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Sample records for addition molecular dynamics

  1. Towards the design of new and improved drilling fluid additives using molecular dynamics simulations.

    PubMed

    Anderson, Richard L; Greenwel, H Christopher; Suter, James L; Jarvis, Rebecca M; Coveney, Peter V

    2010-03-01

    During exploration for oil and gas, a technical drilling fluid is used to lubricate the drill bit, maintain hydrostatic pressure, transmit sensor readings, remove rock cuttings and inhibit swelling of unstable clay based reactive shale formations. Increasing environmental awareness and resulting legislation has led to the search for new, improved biodegradable drilling fluid components. In the case of additives for clay swelling inhibition, an understanding of how existing effective additives interact with clays must be gained to allow the design of improved molecules. Owing to the disordered nature and nanoscopic dimension of the interlayer pores of clay minerals, computer simulations have become an increasingly useful tool for studying clay-swelling inhibitor interactions. In this work we briefly review the history of the development of technical drilling fluids, the environmental impact of drilling fluids and the use of computer simulations to study the interactions between clay minerals and swelling inhibitors. We report on results from some recent large-scale molecular dynamics simulation studies on low molecular weight water-soluble macromolecular inhibitor molecules. The structure and interactions of poly(propylene oxide)-diamine, poly(ethylene glycol) and poly(ethylene oxide)-diacrylate inhibitor molecules with montmorillonite clay are studied.

  2. Molecular dynamics

    SciTech Connect

    Ladd, A.J.C.

    1988-08-01

    The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.

  3. Linearity and additivity in cluster-induced sputtering: A molecular-dynamics study of van der Waals bonded systems

    SciTech Connect

    Anders, Christian; Urbassek, Herbert M.; Johnson, Robert E.

    2004-10-15

    Using molecular-dynamics simulation, we study sputtering of a condensed-gas solid induced by the impact of atomic clusters with sizes 1{<=}n{<=}10{sup 4}. Above a nonlinear onset regime, we find a linear increase of the sputter yield Y with the total energy E of the bombarding cluster. The fitting coefficients in the linear regime depend only on the cluster size n such that for fixed bombardment energy, sputtering decreases with increasing cluster size n. We find that to a good approximation the sputter yield in this regime obeys an additivity rule in cluster size n such that doubling the cluster size at the same cluster velocity amounts to doubling the sputter yield. The sputter-limiting energy {epsilon}{sub s} is introduced which separates erosion ({epsilon}>{epsilon}{sub s}) from growth ({epsilon}<{epsilon}{sub s}) under cluster impact.

  4. Molecular dynamics.

    PubMed

    Cheng, Xiaolin; Ivanov, Ivaylo

    2012-01-01

    Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton's equations of motion. In this review, we present an overview of how the MD simulation can be conducted to address computational toxicity problems. The study cases will cover a standard MD simulation performed to investigate the overall flexibility of a cytochrome P450 (CYP) enzyme and a set of more advanced MD simulations to examine the barrier to ion conduction in a human α7 nicotinic acetylcholine receptor (nAChR).

  5. Rational molecular dynamics scheme for predicting optimum concentration loading of nano-additive in phase change materials

    NASA Astrophysics Data System (ADS)

    Rastogi, Monisha; Vaish, Rahul; Madhar, Niyaz Ahamad; Shaikh, Hamid; Al-Zahrani, S. M.

    2015-10-01

    The present study deals with the diffusion and phase transition behaviour of paraffin reinforced with carbon nano-additives namely graphene oxide (GO) and surface functionalized single walled carbon nanotubes (SWCNT). Bulk disordered systems of paraffin hydrocarbons impregnated with carbon nano-additives have been generated in realistic equilibrium conformations for potential application as latent heat storage systems. Ab initio molecular dynamics(MD) in conjugation with COMPASS forcefield has been implemented using periodic boundary conditions. The proposed scheme allows determination of optimum nano-additive loading for improving thermo-physical properties through analysis of mass, thermal and transport properties; and assists in determination of composite behaviour and related performance from microscopic point of view. It was observed that nanocomposites containing 7.8 % surface functionalised SWCNT and 55% GO loading corresponds to best latent heat storage system. The propounded methodology could serve as a by-pass route for economically taxing and iterative experimental procedures required to attain the optimum composition for best performance. The results also hint at the large unexplored potential of ab-initio classical MD techniques for predicting performance of new nanocomposites for potential phase change material applications.

  6. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics.

