atomic level, the dynamics of ligand binding and activation of these membrane-bound receptors. Here, we discuss and present several representative examples of the application of molecular dynamics simulations to the understanding of the signatures of ligand-binding and -biased signaling at the cannabinoid type 1 and 2 receptors. PMID:28750815

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

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2018-03-13

    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 a complex environment but also very time-consuming. The computational cost of 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 idea. 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 [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] 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

  20. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    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. Study on the Characteristics of Gas Molecular Mean Free Pathin Nanopores by Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Qixin Liu

    2014-07-01

    Full Text Available This paper presents studies on the characteristics of gas molecular mean freepath in nanopores by molecular dynamics simulation. Our study results indicate that themean free path of all molecules in nanopores depend on both the radius of the nanoporeand the gas-solid interaction strength. Besides mean free path of all molecules in thenanopore, this paper highlights the gas molecular mean free path at different positions ofthe nanopore and the anisotropy of the gas molecular mean free path at nanopores. Themolecular mean free path varies with the molecule’s distance from the center of thenanopore. The least value of the mean free path occurs at the wall surface of the nanopore.The present paper found that the gas molecular mean free path is anisotropic when gas isconfined in nanopores. The radial gas molecular mean free path is much smaller than themean free path including all molecular collisions occuring in three directions. Our studyresults also indicate that when gas is confined in nanopores the gas molecule number densitydoes not affect the gas molecular mean free path in the same way as it does for the gas inunbounded space. These study results may bring new insights into understanding the gasflow’s characteristic at nanoscale.

  2. Investigation of Interfacial and Bulk Dissociation of HBr, HCl, and HNO3 Using Density Functional Theory-Based Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Baer, Marcel; Tobias, Douglas J.; Mundy, Christopher J.

    2014-12-18

    In this study we investigate the free energy barrier associated with the dissociation of strong acids, XH (HBr, HCl and HNO3) deprotonation, and subsequent formation of ionpairs, X–___H3O+ in the vicinity of the air-water interface. We will show that the free energy for acid dissociation for HCl and HNO3 show significant differences at the air-water than under bulk solvation conditions producing a picture where at the interface associated molecular species can be stable. For the strongest acid we consider, HBr the more traditional picture of acids is preserved in the vicinity of the air-water interface. Our results have implications for our understanding of acids, and their surface tensions at the air-water interface.

  3. Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006

  4. 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.

  5. Statistical ensembles and molecular dynamics studies of anisotropic solids. II

    International Nuclear Information System (INIS)

    Ray, J.R.; Rahman, A.

    1985-01-01

    We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities

  6. 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.

  7. Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

    International Nuclear Information System (INIS)

    Zhang Junfang; Rivero, Mayela; Choi, S K

    2007-01-01

    We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added

  8. Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)

    2007-02-14

    We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

  9. Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar

    ) 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......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...

  10. Thermal Conductivity of Supercooled Water: An Equilibrium Molecular Dynamics Exploration.

    Science.gov (United States)

    English, Niall J; Tse, John S

    2014-11-06

    The thermal conductivity of both supercooled and ambient-temperature water at atmospheric pressure has been computed over the 140-270 K temperature range for three popular water models via equilibrium molecular dynamics in the Green-Kubo setting. No strong temperature dependence of thermal conductivity was observed. The underlying phonon modes contributing to thermal conduction processes have been examined in the present work, and it has been established that (translational) acoustic modes dominate in supercooled water.

  11. Thermal Transport in Fullerene Derivatives Using Molecular Dynamics Simulations

    OpenAIRE

    Chen, Liang; Wang, Xiaojia; Kumar, Satish

    2015-01-01

    In order to study the effects of alkyl chain on the thermal properties of fullerene derivatives, we perform molecular dynamics (MD) simulations to predict the thermal conductivity of fullerene (C60) and its derivative phenyl-C61-butyric acid methyl ester (PCBM). The results of non-equilibrium MD simulations show a length-dependent thermal conductivity for C60 but not for PCBM. The thermal conductivity of C60, obtained from the linear extrapolation of inverse conductivity vs. inverse length cu...

  12. Spin dynamics of an ultra-small nanoscale molecular magnet

    Directory of Open Access Journals (Sweden)

    Ciftja Orion

    2007-01-01

    Full Text Available AbstractWe present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high Heisenberg spins. We derive exact analytic expressions (in integral form for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail.

  13. Molecular dynamics simulations of freezing of water and salt solutions

    Czech Academy of Sciences Publication Activity Database

    Vrbka, Luboš; Jungwirth, Pavel

    2007-01-01

    Roč. 134, č. 1 (2007), s. 64-70 ISSN 0167-7322 R&D Projects: GA MŠk LC512; GA ČR(CZ) GD203/05/H001 Institutional research plan: CEZ:AV0Z40550506 Keywords : ice freezing * salt ions * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.982, year: 2007

  14. 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.

  15. Identification of potent inhibitors against snake venom metalloproteinase (SVMP) using molecular docking and molecular dynamics studies.

    Science.gov (United States)

    Chinnasamy, Sathishkumar; Chinnasamy, Selvakkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan

    2015-01-01

    Snake venom metalloproteinase (SVMP) (Echis coloratus (Carpet viper) is a multifunctional enzyme that is involved in producing several symptoms that follow a snakebite, such as severe local hemorrhage, nervous system effects and tissue necrosis. Because the three-dimensional (3D) structure of SVMP is not known, models were constructed, and the best model was selected based on its stereo-chemical quality. The stability of the modeled protein was analyzed through molecular dynamics (MD) simulation studies. Structure-based virtual screening was performed, and 15 potential molecules with the highest binding energies were selected. Further analysis was carried out with induced fit docking, Prime/MM-GBSA (ΔGBind calculations), quantum-polarized ligand docking, and density functional theory calculations. Further, the stability of the lead molecules in the SVMP-active site was examined using MD simulation. The results showed that the selected lead molecules were highly stable in the active site of SVMP. Hence, these molecules could potentially be selective inhibitors of SVMP. These lead molecules can be experimentally validated, and their backbone structural scaffold could serve as building blocks in designing drug-like molecules for snake antivenom.

  16. Progress on RNAi-based molecular medicines

    Directory of Open Access Journals (Sweden)

    Chen J

    2012-07-01

    Full Text Available Jing Chen, Jianping XieInstitute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, ChinaAbstract: RNA interference (RNAi is a promising strategy to suppress the expression of disease-relevant genes and induce post-transcriptional gene silencing. Their simplicity and stability endow RNAi with great advantages in molecular medicine. Several RNAi-based drugs are in various stages of clinical investigation. This review summarizes the ongoing research endeavors on RNAi in molecular medicine, delivery systems for RNAi-based drugs, and a compendium of RNAi drugs in different stages of clinical development. Of special interest are RNAi-based drug target discovery and validation, delivery systems for RNAi-based drugs, such as nanoparticles, rabies virus protein-based vehicles, and bacteriophages for RNA packaging.Keywords: RNA interference, delivery systems, liposome, nanoparticle, molecular medicines

  17. Molecular dynamics simulations of solutions at constant chemical potential

    Science.gov (United States)

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

    2015-04-01

    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 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.

  18. 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

  19. 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......In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...

  20. Molecular dynamics algorithms for path integrals at constant pressure

    Science.gov (United States)

    Martyna, Glenn J.; Hughes, Adam; Tuckerman, Mark E.