    PubMed

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems. PMID:27176426

  7. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

  8. Molecular dynamics simulations for the examination of mechanical properties of hydroxyapatite/ poly α-n-butyl cyanoacrylate under additive manufacturing.

    PubMed

    Wang, Yanen; Wei, Qinghua; Pan, Feilong; Yang, Mingming; Wei, Shengmin

    2014-01-01

    Molecular dynamics (MD) simulations emerged to be a helpful tool in the field of material science. In rapid prototyping artificial bone scaffolds process, the binder spraying volume and mechanism are very important for bone scaffolds mechanical properties. In this study, we applied MD simulations to investigating the binding energy of α-n-butyl cyanoacrylate (NBCA) on Hydroxyapatite (HA) crystallographic planes (001, 100 and 110), and to calculating and analyzing the mechanical properties and radial distribution function of the HA(110)/NBCA mixed system. The simulation results suggested that HA (110) has the highest binding energy with NBCA owing to the high planar atom density, and the mechanical properties of HA(110)/NBCA mixed system is stronger than pure HA system. Therefore, the multi-grade strength bone scaffold could be fabricated through spraying various volume NBCA binders during 3D printing process. By calculating the radial distribution function of HA(110)/NBCA, the essence of the interface interaction were successfully elucidated. The forming situation parameters can be referred to calculation results. There exists a strong interaction between HA crystallographic plane (110) and NBCA, it is mainly derived from the hydrogen bonds between O atoms which connect with C atoms of NBCA and H atoms in HA crystal. Furthermore, a strong adsorption effect can be demonstrated between HA and NBCA.

  9. Accelerated molecular dynamics methods

    SciTech Connect

    Perez, Danny

    2011-01-04

    The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.

  10. Additives Effects on Crystal Morphology of Dihydroxylammonium 5,5ʹ-Bistetrazole-1,1ʹ-diolate by Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Xiong, Shu-Ling; Chen, Shu-Sen; Jin, Shao-Hua; Li, Li-Jie

    2016-10-01

    Dihydroxylammonium 5,5‧-bistetrazole-1,1‧-diolate (TKX-50) is a newly synthesized explosive with excellent comprehensive properties: high energy storage, low impact sensitivity, and low toxicity. To understand and improve the crystal morphology of TKX-50, we reported the polymer consistent force field to simulate the crystal morphology of TKX-50 by growth morphology (GM) method. We then used this force field in molecular dynamics (MD) simulations to predict the influences of additives on crystal facets of TKX-50. The calculated results indicate that ethanol, ethylene glycol, and acetic acid are more favorable to the spheroidization of TKX-50, which provides a theoretical support for the additive selection of crystalline system. Furthermore, we added the selected additives in the recrystallization system of TKX-50. The recrystallized samples possessed a small aspect ratio and were close to spherical in shape, which indicates that the experimental results are consistent with the simulated results.

  11. Multiscale reactive molecular dynamics

    PubMed Central

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-01-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062

  12. Ab initio molecular dynamics.

    PubMed

    Laasonen, Kari

    2013-01-01

    In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.

  13. Substructured multibody molecular dynamics.

    SciTech Connect

    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.

  14. Open boundary molecular dynamics

    NASA Astrophysics Data System (ADS)

    Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.

    2015-09-01

    This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.

  15. A sampling of molecular dynamics

    NASA Astrophysics Data System (ADS)

    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

  16. Molecular dynamics simulations.

    PubMed

    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.

  17. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik R

    2008-01-01

    Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.

  18. An Additive Definition of Molecular Complexity.

    PubMed

    Böttcher, Thomas

    2016-03-28

    A framework for molecular complexity is established that is based on information theory and consistent with chemical knowledge. The resulting complexity index Cm is derived from abstracting the information content of a molecule by the degrees of freedom in the microenvironments on a per-atom basis, allowing the molecular complexity to be calculated in a simple and additive way. This index allows the complexity of any molecule to be universally assessed and is sensitive to stereochemistry, heteroatoms, and symmetry. The performance of this complexity index is evaluated and compared against the current state of the art. Its additive character gives consistent values also for very large molecules and supports direct comparisons of chemical reactions. Finally, this approach may provide a useful tool for medicinal chemistry in drug design and lead selection, as demonstrated by correlating molecular complexities of antibiotics with compound-specific parameters.