    1999-02-01

    Extended system path integral molecular dynamics algorithms have been developed that can generate efficiently averages in the quantum mechanical canonical ensemble [M. E. Tuckerman, B. J. Berne, G. J. Martyna, and M. L. Klein, J. Chem. Phys. 99, 2796 (1993)]. Here, the corresponding extended system path integral molecular dynamics algorithms appropriate to the quantum mechanical isothermal-isobaric ensembles with isotropic-only and full system cell fluctuations are presented. The former ensemble is employed to study fluid systems which do not support shear modes while the latter is employed to study solid systems. The algorithms are constructed by deriving appropriate dynamical equations of motions and developing reversible multiple time step algorithms to integrate the equations numerically. Effective parallelization schemes for distributed memory computers are presented. The new numerical methods are tested on model (a particle in a periodic potential) and realistic (liquid and solid para-hydrogen and liquid butane) systems. In addition, the methodology is extended to treat the path integral centroid dynamics scheme, [J. Cao and G. A. Voth, J. Chem. Phys. 99, 10070 (1993)], a novel method which is capable of generating semiclassical approximations to quantum mechanical time correlation functions.

  1. Large scale molecular dynamics simulations of nuclear pasta

    Science.gov (United States)

    Horowitz, C. J.; Berry, D.; Briggs, C.; Chapman, M.; Clark, E.; Schneider, A.

    2014-09-01

    We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. Supported in parts by DOE Grants No. DE-FG02-87ER40365 (Indiana University) and No. DE-SC0008808 (NUCLEI SciDAC Collaboration).

  2. 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.

  3. The dynamics of molecular evolution over 60,000 generations.

    Science.gov (United States)

    Good, Benjamin H; McDonald, Michael J; Barrick, Jeffrey E; Lenski, Richard E; Desai, Michael M

    2017-11-02

    The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population. Interactions between ecological and evolutionary processes play an important role, as long-term quasi-stable coexistence arises spontaneously in most populations, and evolution continues within each clade. We also present evidence that the targets of natural selection change over time, as epistasis and historical contingency alter the strength of selection on different genes. Together, these results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed.

  4. Molecular dynamics of polarizable point dipole models for molten NaI. Comparison with first principles simulations

    Directory of Open Access Journals (Sweden)

    Trullàs J.

    2011-05-01

    Full Text Available Molecular dynamics simulations of molten NaI at 995 K have been carried out using polarizable ion models based on rigid ion pair potentials to which the anion induced dipole polarization is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and deformation short-range damping interactions that oppose the electrically induced dipole moments. The structure and self-diffusion results are compared with those obtained by Galamba and Costa Cabral using first principles Hellmann-Feynman molecular dynamics simulations and using classical molecular dynamics of a shell model which allows only the iodide polarization

  5. 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.

  6. 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.

  7. Liquid-vapor coexistence by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Baranyai, Andras; Cummings, Peter T.

    2000-01-01

    We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics

  8. 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.

  9. Molecular dynamics of coalescence and collisions of silver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Guevara-Chapa, Enrique, E-mail: enrique_guevara@hotmail.com [Universidad Autónoma de Nuevo León, Facultad de Ciencias Físico Matemáticas (Mexico); Mejía-Rosales, Sergio [Universidad Autónoma de Nuevo León, Center for Innovation, Research and Development in Engineering and Technology (CIIDIT), and CICFIM-Facultad de Ciencias Físico Matemáticas (Mexico)

    2014-12-15

    We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy.

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

    International Nuclear Information System (INIS)

    Lerbret, A.; Affouard, F.; Bordat, P.; Hedoux, A.; Guinet, Y.; Descamps, M.

    2008-01-01

    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

  11. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    International Nuclear Information System (INIS)

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

    2015-01-01

    The dynamic properties of liquid B 2 O 3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B 2 O 3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  12. A Hadoop-based Molecular Docking System

    Science.gov (United States)

    Dong, Yueli; Guo, Quan; Sun, Bin

    2017-10-01

    Molecular docking always faces the challenge of managing tens of TB datasets. It is necessary to improve the efficiency of the storage and docking. We proposed the molecular docking platform based on Hadoop for virtual screening, it provides the preprocessing of ligand datasets and the analysis function of the docking results. A molecular cloud database that supports mass data management is constructed. Through this platform, the docking time is reduced, the data storage is efficient, and the management of the ligand datasets is convenient.

  13. Non-Watson-Crick base pairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E

    Czech Academy of Sciences Publication Activity Database

    Réblová, K.; Špačková, Naďa; Koča, J.; Leontis, N. B.; Šponer, Jiří

    2003-01-01

    Roč. 20, č. 6 (2003), s. 986 ISSN 0739-1102. [Albany 2003: Conversation 13. 17.06.2003-21.06.2003, Albany] Institutional research plan: CEZ:AV0Z5004920 Keywords : non- Watson -Crick base pairs * Loop E * RNA Subject RIV: BO - Biophysics

  14. Molecular origin of limiting shear stress of elastohydrodynamic lubrication oil film studied by molecular dynamics

    Science.gov (United States)

    Washizu, Hitoshi; Ohmori, Toshihide; Suzuki, Atsushi

    2017-06-01

    All-atom molecular dynamics simulations of an elastohydrodynamic lubrication oil film are performed to study the effect of pressure. Fluid molecules of n-hexane are confined between two solid plates under a constant normal force of 0.1-8.0 GPa. Traction simulations are performed by applying relative sliding motion to the solid plates. A transition in the traction behavior is observed around 0.5-2.0 GPa, which corresponds to the viscoelastic region to the plastic-elastic region, which are experimentally observed. This phase transition is related to the suppression of the fluctuation in molecular motion.

  15. 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

  16. Accelerated molecular dynamics methods: introduction and recent developments

    International Nuclear Information System (INIS)

    Uberuaga, Blas Pedro; Voter, Arthur F.; Perez, Danny; Shim, Y.; Amar, J.G.

    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. Ultrathin inorganic molecular nanowire based on polyoxometalates

    Science.gov (United States)

    Zhang, Zhenxin; Murayama, Toru; Sadakane, Masahiro; Ariga, Hiroko; Yasuda, Nobuhiro; Sakaguchi, Norihito; Asakura, Kiyotaka; Ueda, Wataru

    2015-01-01

    The development of metal oxide-based molecular wires is important for fundamental research and potential practical applications. However, examples of these materials are rare. Here we report an all-inorganic transition metal oxide molecular wire prepared by disassembly of larger crystals. The wires are comprised of molybdenum(VI) with either tellurium(IV) or selenium(IV): {(NH4)2[XMo6O21]}n (X=tellurium(IV) or selenium(IV)). The ultrathin molecular nanowires with widths of 1.2 nm grow to micrometre-scale crystals and are characterized by single-crystal X-ray analysis, Rietveld analysis, scanning electron microscopy, X-ray photoelectron spectroscopy, ultraviolet–visible spectroscopy, thermal analysis and elemental analysis. The crystals can be disassembled into individual molecular wires through cation exchange and subsequent ultrasound treatment, as visualized by atomic force microscopy and transmission electron microscopy. The ultrathin molecular wire-based material exhibits high activity as an acid catalyst, and the band gap of the molecular wire-based crystal is tunable by heat treatment. PMID:26139011

  18. 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.

  19. Seeking new mutation clues from Bacillus licheniformis amylase by molecular dynamics simulations

    Science.gov (United States)

    Lu, Tao

    2009-07-01

    Amylase is one of the most important industrial enzymes in the world. Researchers have been searching for a highly thermal stable mutant for many years, but most focus on point mutations of one or few nitrogenous bases. According to this molecular dynamic simulation of amylase from Bacillus licheniformis (BLA), the deletion of some nitrogenous bases would be more efficacious than point mutations. The simulation reveals strong fluctuation of the BLA structure at optimum temperature. The fluctuation of the outer domains of BLA is stronger than that of the core domain. Molecular simulation provides a clue to design thermal stable amylases through deletion mutations in the outer domain.