  19. An Additive Definition of Molecular Complexity.

    PubMed

    Böttcher, Thomas

    2016-03-28

    A framework for molecular complexity is established that is based on information theory and consistent with chemical knowledge. The resulting complexity index Cm is derived from abstracting the information content of a molecule by the degrees of freedom in the microenvironments on a per-atom basis, allowing the molecular complexity to be calculated in a simple and additive way. This index allows the complexity of any molecule to be universally assessed and is sensitive to stereochemistry, heteroatoms, and symmetry. The performance of this complexity index is evaluated and compared against the current state of the art. Its additive character gives consistent values also for very large molecules and supports direct comparisons of chemical reactions. Finally, this approach may provide a useful tool for medicinal chemistry in drug design and lead selection, as demonstrated by correlating molecular complexities of antibiotics with compound-specific parameters. PMID:26857537

  20. Dynamic fracture toughness determined using molecular dynamics

    SciTech Connect

    Swadener, J. G.; Baskes, M. I.; Nastasi, Michael Anthony,

    2004-01-01

    Molecular dynamics (MD) simulations of fracture in crystalline silicon are conducted in order to determine the dynamic fracture toughness. The MD simulations show how the potential energy released during fracture is partitioned into surface energy, energy stored in defects and kinetic energy. First, the MD fracture simulations are shown to produce brittle fracture and be in reasonable agreement with experimental results. Then dynamic hcture toughness is calculated as the sum of the surface energy and the energy stored as defects directly from the MD models. Models oriented to produce fracture on either (111) or (101) planes are used. For the (101) fracture orientation, equilibrium crack speeds of greater than 80% of the Rayleigh wave speed are obtained. Crack speeds initially show a steep increase with increasing energy release rate followed by a much more gradual increase. No plateau in crack speed is observed for static energy release rates up to 20 J/m{sup 2}. At the point where the change in crack speed behavior occur, the dynamic fracture toughness (J{sub d}) is still within 10% of two times the surface energy (2{gamma}{sub 0}) and changing very slowly. From these MD simulations, it appears that the change in crack speed behavior is due to a change in the kinetic energy generation during dynamic fracture. In addition, MD simulations of facture in silicon with defects were conducted. The addition of defects increases the inelastic dissipation and the energy stored in defects.

  1. Interactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    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.

  2. Theory of atomic additivity in molecular hyperpolizabilities

    NASA Technical Reports Server (NTRS)

    Baird, James K.

    1987-01-01

    Hyperpolarizability is a function of frequency. This is called dispersion. Because of the Kramers-Kronig relations, researchers expect that a material that is dispersing light is also absorbing it. Where there is both dispersion and absorption, the molecular polarizabilities are complex functions of the frequency. This led researchers to consider atomic additivity in both the real and imaginary parts of the ordinary and hyperpolarizabilities. This effort is desirable not only from a theoretical point of view, but also because of the existence of a large body of complex refractive index data, which may be used to test the additivity principle with the complex valued ordinary dipole polarizability.

  3. Introduction to Accelerated Molecular Dynamics

    SciTech Connect

    Perez, Danny

    2012-07-10

    Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.

  4. NMR investigations of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  5. Nonlinear dynamics of additive pulse modelocked lasers

    SciTech Connect

    Sucha, G.; Bolton, S.R.; Chemla, D.S.

    1995-04-01

    Nonlinear dynamics have been studied in a number of modelocked laser systems, primarily in actively modelocked systems. However, less attention has been paid to the dynamics of passively modelocked laser systems. With the recent revolutionary advances in femtosecond modelocked laser technology, the understanding of instabilities and dynamics in passively modelocked lasers is an important issue. Here, the authors present experimental and numerical studies of the dynamics of an additive-pulse modelocked (APM) color-center laser.

  6. Molecular photoionization dynamics

    SciTech Connect

    Dehmer, Joseph L.

    1982-05-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)

  7. PDII- Additional discussion of the dynamic aperture

    SciTech Connect

    Norman M. Gelfand

    2002-07-23

    This note is in the nature of an addition to the dynamic aperture calculations found in the report on the Proton Driver, FERMILAB-TM-2169. A extensive discussion of the Proton Driver lattice, as well as the nomenclature used to describe it can be found in TM-2169. Basically the proposed lattice is a racetrack design with the two arcs joined by two long straight sections. The straight sections are dispersion free. Tracking studies were undertaken with the objective of computing the dynamic aperture for the lattice and some of the results have been incorporated into TM-2169. This note is a more extensive report of those calculations.