  20. An improved version of the Green's function molecular dynamics method

    Science.gov (United States)

    Kong, Ling Ti; Denniston, Colin; Müser, Martin H.

    2011-02-01

    This work presents an improved version of the Green's function molecular dynamics method (Kong et al., 2009; Campañá and Müser, 2004 [1,2]), which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only atoms near the surface. In the previous implementation, the effective elastic coefficients measured at the Γ-point were altered to reduce finite size effects: their eigenvalues corresponding to the acoustic modes were set to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. It turns out that a violation of the acoustic sum rule for the effective elastic coefficients at Γ (Kong, 2010 [3]) was responsible for this behavior. In the new version, the acoustic sum rule is enforced by adopting an iterative procedure, which is found to be physically more meaningful than the previous one. In addition, the new algorithm allows one to treat lattices with bases and the Green's function slab is no longer confined to one layer. New version program summaryProgram title: FixGFC/FixGFMD v1.12 Catalogue identifier: AECW_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_1.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.: 206 436 No. of bytes in distributed program, including test data, etc.: 4 314 850 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Yes. Code has been parallelized using MPI directives. RAM: Depends on the problem Classification: 7.7 External routines: LAMMPS ( http://lammps.sandia.gov/), MPI ( http

  1. Molecular dynamics studies of protein folding and aggregation

    Science.gov (United States)

    Ding, Feng

    This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism

  2. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations

    NARCIS (Netherlands)

    Risselada, H. Jelger; Marrink, Siewert J.

    2009-01-01

    The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high

  3. Reaction Ensemble Molecular Dynamics: Direct Simulation of the Dynamic Equilibrium Properties of Chemically Reacting Mixtures

    Czech Academy of Sciences Publication Activity Database

    Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.

    2004-01-01

    Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004

  4. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

    NARCIS (Netherlands)

    Marrink, SJ; Mark, AE

    2003-01-01

    Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at

  5. 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.)

  6. Physical properties of Cu nanoparticles: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Kart, H.H., E-mail: hkart@pau.edu.tr [Department of Physics, Pamukkale University, Kınıklı Campus, 20017 Denizli (Turkey); Yildirim, H.; Ozdemir Kart, S. [Department of Physics, Pamukkale University, Kınıklı Campus, 20017 Denizli (Turkey); Çağin, T. [Department of Materials Science and Engineering, Texas A and M University, College Station, TX 77845-3003 (United States); Department of Chemical Engineering, Texas A and M University, College Station, TX 77845-3122 (United States)

    2014-09-15

    Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index.

  7. Physical properties of Cu nanoparticles: A molecular dynamics study

    International Nuclear Information System (INIS)

    Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.

    2014-01-01

    Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index

  8. Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

    International Nuclear Information System (INIS)

    Dellerue, Serge

    2000-01-01

    Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

  9. Gas Sensors Based on Molecular Imprinting Technology.

    Science.gov (United States)

    Zhang, Yumin; Zhang, Jin; Liu, Qingju

    2017-07-04

    Molecular imprinting technology (MIT); often described as a method of designing a material to remember a target molecular structure (template); is a technique for the creation of molecularly imprinted polymers (MIPs) with custom-made binding sites complementary to the target molecules in shape; size and functional groups. MIT has been successfully applied to analyze; separate and detect macromolecular organic compounds. Furthermore; it has been increasingly applied in assays of biological macromolecules. Owing to its unique features of structure specificity; predictability; recognition and universal application; there has been exploration of the possible application of MIPs in the field of highly selective gas sensors. In this present study; we outline the recent advances in gas sensors based on MIT; classify and introduce the existing molecularly imprinted gas sensors; summarize their advantages and disadvantages; and analyze further research directions.

  10. Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

    2015-05-01

    Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

  11. Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping

    Science.gov (United States)

    Lu, Jianfeng; Zhou, Zhennan

    2018-02-01

    To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limit, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer and thus connects the surface hopping approach to the mean-field path-integral molecular dynamics. A multiscale integrator for the infinite swapping limit is also proposed to enable efficient sampling based on the limiting dynamics. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path-integral molecular dynamics with surface hopping.

  12. Imaging molecular structure and dynamics using laser driven recollisions

    International Nuclear Information System (INIS)

    Marangos, J.P.; Baker, S.; Torres, R.; Kajumba, N.; Haworth, C.; Robinson, J.; Tisch, J.W.G.; Lein, M.; Chirila, C.; Vozzi, C.

    2006-01-01

    Complete test of publication follows. Laser driven electron recollision provides a unique tool for measuring the structure and dynamics of matter. We illustrate this with experiments that use HHG to measure molecular structure with sub-Angstrom spatial and sub-femtosecond temporal resolution. Our recent work has looked in particular at the signal from high order harmonic generation which contains rich information about the structure and intra-molecular dynamics of small molecules. This we will illustrate by two types of experiment; (a) measurements of HHG from aligned molecular samples to observe two-centre recombination interference and electronic structure dependence of the angle dependent yield, (b) reconstruction of intra-molecular proton dynamics from the spectral dependence of the HHG using the intrinsic chirp of recolliding electrons. We experimentally investigate the process of intramolecular quantum interference in high-order harmonic generation in impulsively aligned CO 2 molecules. The recombination interference effect is clearly seen through the order dependence of the harmonic yield in an aligned sample. This confirms that the effective de Broglie wavelength of the returning electron wave is not significantly altered by acceleration in the Coulomb field of the molecular ion. For the first time, to our knowledge, we demonstrate that such interference effects can be effectively controlled by changing the ellipticity of the driving laser field. Here we also report the results of angular dependence measurements of high order harmonics (17 tt h - 27 th ) from impulsively aligned organic molecules: Acetylene, Ethylene, and Allene. Since these molecules have a relatively low I p an appropriately short pulse is required to produce as many harmonic orders as possible. This was provided by the ∼ 10 fs beam line of the ASTRA laser at Rutherford Appleton Laboratory whilst a somewhat longer pulse, properly forwarded with respect to the driving pulse, induced the

  13. Thermal Transport in Carbon Nanotubes using Molecular Dynamics

    Science.gov (United States)

    Moore, Andrew; Khatun, Mahfuza

    2011-10-01

    We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.

  14. 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...... details of lactose interaction with the lumen of LacY during its permeation. Lactose induces a widening of the narrowest parts of the channel during permeation, the widening being largest within the periplasmic half-channel. During permeation, the water-filled lumen of LacY only partially hydrates lactose......, 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...

  15. Spotting the difference in molecular dynamics simulations of biomolecules

    Science.gov (United States)

    Sakuraba, Shun; Kono, Hidetoshi

    2016-08-01

    Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories.

  16. 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.

  17. Thermal conductivity of ionic systems from equilibrium molecular dynamics.

    Science.gov (United States)

    Salanne, Mathieu; Marrocchelli, Dario; Merlet, Céline; Ohtori, Norikazu; Madden, Paul A

    2011-03-16

    Thermal conductivities of ionic compounds (NaCl, MgO, Mg(2)SiO(4)) are calculated from equilibrium molecular dynamics simulations using the Green-Kubo method. Transferable interaction potentials including many-body polarization effects are employed. Various physical conditions (solid and liquid states, high temperatures, high pressures) relevant to the study of the heat transport in the Earth's mantle are investigated, for which experimental measures are very challenging. By introducing a frequency-dependent thermal conductivity, we show that important coupled thermoelectric effects occur in the energy conduction mechanism in the case of liquid systems.