  8. State-dependent molecular dynamics.

    PubMed

    Yang, Ciann-Dong; Weng, Hung-Jen

    2014-01-01

    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. Molecular Aluminum Additive for Burn Enhancement of Hydrocarbon Fuels.

    PubMed

    Guerieri, Philip M; DeCarlo, Samantha; Eichhorn, Bryan; Connell, Terrence; Yetter, Richard A; Tang, Xin; Hicks, Zachary; Bowen, Kit H; Zachariah, Michael R

    2015-11-12

    Additives to hydrocarbon fuels are commonly explored to change the combustion dynamics, chemical distribution, and/or product integrity. Here we employ a novel aluminum-based molecular additive, Al(I) tetrameric cluster [AlBrNEt3]4 (Et = C2H5), to a hydrocarbon fuel and evaluate the resultant single-droplet combustion properties. This Al4 cluster offers a soluble alternative to nanoscale particulate additives that have recently been explored and may mitigate the observed problems of particle aggregation. Results show the [AlBrNEt3]4 additive to increase the burn rate constant of a toluene-diethyl ether fuel mixture by ∼20% in a room temperature oxygen environment with only 39 mM of active aluminum additive (0.16 wt % limited by additive solubility). In comparison, a roughly similar addition of nano-aluminum particulate shows no discernible difference in burn properties of the hydrocarbon fuel. High speed video shows the [AlBrNEt3]4 to induce microexplosive gas release events during the last ∼30% of the droplet combustion time. We attribute this to HBr gas release based on results of temperature-programmed reaction (TPR) experiments of the [AlBrNEt3]4 dosed with O2 and D2O. A possible mechanism of burn rate enhancement is presented that is consistent with microexplosion observations and TPR results. PMID:26488461

  10. Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

    PubMed Central

    Savelyev, Alexey; MacKerell, Alexander D.

    2015-01-01

    In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286

  11. Dynamic signature of molecular association in methanol.

    PubMed

    Bertrand, C E; Self, J L; Copley, J R D; Faraone, A

    2016-07-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids. PMID:27394112

  12. Dynamic signature of molecular association in methanol

    NASA Astrophysics Data System (ADS)

    Bertrand, C. E.; Self, J. L.; Copley, J. R. D.; Faraone, A.

    2016-07-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

  13. Thomas-Fermi molecular dynamics

    SciTech Connect

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

    1992-10-15

    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.

  14. MDMovie: a molecular dynamics viewing tool.

    PubMed

    Greenberg, J P

    1996-10-01

    The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.

  15. Available Instruments for Analyzing Molecular Dynamics Trajectories.

    PubMed

    Likhachev, I V; Balabaev, N K; Galzitskaya, O V

    2016-01-01

    Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. PMID:27053964

  16. Available Instruments for Analyzing Molecular Dynamics Trajectories

    PubMed Central

    Likhachev, I. V.; Balabaev, N. K.; Galzitskaya, O. V.

    2016-01-01

    Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. PMID:27053964

  17. From molecular dynamics to Brownian dynamics

    PubMed Central

    Erban, Radek

    2014-01-01

    Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane. PMID:25002825

  18. Scalable Molecular Dynamics with NAMD

    PubMed Central

    Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus

    2008-01-01

    NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654

  19. Better, Cheaper, Faster Molecular Dynamics

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

  20. Molecular dynamics of polymer growth

    NASA Astrophysics Data System (ADS)

    Akkermans, Reinier L. C.; Toxvaerd, Søren; Briels, W. J.

    1998-08-01

    The irreversible polymerization of a monomer liquid has been studied by molecular-dynamics simulation in two and three dimensions. The growth process is studied under good solvent conditions in the dilute regime and up to semidilute and concentrated regimes. In the dilute regime we observe a reaction limitation due to trapping of the growing centers, which is more pronounced in the lower dimension. At higher concentrations the presence of other chains decreases the monomer mobility and reaction rate. Conformational properties are studied by scaling analysis of end-to-end and gyration radii. A crossover from swollen conformations towards screened conformations is observed as growth proceeds.

  1. Radiation in molecular dynamic simulations

    SciTech Connect

    Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M

    2008-10-13

    Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.

  2. Molecular dynamics of interface rupture

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

    Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

  3. A concurrent multiscale micromorphic molecular dynamics

    SciTech Connect

    Li, Shaofan Tong, Qi

    2015-04-21

    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.