  18. Molecular dynamics study on microstructure of near grain boundary

    CERN Document Server

    Wang, J Y; Rifkin, J; Li, D X

    2001-01-01

    The molecular dynamics method is used to simulate a uniaxial tensile deformation of 3.8nm nano-NiAl alloy with curved amorphous-like interfaces at 0K. Plastic deformation behaviour is studied by examining the strain-stress relationship and the microstructural evolution characteristic. Atomic level analysis showed that the micro-strain is essentially heterogeneous in simulated nano-phase samples. The plastic deformation is not only attributed to the plasticity of interfaces, but also accompanied with the plastic shear strain mechanism inside lattice distortion regions and grains.

  19. Ti and Zr surfaces studied by molecular dynamics

    International Nuclear Information System (INIS)

    Pascuet, Maria I.; Passianot, Roberto C.; Monti, Ana M.

    2003-01-01

    The interaction between point defects technique and the (0001), (1-210), (10-10) surfaces in Ti and Zr is studied by the molecular dynamics technique. Both of metals are in the hexagonal structure and within a temperature range of 100 to 900 K. The atomic interactions are modeled by EAM-type many-body potentials, that were used previously in static simulations. New migration mechanisms are unraveled and others are verified with respect to those already proposed in the static studies. Also included is an analysis of the vacancy stability in the sub-surface layers of the prismatic surfaces. (author)

  20. The density functional theory and the charged fluid molecular dynamics

    International Nuclear Information System (INIS)

    Hansen, J.P.; Zerah, G.

    1993-01-01

    Car and Parrinello had the idea of combining the density functional theory (Hohenberg, Kohn and Sham) to the 'molecular dynamics' numerical modelling method, in order to simulate metallic or co-valent solids and liquids from the first principles. The objective of this paper is to present a simplified version of this method ab initio, applicable to classical and quantal charged systems. The method is illustrated with recent results on charged colloidal suspensions and highly correlated electron-proton plasmas. 1 fig., 21 refs

  1. Dynamical evolution of supernova remnants breaking through molecular clouds

    OpenAIRE

    Cho, Wankee; Kim, Jongsoo; Koo, Bon-Chul

    2015-01-01

    We carry out three-dimensional hydrodynamic simulations of the supernova remnants (SNRs) produced inside molecular clouds (MCs) near their surface using the HLL code (Harten et al. 1983). We explore the dynamical evolution and the X-ray morphology of SNRs after breaking through the MC surface for ranges of the explosion depths below the surface and the density ratios of the clouds to the intercloud media (ICM). We find that if an SNR breaks out through an MC surface in its Sedov stage, the ou...

  2. Porting of serial molecular dynamics code on MIMD platforms

    International Nuclear Information System (INIS)

    Celino, M.

    1995-05-01

    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 Mechanics theory. Furthermore, techniques and parallelization strategies utilized and the MD parallel code are described in detail. Benchmarks on several MIMD platforms (IBM SP1 and SP2, Cray T3D, Cluster of workstations) allow performances evaluation of the code versus the different characteristics of the parallel platforms

  3. Hydrogen diffusion in liquid aluminum from ab initio molecular dynamics

    Science.gov (United States)

    Jakse, N.; Pasturel, A.

    2014-05-01

    Ab initio molecular dynamics simulations are used to describe the diffusion of hydrogen in liquid aluminum at different temperatures. Quasi-instantaneous jumps separating periods of localized vibrations around a mean position are found to characterize the hydrogen motion at the microscopic scale. The hydrogen motion is furthermore analyzed using the van Hove function. We highlight a non-Fickian behavior for the hydrogen diffusion due to a large spatial distribution of hydrogen jumps. We show that a generalized continuous time random walk (CTRW) model describes the experimental diffusion coefficients in a satisfactory manner. Finally, the impact of impurities and alloying elements on hydrogen diffusion in aluminum is discussed.

  4. 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.

  5. 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

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

    International Nuclear Information System (INIS)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-01-01

    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

  7. Haptization of molecular dynamics simulation with thermal display

    International Nuclear Information System (INIS)

    Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki

    2010-01-01

    Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)

  8. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

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

    1996-01-01

    Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111......)7X7 and Si(100)2X1. Strong phonon-assisted sticking was observed for gases at 300 K and surface temperatures between 550 K and 1050 K. The absolute values as well as the temperature variation of the adsorption and desorption rates show surprisingly little isotope effect, and they differ only little...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective...

  9. Deformation mechanisms in nanotwinned copper by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Zhao, Xing; Lu, Cheng; Tieu, Anh Kiet; Pei, Linqing; Zhang, Liang; Su, Lihong; Zhan, Lihua

    2017-01-01

    Nanotwinned materials exhibit simultaneous ultrahigh strength and high ductility which is attributed to the interactions between dislocations and twin boundaries but the specific deformation mechanisms are rarely seen in experiments at the atomic level. Here we use large scale molecular dynamics simulations to explore this intricate interplay during the plastic deformation of nanotwinned Cu. We demonstrate that the dominant deformation mechanism transits dynamically from slip transfer to twin boundary migration to slip-twin interactions as the twin boundary orientation changes from horizontal to slant, and then to a vertical direction. Building on the fundamental physics of dislocation processes from computer simulations and combining the available experimental investigations, we unravel the underlying deformation mechanisms for nanotwinned Cu, incorporating all three distinct dislocation processes. Our results give insights into systematically engineering the nanoscale twins to fabricate nanotwinned metals or alloys that have high strength and considerable ductility.

  10. 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.

  11. 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...

  12. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    Science.gov (United States)

    Shekhar, Adarsh

    Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

  13. Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann

    Energy Technology Data Exchange (ETDEWEB)

    Melenev, Petr, E-mail: melenev@icmm.ru [Ural Federal University, 4, Turgeneva str., 620000 Ekaterinburg (Russian Federation); Institute of Continuous Media Mechanics, 1, Koroleva str., 614013 Perm (Russian Federation)

    2017-06-01

    Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces. - Highlights: • The combination of molecular dynamics and lattice Boltzmann method is utilized for the reveal of the role of hydrodynamic interaction in rotational dynamics of colloid particles. • The verification of the model parameters is done based on the comparison with the results of Langevin dynamics. • For the task of free rotational diffusion of the pair of colloid particles the influence of the hydrodynamic interactions on the relaxation time is examined in the case of nonmagnetic particles and at the presence of weak dipolar interaction.

  14. Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann

    International Nuclear Information System (INIS)

    Melenev, Petr

    2017-01-01

    Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces. - Highlights: • The combination of molecular dynamics and lattice Boltzmann method is utilized for the reveal of the role of hydrodynamic interaction in rotational dynamics of colloid particles. • The verification of the model parameters is done based on the comparison with the results of Langevin dynamics. • For the task of free rotational diffusion of the pair of colloid particles the influence of the hydrodynamic interactions on the relaxation time is examined in the case of nonmagnetic particles and at the presence of weak dipolar interaction.