  4. Molecular Dynamics Simulation of Dynamic Response of Beryllium

    NASA Astrophysics Data System (ADS)

    Thompson, Aidan P.; Lane, J. Matthew D.; Baskes, Michael I.; Desjarlais, Michael P.

    2009-06-01

    The response of beryllium to dynamic loading has been extensively studied, both experimentally and theoretically, due to its importance in several technological areas. Compared to other metals, it is quite challenging to accurately represent the various anomalous behaviors of beryllium using classical interatomic potentials. The spherically-symmetric EAM potential can not reproduce the observed c/a ratio for α-Be under ambient conditions, which is significantly smaller than the ideal HCP value. The directional-dependence of the MEAM potential overcomes this problem, but introduces additional complexity. We will compare predictions of these classical potentials to experimental measurements of beryllium at ambient conditions, and also to theoretical calculations at high temperatures and pressures. Finally, we will present initial results from non-equilibrium molecular dynamics simulations of beryllium under dynamic loading. This work is supported by the Laboratory Directed Research and Development program at Sandia National Laboratories.

  5. Molecular crowding and protein enzymatic dynamics.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2012-05-21

    The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding. PMID:22476233

  6. Shear flow by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Heyes, D. M.

    1985-08-01

    A detailed comparison is made between a number of methods for generating shear flow in Molecular Dynamics computer simulation. Algorithms which closely mimic most experimental methods for producing shear flow are those by Trozzi and Ciccotti, and Ashurst and Hoover. They employ hard wall boundaries and fluid walls respectively (with sheared cell periodicity being only in two dimensions). The sheared fluid properties are therefore inextricably linked with interfacial effects. These problems are largely eliminated by the Lees and Edwards scheme which creates a pseudo-infinite sheared material. There are a number of derivatives of this model including one favoured by the author for investigating non-linear viscoelastic phenomena. A number of results from this scheme pertaining to the Lennard-Jones liquid are presented.

  7. Buckybomb: Reactive Molecular Dynamics Simulation.

    PubMed

    Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V

    2015-03-01

    Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672

  8. Emergent Phenomena via Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Rapaport, D. C.

    Emergent phenomena are unusual because they are not obvious consequences of the design of the systems in which they appear, a feature no less relevant when they are being simulated. Several systems that exhibit surprisingly rich emergent behavior, each studied by molecular dynamics (MD) simulation, are described: (i) Modeling self-assembly processes associated with virus growth reveals the ability to achieve error-free assembly, where paradoxically, near-maximum yields are due to reversible bond formation. (ii) In fluids studied at the atomistic level, complex hydrodynamic phenomena in rotating and convecting fluids - the Taylor- Couette and Rayleigh-Bénard instabilities - can be reproduced, despite the limited length and time scales accessible by MD. (iii) Segregation studies of granular mixtures in a rotating drum reproduce the expected, but counterintuitive, axial and radial segregation, while for the case of a vertically vibrated layer a novel form of horizontal segregation is revealed.

  9. Buckybomb: Reactive Molecular Dynamics Simulation.

    PubMed

    Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V

    2015-03-01

    Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material.

  10. Molecular dynamics of membrane proteins.

    SciTech Connect

    Woolf, Thomas B.; Crozier, Paul Stewart; Stevens, Mark Jackson

    2004-10-01

    Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

  11. Dynamical Localization in Molecular Systems.

    NASA Astrophysics Data System (ADS)

    Wang, Xidi

    In the first four chapters of this thesis we concentrate on the Davydov model which describes the vibrational energy quanta of Amide I bonds (C=O bonds on the alpha -helix) coupled to the acoustic phonon modes of the alpha-helix backbone in the form of a Frohlich Hamiltonian. Following a brief introduction in chapter one, in chapter two we formulate the dynamics of vibrational quanta at finite temperature by using coherent state products. The fluctuation-dissipation relation is derived. At zero temperature, in the continuum limit, we recover the original results of Davydov. We also achieve good agreement with numerical simulations. In chapter three, the net contraction of the lattice is calculated exactly at any temperature, and its relation to the so -call "topological stability" of the Davydov soliton is discussed. In the second section of the chapter three we calculate the overtone spectra of crystalline acetanilide (according to some opinions ACN provides experimental evidence for the existence of Davydov solitons). Good agreement with experimental data has been obtained. In chapter four we study the self-trapped vibrational excitations by the Quantum Monte Carlo technique. For a single excitation, the temperature dependence of different physical observables is calculated. The quasi-particle which resembles the Davydov soliton has been found to be fairly narrow using the most commonly used data for the alpha -helix; at temperatures above a few Kelvin, the quasi-particle reaches its smallest limit (extends over three sites), which implies diffusive motion of the small polaron-like quasi-particle at high temperatures. For the multi-excitation case, bound pairs and clusters of excitations are found at low temperatures; they gradually dissociate when the temperature of the system is increased as calculated from the density-density correlation function. In the last chapter of this thesis, we study a more general model of dynamical local modes in molecular systems