  15. Fluorescence based molecular in vivo imaging

    International Nuclear Information System (INIS)

    Ebert, Bernd

    2008-01-01

    Molecular imaging represents a modern research area that allows the in vivo study of molecular biological process kinetics using appropriate probes and visualization methods. This methodology may be defined- apart from the contrast media injection - as non-abrasive. In order to reach an in vivo molecular process imaging as accurate as possible the effects of the used probes on the biological should not be too large. The contrast media as important part of the molecular imaging can significantly contribute to the understanding of molecular processes and to the development of tailored diagnostics and therapy. Since more than 15 years PTB is developing optic imaging systems that may be used for fluorescence based visualization of tissue phantoms, small animal models and the localization of tumors and their predecessors, and for the early recognition of inflammatory processes in clinical trials. Cellular changes occur during many diseases, thus the molecular imaging might be of importance for the early diagnosis of chronic inflammatory diseases. Fluorescent dyes can be used as unspecific or also as specific contrast media, which allow enhanced detection sensitivity

  16. Molecular phylogeny of Ranunculaceae based on internal ...

    African Journals Online (AJOL)

    The botanical family Ranunculaceae contains important medicinal plants. To obtain new evolutionary evidence regarding the systematic classification of Ranunculaceae plants, we used molecular phylogenies to test relationships based on the internal transcribed spacer region. The results of phylogenetic analysis of 92 ...

  17. Molecular phylogeny of Ranunculaceae based on internal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... The botanical family Ranunculaceae contains important medicinal plants. To obtain new evolutionary evidence regarding the systematic classification of Ranunculaceae plants, we used molecular phylogenies to test relationships based on the internal transcribed spacer region. The results of phylogenetic ...

  18. Environmental Phosphorus Recovery Based on Molecular Bioscavengers

    DEFF Research Database (Denmark)

    Gruber, Mathias Felix

    -scale quantum calculations to macro-scale fluid simulations, are employed to hint at the potential of a recovery technology based on molecular bioscavengers. As a first approach, data mining is used to obtain statistical information about how proteins in nature interact with phosphate groups, thereby revealing...

  19. Measurements based dynamic climate observer

    Energy Technology Data Exchange (ETDEWEB)

    Chaabene, Maher [The High Institute of Technological Studies (ISET), Sfax (Tunisia); Unite de Commande de Machines et Reseaux de Puissance CMERP-ENIS, Tunisia, Rte Mahdia Km 2, BP88A, ElBustan 3099 Sfax (Tunisia)

    2008-09-15

    This paper introduces a dynamic prediction of solar radiation and ambient temperature. Medium term prediction is based on climatic parameters behaviours during the day before and on time distribution models. As for short term prediction, it is ensured by an ARMA predictor using Kalman filter. Herein, we describe our method and present prediction results. Validation is based on measures taken during the year 2005 in the north of Tunisia. The work effectiveness is illustrated by a short term and medium term prediction of the electric energy produced by a 1 KWp photovoltaic panel (PVP) installed at the Energy and Thermal Research Centre (CRTEn) in the north of Tunisia. Since our work delivers accurate climatic parameters prediction, the obtained results can be easily adapted to predict any other solar conversion system output. (author)

  20. Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases.

    Science.gov (United States)

    Moffett, Alexander S; Bender, Kyle W; Huber, Steven C; Shukla, Diwakar

    2017-07-28

    The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Static and dynamic properties of grafted ring polymer: Molecular dynamics simulation

    Science.gov (United States)

    He, Su-Zhen; Holger, Merlitz; Su, Chan-Fei; Wu, Chen-Xu

    2013-01-01

    The static and dynamic properties of a system of end-grafted flexible ring polymer chains grafted to a flat substrate and exposed to a good solvent are studied by using a molecular dynamics method. The monomers are described by a coarse-grained bead-spring model. Varying the grafting density ρ and the degree of polymerization or chain length N, we obtain the density profiles of monomers, study the structural properties of the chain (radius of gyration, bond orientational parameters, etc.), and also present the dynamic characteristics such as chain energy and bond force. Compared with a linear polymer brush, the ring polymer brush exhibits different static and dynamic properties for moderate or short chain length, while it behaves like linear polymer brush in the regime of long chain length.

  2. Simulation of a lipid monolayer using molecular dynamics

    Science.gov (United States)

    Kox, A. J.; Michels, J. P. J.; Wiegel, F. W.

    1980-09-01

    Numerical simulation is often a useful tool f or investigating the behaviour of complex systems with many degrees of freedom. Of the two major methods in this field, the Monte Carlo method and the molecular dynamics method, only the first has been applied to realistic models of lipid monolayers1-5. The term lipid monolayer is used here to describe a class of systems consisting of chain molecules on a liquid substrate, the characteristic properties of which can be summarized as follows. (1) The constituent molecules are amphipathic, that is they consist of a hydrophilic (polar) head group and one or more hydrophobic hydrocarbon chains. (2) Due to the amphipathic character of the molecules, the head groups are constrained to the plane of the substrate, whereas the tails are directed outwards from this plane. (3) The collective properties of the molecules are determined by their short-range repulsive and long-range attractive interactions and by the steric repulsion of the tails. We now present what we believe to be the first molecular dynamics simulation of a realistic model of a lipid monolayer. The model system, which has all three properties enumerated above, shows a first order phase transition from an ordered fluid-like state to a disordered, gas-like state.

  3. Molecular dynamics simulations through GPU video games technologies.

    Science.gov (United States)

    Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

    Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations.

  4. Sex speeds adaptation by altering the dynamics of molecular evolution.

    Science.gov (United States)

    McDonald, Michael J; Rice, Daniel P; Desai, Michael M

    2016-03-10

    Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.

  5. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.

    Science.gov (United States)

    Okumura, Hisashi

    2008-09-28

    Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo simulations. The partial multicanonical simulation samples a wide range of a part of the potential-energy terms, which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm. Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation. The partial multicanonical, multicanonical, and canonical molecular dynamics algorithms were applied to an alanine dipeptide in explicit water solvent. The canonical simulation sampled the states of P(II), C(5), alpha(R), and alpha(P). The multicanonical simulation covered the alpha(L) state as well as these states. The partial multicanonical simulation also sampled the C(7) (ax) state in addition to the states that were sampled by the multicanonical simulation. In the partial multicanonical simulation, furthermore, backbone dihedral angles phi and psi rotated more frequently than those in the multicanonical and canonical simulations. These results mean that the partial multicanonical algorithm has a higher sampling efficiency than the multicanonical and canonical algorithms.

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

    Science.gov (United States)

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

    2013-08-13

    Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules. To improve the stability and accuracy of coarse-grained molecular dynamics simulations, we propose two approaches. The first makes use of improved forms for the angle potentials: the restricted bending (ReB) potential prevents torsion angles from visiting unstable or unphysical configurations and the combined bending-torsion (CBT) potential smoothly flattens the interactions when such configurations are sampled. In the second approach, dummy-assisted dihedral (DAD), the torsion potential is applied differently: instead of acting directly on the beads, it acts on virtual beads, bound to the real ones. For simple geometrical reasons, the unstable region is excluded from the accessible conformational space. The benefits of the new approaches are demonstrated in simulations of polyethylene glycol (PEG), polystyrene (PS), and polypeptide molecules described by the MARTINI coarse-grained force field. The new potentials are implemented in an in-house version of the Gromacs package, publicly available.

  7. Animated molecular dynamics simulations of hydrated Cesium-smectite interlayers

    International Nuclear Information System (INIS)

    Sutton, Rebecca; Sposito, Garrison

    2002-01-01

    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 analytical methods. Cs+ could be seen to jump from one attracting location near a layer charge site to the next, and 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. The extent of this sharing interaction in the interlayer was determined by the smectite charge distribution, but increased with increasing water content. Water molecules also could be seen to interact directly with the mineral surface, entering its ditrigonal cavities to approach attracting charge sites. The frequency and duration of cavity habitation increased with increasing water content and tetrahedral charge, and was inhibited the more perpendicular was the structural hydroxyl orientation relative to the mineral surface. 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

  8. A new parallel molecular dynamics algorithm for organic systems

    International Nuclear Information System (INIS)

    Plimpton, S.; Hendrickson, B.; Heffelfinger, G.

    1993-01-01

    A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed

  9. 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.