  12. Molecular dynamics on APE100

    NASA Astrophysics Data System (ADS)

    Barone, Luciano Maria; Simonazzi, Riccardo; Tenenbaum, Alexander

    1995-09-01

    We have studied portability, efficiency and accuracy of a standard Molecular Dynamics simulation on the SIMD parallel computer APE100. Computing speed performance and physical system size range have been analyzed and compared with those of a conventional computer. Short range and long range potentials have been considered, and the comparative advantage of different simulation approaches has been assessed. For long range potentials, APE turns out to be faster than a conventional computer; large systems can be conveniently simulated using either the cloning approach (up to ˜ 10 5 particles) or a domain decomposition with the systolic method. In the case of short range potentials and systems with diffusion (like a liquid), APE is convenient only when using a large number of processors. In a special case (a crystal without diffusion), a specific domain decomposition technique with frames makes APE advantageous for intermediate and large systems. Using the latter technique we have studied in detail the effect of different numerical error sources, and compared the accuracy of APE with that of a conventional computer.

  13. Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics.

    PubMed

    Hele, Timothy J H; Willatt, Michael J; Muolo, Andrea; Althorpe, Stuart C

    2015-05-21

    We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the "Classical Wigner" approximation. Here, we show that the further approximation of this "Matsubara dynamics" gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.

  14. Exact dynamic properties of molecular motors

    NASA Astrophysics Data System (ADS)

    Boon, N. J.; Hoyle, R. B.

    2012-08-01

    Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.

  15. Time-Dependent Molecular Reaction Dynamics

    NASA Astrophysics Data System (ADS)

    Öhrn, Yngve

    2007-11-01

    This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefcients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions.

  16. Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics

    SciTech Connect

    Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.

    2015-05-21

    We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.

  17. Classical Molecular Dynamics Simulation of Nuclear Fuel

    SciTech Connect

    Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

    2015-10-10

    Molecular dynamics simulation 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 thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.

  18. Molecular dynamics simulations of wear processes

    NASA Astrophysics Data System (ADS)

    Yu, Hualiang

    Wear has been recognized as a vital problem in many industries. It results in a loss of durability, reliability, and efficiency and costs tens of billions of dollars annually. Significant effort has been devoted in both experimental and theoretical studies. However, the mechanisms of wear are still poorly understood and therefore wear control is far behind its demand. One way to study wear process is via computer simulation, which has become more powerful with the rapid development in computer facilities and efficient algorithms. It allows observation of atomic scale deformation and therefore it is a very good tool to study wear mechanisms at the nano-scale. This study presents a series of molecular dynamic simulation of some nano-scale wear processes, such as indentation and plowing, with the goal of exploring the factors that affect wear and predicting wear for different conditions. Molecular Dynamics simulations were carried out on a system that includes an aluminum substrate and a hard tip. Embedded atom method (EAM) and Lennard-Jones potentials were used to describe interactions between atoms. For nano-indentation simulations, both constant indent force and constant loading speed were applied to study the wear mechanisms as well as material properties. Some phenomenon, such as jump-to-contact, local melting, and dislocation nucleation were observed. More importantly, the effects of system temperature, indent force, substrate orientation, tip-substrate bond, indenter shape, boundary condition, and defect concentrations of the substrate were systematically investigated during indentation. The results are in qualitative agreement with limited experimental data. Similar simulations were carried out for plowing. The effects of plowing force, substrate orientation, the tip-substrate bond, and alloy elements are discussed based on the simulation results. In addition, a simple analytic model of plowing behavior is provided. The model reveals two parameters, static

  19. Molecular ions, Rydberg spectroscopy and dynamics

    SciTech Connect

    Jungen, Ch.

    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.