  10. 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.

  11. Kinetic distance and kinetic maps from molecular dynamics simulation.

    Science.gov (United States)

    Noé, Frank; Clementi, Cecilia

    2015-10-13

    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 metric 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 pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets.

  12. 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.

    2018-01-01

    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

  13. Graphene-based nanoprobes for molecular diagnostics.

    Science.gov (United States)

    Chen, Shixing; Li, Fuwu; Fan, Chunhai; Song, Shiping

    2015-10-07

    In recent years, graphene has received widespread attention owing to its extraordinary electrical, chemical, optical, mechanical and structural properties. Lately, considerable interest has been focused on exploring the potential applications of graphene in life sciences, particularly in disease-related molecular diagnostics. In particular, the coupling of functional molecules with graphene as a nanoprobe offers an excellent platform to realize the detection of biomarkers, such as nucleic acids, proteins and other bioactive molecules, with high performance. This article reviews emerging graphene-based nanoprobes in electrical, optical and other assay methods and their application in various strategies of molecular diagnostics. In particular, this review focuses on the construction of graphene-based nanoprobes and their special advantages for the detection of various bioactive molecules. Properties of graphene-based materials and their functionalization are also comprehensively discussed in view of the development of nanoprobes. Finally, future challenges and perspectives of graphene-based nanoprobes are discussed.

  14. Molecular dynamics and binary collision modeling of the primary damage state of collision cascades

    DEFF Research Database (Denmark)

    Heinisch, H.L.; Singh, B.N.

    1992-01-01

    Quantitative information on defect production in cascades in copper obtained from recent molecular dynamics simulations is compared to defect production information determined earlier with a model based on the binary collision approximation (BCA). The total numbers of residual defects, the fracti...... that is practical for simulating much higher energies and longer times than MD alone can achieve. The extraction of collisional phase information from MD simulations and the correspondence of MD and BCA versions of the collisional phase is demonstrated at low energy.......Quantitative information on defect production in cascades in copper obtained from recent molecular dynamics simulations is compared to defect production information determined earlier with a model based on the binary collision approximation (BCA). The total numbers of residual defects...

  15. Molecular dynamics study of the ternary Cu50Ti25Zr25 bulk glass forming alloy

    Directory of Open Access Journals (Sweden)

    Celtek M.

    2011-05-01

    Full Text Available The structure and thermodynamic properties of a ternary Cu50Ti25Zr25 metallic glass forming alloy in solid-liquid to glass phases were studied using molecular dynamics (MD method based on tight-binding (TB potentials. An atomic description of the melting, glass formation and crystallization process has been analyzed using different heating and cooling rates. The computed Glass Forming Ability (GFA parameters are in good agreement with experimental data. The structure analysis of the Cu50Ti25Zr25 based on molecular dynamics simulation will be also presented and compared with available MD results. We have also discussed the crystallization transition with two different interatomic potentials used in this work

  16. Nucleation of Salt Crystals in Clay Minerals: Molecular Dynamics Simulation.

    Science.gov (United States)

    Dashtian, Hassan; Wang, Haimeng; Sahimi, Muhammad

    2017-07-20

    Nucleation of salt crystals in confined media occurs in many processes of high importance, such as injection of CO 2 in geological formations for its sequestration. In particular, salt precipitation in clays, a main component of sedimentary rock, is an important phenomenon. The crystals precipitate on the pores' surface, modify the pore space morphology, and reduce its flow and transport properties. Despite numerous efforts to understand the mechanisms of nucleation of salt crystals in confined media, the effect of the clay's chemistry on the growth, distribution, and properties of the crystals is not well understood. We report the results of extensive molecular dynamics simulation of nucleation and growth of NaCl crystals in a clay pore using molecular models of two types of clay minerals, Na-montmorillonite and kaolinite. Clear evidence is presented for the nucleation of the salt crystals that indicates that the molecular structure of clay minerals affects their spatial distribution, although the nucleation mechanism is the same in both types of clays.

  17. Combined multi-pharmacophore, molecular docking and molecular dynamic study for discovery of promising MTH1 inhibitors

    Science.gov (United States)

    Dai, Duoqian; Zhou, Lu; Zhu, Xiaohong; You, Rong; Zhong, Liangliang

    2017-06-01

    MutT homolog 1 (MTH1), a nudix phosphohydrolase enzyme participates in the process of repairing of DNA damage by hydrolyzing oxidized deoxy-ribonucleoside triphosphate in cancer cells, is regarded as a potential target for anticancer therapy. In order to seek for promising inhibitor of MTH1, structured-based pharmacophore and 3D-QSAR pharmacophore hypotheses combine with the ADMET analysis and Lipinski's rule of five were used for screening the public molecules libraries (Asinex, Ibscreen and Natural). Then molecular docking studies were performed on screened hits via various docking programs (Glide SP, GOLD and Glide XP), five molecules with three scaffolds were picked out as potential inhibitors against MTH1. Eventually, 20 ns molecular dynamics simulation was implemented on the potential inhibitors. The RMSD (Root Mean Square Deviation) values were used to illustrate bind stability between potential molecules and MTH1. Therefore, the five hits may be considered as promising MTH1 inhibitors by all above studies.

  18. Molecular Docking and Molecular Dynamics Simulation studies of DHFR inhibitors in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Prachi Bhole

    2017-10-01

    Full Text Available Malaria, caused by Plasmodium falciparum is a very common disease that causes 2.5 million deaths worldwide. This makes designing of lead molecules for malaria very exigent. DHFR has been known to be one of the major targets of antimalarial drug therapy which functions as a fundamental cofactor in the synthesis of histidine and methionine as well as purine nucleotides. Inhibition of this DHFR blocks the reduction of Dihydrofolate (DHF to Tetrahydrofolate (THF and hence prevents the synthesis of DNA, resulting in death of Plasmodium falciparum. Pyrimethamine is a Diaminopyrimidine that inhibits pfDHFR (Plasmodium falciparum DHFR at a concentration that is 1000 times less than that required to inhibit the mammalian DHFR. Virtual screening is performed to find Pyrimethamine analogs from PubChem database. Docking studies are performed on DHFR (PDB ID: 3QGT with Pyrimethamine and its 193 derivatives and the differences in their binding modes are investigated. The binding score suggests 53 derivatives to be more potent than Pyrimethamine which has a score of -24.7 showing interaction with Ile14, Asp54 and Ile164. The compound with best binding score (-35 showed interaction with Ile14, Cys15, Asp54, Phe58, Ser108, Ser111, Ile164 and Tyr170. The compounds are screened based on hydrogen bonding, π-π interactions, halogen bonding and orientation within the binding site with high binding score using Maestro (v.11.0.014, Schrodinger. The best screened compound is selected for Molecular Dynamic Simulation analysis up to 20ns using Desmond (v.4.8, Schrodinger which represents a good starting point for further in vivo experimentation and can probably serve as an ideal lead compound for the treatment of Malaria.

  19. Action-Derived Molecular Dynamics in the Study of Rare Events

    Energy Technology Data Exchange (ETDEWEB)

    Passerone, Daniele; Parrinello, Michele

    2001-09-03

    We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions.

  20. Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics

    OpenAIRE

    Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele

    2003-01-01

    The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metady- namics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.