  20. Modeling the Hydrogen Bond within Molecular Dynamics

    ERIC Educational Resources Information Center

    Lykos, Peter

    2004-01-01

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

  1. Protein dynamics: Moore's law in molecular biology.

    PubMed

    Vendruscolo, Michele; Dobson, Christopher M

    2011-01-25

    The millisecond barrier has been broken in molecular dynamics simulations of proteins. Such simulations are increasingly revealing the inner workings of biological systems by generating atomic-level descriptions of their behaviour that make testable predictions about key molecular processes.

  2. Molecular Dynamics Simulations of Simple Liquids

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  3. Parallel Molecular Dynamics Program for Molecules

    SciTech Connect

    Plimpton, Steve

    1995-03-07

    ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.

  4. Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics

    NASA Astrophysics Data System (ADS)

    Rakesh, L.

    2009-09-01

    Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the

  5. Dynamic molecular crystals with switchable physical properties.

    PubMed

    Sato, Osamu

    2016-06-21

    The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials. PMID:27325090

  6. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

  7. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.

  8. Molecular dynamics simulations of large macromolecular complexes

    PubMed Central

    Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

    2015-01-01

    Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770

  9. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect

    Nesbitt, David J.

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  10. Molecular scale dynamics of large ring polymers.

    PubMed

    Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D

    2014-10-17

    We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture. PMID:25361284

  11. Molecular scale dynamics of large ring polymers.

    PubMed

    Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D

    2014-10-17

    We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.

  12. Numerical methods for molecular dynamics

    SciTech Connect

    Skeel, R.D.

    1991-01-01

    This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.

  13. Semiclassical guided optimal control of molecular dynamics

    SciTech Connect

    Kondorskiy, A.; Mil'nikov, G.; Nakamura, H.

    2005-10-15

    An efficient semiclassical optimal control theory applicable to multidimensional systems is formulated for controlling wave packet dynamics on a single adiabatic potential energy surface. The approach combines advantages of different formulations of optimal control theory: quantum and classical on one hand and global and local on the other. Numerical applications to the control of HCN-CNH isomerization demonstrate that this theory can provide an efficient tool to manipulate molecular dynamics of many degrees of freedom by laser pulses.

  14. Thermal Conductivity of Natural Rubber Using Molecular Dynamics Simulation.

    PubMed

    He, Yan; Ma, Lian-Xiang; Tang, Yuan-Zheng; Wang, Ze-Peng; Li, Wei; Kukulka, David

    2015-04-01

    Thermal conductivity of natural rubber has been studied by classic molecular dynamics simulations. These simulations are performed on natural rubber models using the adaptive intermolecular reactive empirical bond order (AIREBO) and the Green-Kubo molecular dynamics (MD) simulations. Thermal conductivity results are found to be very sensitive to the time step used in the simulations. For a time step of 0.1 fs, the converged thermal conductivity is 0.35 W/mK. Additionally the anisotropic thermal conductivity of a specially-modeled natural rubber model with straight molecular chains was studied and values of thermal conductivity parallel to the molecular chains was found to be 1.71 W/mK and the anisotropy, 2Kz/(Kx + Ky), was 2.67.

  15. Molecular dynamics studies on nanoscale gas transport

    NASA Astrophysics Data System (ADS)

    Barisik, Murat

    wall force penetration region at different flow conditions. Shear stress results are utilized to calculate the tangential momentum accommodation coefficient (TMAC) between argon gas and FCC walls. The TMAC value is shown to he independent of the now properties and Knudsen number in all simulations. Velocity profiles show distinct deviations from the kinetic theory based solutions inside the wall force penetration depth, while they match the linearized Boltzmann equation solution outside these zones. Afterwards, surface effects are studied as a function of the surface-gas potential strength ratio (epsilon wf/epsilonff) for the shear driven argon gas flows in the early transition and tree molecular flow regimes. Results show that increased epsilonwf/epsilon ff results in increased gas density, leading towards monolayer adsorption on surfaces. The near wall velocity profile shows reduced gas slip, and eventually velocity stick with increased epsilonwf/epsilon ff. Similarly, using MD predicted shear stress values and kinetic theory, TMAC are calculated as a function of epsilonwf/epsilon ff and TMAC values are shown to be independent of the Knudsen number. Results indicate emergence of the wall force field penetration depth as an additional length scale for gas flows in nano-channels, breaking the dynamic similarity between rarefied and nano-scale gas flows solely based on the Knudsen and Mach numbers.

  16. Molecular Exchange Dynamics in Block Copolymer Micelles

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  17. Reaction dynamics in polyatomic molecular systems

    SciTech Connect

    Miller, W.H.

    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.