  1. Action-Derived Molecular Dynamics in the Study of Rare Events

    International Nuclear Information System (INIS)

    Passerone, Daniele; Parrinello, Michele

    2001-01-01

    We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions

  2. Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Federica Chiappori

    Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

  3. A nanoplasmonic switch based on molecular machines

    KAUST Repository

    Zheng, Yue Bing

    2009-06-01

    We aim to develop a molecular-machine-driven nanoplasmonic switch for its use in future nanophotonic integrated circuits (ICs) that have applications in optical communication, information processing, biological and chemical sensing. Experimental data show that an Au nanodisk array, coated with rotaxane molecular machines, switches its localized surface plasmon resonances (LSPR) reversibly when it is exposed to chemical oxidants and reductants. Conversely, bare Au nanodisks and disks coated with mechanically inert control compounds, do not display the same switching behavior. Along with calculations based on time-dependent density functional theory (TDDFT), these observations suggest that the nanoscale movements within surface-bound "molecular machines" can be used as the active components in plasmonic devices. ©2009 IEEE.

  4. Molecular Docking and Molecular Dynamics to Identify a Novel Human Immunodeficiency Virus Inhibitor from Alkaloids of Toddalia asiatica.

    Science.gov (United States)

    Priya, R; Sumitha, Rajendrarao; Doss, C George Priya; Rajasekaran, C; Babu, S; Seenivasan, R; Siva, R

    2015-10-01

    Acquired immunodeficiency syndrome caused by human immunodeficiency virus (HIV) is an immunosuppressive disease. Over the past decades, it has plagued human health due to the grave consequences in its harness. For this reason, anti-HIV agents are imperative, and the search for the same from natural resources would assure the safety. In this investigation we have performed molecular docking, molecular property prediction, drug-likeness score, and molecular dynamics (MD) simulation to develop a novel anti-HIV drug. We have screened 12 alkaloids from a medicinal plant Toddalia asiatica for its probabilistic binding with the active site of the HIV-1-reverse transcriptase (HIV-1-RT) domain (the major contributor to the onset of the disease). The docking results were evaluated based on free energies of binding (ΔG), and the results suggested toddanol, toddanone, and toddalenone to be potent inhibitors of HIV-1-RT. In addition, the alkaloids were subjected to molecular property prediction analysis. Toddanol and toddanone with more rotatable bonds were found to have a drug-likeness score of 0.23 and 0.11, respectively. These scores were comparable with the standard anti-HIV drug zidovudine with a model score 0.28. Finally, two characteristic protein-ligand complexes were exposed to MD simulation to determine the stability of the predicted conformations. The toddanol-RT complex showed higher stability and stronger H-bonds than toddanone-RT complex. Based on these observations, we firmly believe that the alkaloid toddanol could aid in efficient HIV-1 drug discovery. In the present study, the molecular docking and MD simulations are performed to explore the possible binding mode of HIV 1 RT with 12 alkaloids of T. asiatica. Molecular docking by AutoDock4 revealed three alkaloids toddanol, toddanone, and toddalenone with highest binding affinity towards HIV 1 RT. The drug likeness model score revealed a positive score for toddanol and toddanone which is comparable to the drug

  5. Molecular dynamics simulation of nanomaterials using an artificial neural net

    Science.gov (United States)

    Benedict, Mark; Maguire, John F.

    2004-11-01

    We report a method of conducting molecular dynamics (MD) simulations that uses an artificial neural net (ANN) to significantly increase computational speed. The technique enables dynamical simulation of hard objects with essentially arbitrarily complex geometry and is well suited to the simulation of granular matter over a wide range of densities. In hard systems, binary collisions are well defined and the ANN approach enables an efficient algorithm to determine the time to next collision with high accuracy. The method has been used to enable an MD study of an ensemble of 1800 hard, smooth, impenetrable equilateral triangles in a two-dimensional periodic space. At high packing fraction (0.6translational order but in which there is nearly perfect long-range orientational order. As the packing fraction decreases, the LCP undergoes a transition to a fluid state in which the long-range orientational correlation vanishes but short-range order is retained. Long-lived clusters, notably hexamers, are clearly apparent in the liquid phase and appear to be stabilized by a sort of internal “orientational” osmotic pressure. Insofar as can be inferred from our machine calculations, the transition between the LCP and the liquid occurs around ρ˜0.57 and appears to be second order. At low density, the hard-triangle system undergoes “chattering” collisions in which pairs of triangles collide and become associated, undergoing multiple collisions with each other before colliding with a third particle. The radial distribution function obtained from both molecular dynamics and Monte Carlo calculations shows a weak peak at low packing fraction.

  6. Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods.

    Science.gov (United States)

    Chergui, Majed; Collet, Eric

    2017-08-23

    We review the tremendous advances in ultrafast X-ray science, over the past 15 years, making the best use of new ultrashort X-ray sources including table-top or large-scale facilities. Different complementary X-ray-based techniques, including spectroscopy, scattering, and diffraction, are presented. The broad and expanding spectrum of these techniques in the ultrafast time domain is delivering new insight into the dynamics of molecular systems, of solutions, of solids, and of biosystems. Probing the time evolution of the electronic and structural degrees of freedom of these systems on the time scales of femtosecond to picoseconds delivers new insight into our understanding of dynamical matter.

  7. Tissue organization by cadherin adhesion molecules: dynamic molecular and cellular mechanisms of morphogenetic regulation

    Science.gov (United States)

    Niessen, Carien M.; Leckband, Deborah; Yap, Alpha S.

    2013-01-01

    This review addresses the cellular and molecular mechanisms of cadherin-based tissue morphogenesis. Tissue physiology is profoundly influenced by the distinctive organizations of cells in organs and tissues. In metazoa, adhesion receptors of the classical cadherin family play important roles in establishing and maintaining such tissue organization. Indeed, it is apparent that cadherins participate in a range of morphogenetic events that range from support of tissue integrity to dynamic cellular rearrangements. A comprehensive understanding of cadherin-based morphogenesis must then define the molecular and cellular mechanisms that support these distinct cadherin biologies. Here we focus on four key mechanistic elements: the molecular basis for adhesion through cadherin ectodomains; the regulation of cadherin expression at the cell surface; cooperation between cadherins and the actin cytoskeleton; and regulation by cell signaling. We discuss current progress and outline issues for further research in these fields. PMID:21527735

  8. Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

    International Nuclear Information System (INIS)

    White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-01-01

    Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantum mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement

  9. Temperature dependent conformation studies of Calmodulin Protein using Molecular Dynamics

    Science.gov (United States)

    Aneja, Sahil; Bhartiya, Vivek Kumar; Negi, Sunita

    2016-10-01

    Calmodulin (CaM) protein plays a very crucial role in the calcium signaling inside the eukaryotic cell structure [1, 2]. It can also bind to other proteins/targets and facilitate various activities inside the cell [3, 4]. Temperature dependent conformation changes in the CaM protein are studied with extensive molecular dynamics simulations. The quantitative comparison of simulation data with various forms of experimental results probing different aspects of the folding process can facilitate robust assessment of the accuracy of the calculations. It can also provide a detailed structural interpretation for the experimental observations as well as physical interpretation for theory behind different aspects of the experiment. Earlier these kinds of studies have been performed experimentally using fluorescence measurements as in [5]. The calcium bound form of CaM is observed to undergo a reversible conformation change in the range 295-301 K at calcium ion concentration 150 mM. The transition temperature was observed to depend on the calcium ion concentration of the protein. Leap-dynamics approach was used earlier to study the temperature dependent conformation change of CaM [6]. At 290 K, both the N- and C-lobes were stable, at 325 K, the C-lobe unfolds whereas at 360 both the lobes unfold [6]. In this work, we perform molecular dynamics simulations of 100 ns each for the temperatures 325 K and 375 K on the apo form of CaM, 3CLN and 1CFD. A remarkable dependence of the temperature is observed on the overall dynamics of both the forms of the protein as reported in our earlier study [7, 8]. 1CFD shows a much flexible linker as compared to 3CLN whereas the overall dynamics of the lobes mainly N-lobe is observed to be more in later case. Salt bridge formation between the residues 2 (ASP) and 148 (LYS) leads to a more compact form of 1CFD at 325 K. The unfolding of the protein is observed to increase with the increase in the temperature similar to the earlier reported

  10. Dynamic signaling cascades: reversible covalent reaction-coupled molecular switches.

    Science.gov (United States)

    Ren, Yulong; You, Lei

    2015-11-11

    The research of systems chemistry exploring complex mixtures of interacting synthetic molecules has been burgeoning recently. Herein we demonstrate for the first time the coupling of molecular switches with a dynamic covalent reaction (DCR) and the modulation of created chemical cascades with a variety of inputs, thus closely mimicking a biological signaling system. A novel Michael type DCR of 10-methylacridinium perchlorate and monothiols exhibiting excellent regioselectivity and tunable affinity was discovered. A delicate balance between the unique reactivity of the reactant and the stability of the adduct leads to the generation of a strong acid in a thermodynamically controlled system. The dynamic cascade was next created via coupling of the DCR and a protonation-induced configurational switch (E/Z isomerization) through a proton relay. Detailed examination of the interdependence of the equilibrium enabled us to rationally optimize the cascade and also shed light on the possible intermediate of the switching process. Furthermore, relative independence of the coupled reactions was verified by the identification of stimuli that are able to facilitate one reaction but suppress the other. To further enhance systematic complexity, a second DCR of electrophilic aldehydes and thiols was employed for the reversible inhibition of the binary system, thus achieving the interplay of multiple equilibria. Finally, a fluorescence switch was turned on through coupling with the DCR, showcasing the versatility of our strategy. The results described herein should pave the way for the exploitation of multifunctional dynamic covalent cascades.

  11. Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

    Science.gov (United States)

    Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

    2010-06-01

    Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

  12. Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

    2007-01-01

    The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental dat....... The average lateral area per chain in this region expands, resulting in a looser packing density. The net effect in the core is a 2–3% decrease in density corresponding to a total volume increase of ∼ 14 cm3 mol−1 hexanol partitioned.......) is stretched by about 4%. Concomitantly, the average lateral area per chain decreases and these two effects compensate so that the overall packing density in the outer region, where the hexanol molecules are located, remains practically constant. The core of the bilayer (C9–C13) is slightly thinned...

  13. The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics.

    Science.gov (United States)

    Nowosielski, Marcin; Hoffmann, Marcin; Kuron, Aneta; Korycka-Machala, Malgorzata; Dziadek, Jaroslaw

    2013-04-05

    The use of the MM2QM tool in a combined docking + molecular dynamics (MD) + molecular mechanics (MM) + quantum mechanical (QM) binding affinity prediction study is presented, and the tool itself is discussed. The system of interest is Mycobacterium tuberculosis (MTB) pantothenate synthetase in complexes with three highly similar sulfonamide inhibitors, for which crystal structures are available. Starting from the structure of MTB pantothenate synthetase in the "open" conformation and following the combined docking + MD + MM + QM procedure, we were able to capture the closing of the enzyme binding pocket and to reproduce the position of the ligands with an average root mean square deviation of 1.6 Å. Protein-ligand interaction energies were reproduced with an average error lower than 10%. The discussion on the MD part and a protein flexibility importance is carried out. The presented approach may be useful especially for finding analog inhibitors or improving drug candidates. Copyright © 2012 Wiley Periodicals, Inc.

  14. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  15. Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.

    Science.gov (United States)

    Sixto-López, Yudibeth; Bello, Martiniano; Correa-Basurto, José

    2018-03-06

    Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K + ) in both sites (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). We found that the presence or absence of K + not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.

  16. Equation of state of warm dense deuterium and its isotopes from density-functional theory molecular dynamics

    Science.gov (United States)

    Danel, J.-F.; Kazandjian, L.; Piron, R.

    2016-04-01

    Of the two approaches of density-functional theory molecular dynamics, quantum molecular dynamics is limited at high temperature by computational cost whereas orbital-free molecular dynamics, based on an approximation of the kinetic electronic free energy, can be implemented in this domain. In the case of deuterium, it is shown how orbital-free molecular dynamics can be regarded as the limit of quantum molecular dynamics at high temperature for the calculation of the equation of state. To this end, accurate quantum molecular dynamics calculations are performed up to 20 eV at mass densities as low as 0.5 g /cm3 and up to 10 eV at mass densities as low as 0.2 g /cm3 . As a result, the limitation in temperature so far attributed to quantum molecular dynamics is overcome and an approach combining quantum and orbital-free molecular dynamics is used to construct an equation of state of deuterium. The thermodynamic domain addressed is that of the fluid phase above 1 eV and 0.2 g /cm3 . Both pressure and internal energy are calculated as functions of temperature and mass density, and various exchange-correlation contributions are compared. The generalized gradient approximation of the exchange-correlation functional, corrected to approximately include the influence of temperature, is retained and the results obtained are compared to other approaches and to experimental shock data; in parts of the thermodynamic domain addressed, these results significantly differ from those obtained in other first-principles investigations which themselves disagree. The equations of state of hydrogen and tritium above 1 eV and above, respectively, 0.1 g /cm3 and 0.3 g /cm3 , can be simply obtained by mass density scaling from the results found for deuterium. This ab initio approach allows one to consistently cover a very large domain of temperature on the domain of mass density outlined above.

  17. Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses

    Directory of Open Access Journals (Sweden)

    Jinxiang Xi

    2018-03-01

    Full Text Available Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of

  18. Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses.

    Science.gov (United States)

    Xi, Jinxiang; Hu, Qin; Zhao, Linlin; Si, Xiuhua April

    2018-03-27

    Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high

  19. Predicting Intersystem Crossing Rates with AIMS-DFT Molecular Dynamics.

    Science.gov (United States)

    Fedorov, Dmitry A; Lykhin, Aleksandr O; Varganov, Sergey A

    2018-03-23

    Accurate prediction of the intersystem crossing rates is important for many different applications in chemistry, physics, and biology. Recently, we implemented the ab initio multiple spawning (AIMS) molecular dynamics method to describe the intersystem crossing processes, where nonradiative transitions between electronic states with different spin multiplicities are mediated by spin-orbit coupling. Our original implementation of the direct AIMS dynamics used the complete active space self-consistent field (CASSCF) method to describe multiple coupled electronic states on which multidimensional Gaussian wave packets were propagated. In this work, we improve the computational efficiency and versatility of the AIMS dynamics by interfacing it with the density functional theory (DFT). The new AIMS-DFT and the earlier AIMS-CASSCF implementations are used to investigate the effects of electronic structure methods on the predicted intersystem crossing rate constants and the lowest triplet state lifetime in the GeH 2 molecule. We also compare the rates and lifetimes obtained from the AIMS simulations with those predicted by the statistical nonadiabatic transition state theory (NA-TST). In NA-TST, the probabilities of spin transitions are calculated using the Landau-Zener, weak coupling, and Zhu-Nakamura formulas. Convergence of the AIMS rate constants with respect to the simulation time and the number of initial trajectories (Gaussian wave packets) is analyzed. An excellent agreement between AIMS-DFT and AIMS-CASSCF can be explained by cancelation of two effects: higher energy barriers and a stronger spin-orbit coupling in DFT relative to CASSCF. The rate constants obtained with the AIMS-DFT dynamics are about a factor of 2 larger than those predicted by the statistical NA-TST. This is likely due to the importance of the nonlocal interstate transitions missing from the NA-TST description.

  20. 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.