  18. Fracture simulations via massively parallel molecular dynamics

    SciTech Connect

    Holian, B.L.; Abraham, F.F.; Ravelo, R.

    1993-09-01

    Fracture simulations at the atomistic level have heretofore been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 {mu}m on a side. We report on recent MD simulations of mode I crack extension under tensile loading at high strain rates. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. We found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly in this paper will be especially important to carrying out feasible massively parallel 3D simulations via MD.

  19. Probing Molecular Dynamics by Laser-Induced Backscattering Holography.

    PubMed

    Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B

    2016-04-01

    We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H_{2} and D_{2} molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H_{2} and D_{2} with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules. PMID:27081975

  20. Probing Molecular Dynamics by Laser-Induced Backscattering Holography

    NASA Astrophysics Data System (ADS)

    Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B.

    2016-04-01

    We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H2 and D2 molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H2 and D2 with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules.

  1. Multiscale coupling of molecular dynamics and peridynamics

    NASA Astrophysics Data System (ADS)

    Tong, Qi; Li, Shaofan

    2016-10-01

    We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.

  2. Polar solvation dynamics of lysozyme from molecular dynamics studies

    NASA Astrophysics Data System (ADS)

    Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

    2012-05-01

    The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the α-helices and β-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.

  3. Combined molecular dynamics-spin dynamics simulations of bcc iron

    SciTech Connect

    Perera, Meewanage Dilina N; Yin, Junqi; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Brown, Greg

    2014-01-01

    Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.

  4. Dynamic strength of molecular adhesion bonds.

    PubMed Central

    Evans, E; Ritchie, K

    1997-01-01

    In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale

  5. Dynamical quenching of tunneling in molecular magnets

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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.

  6. Exciton dynamics in perturbed vibronic molecular aggregates

    PubMed Central

    Brüning, C.; Wehner, J.; Hausner, J.; Wenzel, M.; Engel, V.

    2015-01-01

    A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840

  7. Molecular dynamic simulation methods for anisotropic liquids.

    PubMed

    Aoki, Keiko M; Yoneya, Makoto; Yokoyama, Hiroshi

    2004-03-22

    Methods of molecular dynamics simulations for anisotropic molecules are presented. The new methods, with an anisotropic factor in the cell dynamics, dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under constant hydrostatic pressure or constant volume. The methods are especially effective for anisotropic liquids, such as smectic liquid crystals and membranes, of which the stacks of layers are compressible (elastic in direction perpendicular to the layers) while the layer itself is liquid and only elastic under uniform compressive force. The methods can also be used for crystals and isotropic liquids as well.

  8. Molecular Dynamics Simulations of Alpha-synuclein

    NASA Astrophysics Data System (ADS)

    Sammalkorpi, Maria; Schreck, Carl; Nath, Abhinav; Dewitt, David; Rhoades, Elizabeth; O'Hern, Corey

    2011-03-01

    We investigate the conformational dynamics of single alpha-synuclein proteins, which have been implicated in amyloid diseases such as Parkinson's and Alzheimer's disease, in solution using unconstrained and constrained all-atom, explicit solvent molecular dynamics simulations. The constraints on inter-residue separations are obtained from our single-molecule FRET measurements of eleven FRET pairs that span the protein. By comparing the simulation data satisfying different combinations of FRET constraints, we are able to identify those constraints that are most important in determining the radius of gyration and key features of the contact map of the protein.

  9. Molecular dynamics at constant Cauchy stress

    NASA Astrophysics Data System (ADS)

    Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio

    2016-05-01

    The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

  11. New faster CHARMM molecular dynamics engine

    PubMed Central

    Hynninen, Antti-Pekka; Crowley, Michael F

    2014-01-01

    We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199

  12. Nanoindentation of Zr by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.

    2015-12-01

    Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.

  13. Molecular dynamics modelling of solidification in metals

    SciTech Connect

    Boercker, D.B.; Belak, J.; Glosli, J.

    1997-12-31

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

  14. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  15. Roaming dynamics in radical addition-elimination reactions.

    PubMed

    Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G; Mebel, Alexander M

    2014-06-06

    Radical addition-elimination reactions are a major pathway for transformation of unsaturated hydrocarbons. In the gas phase, these reactions involve formation of a transient strongly bound intermediate. However, the detailed mechanism and dynamics for these reactions remain unclear. Here we show, for reaction of chlorine atoms with butenes, that the Cl addition-HCl elimination pathway occurs from an abstraction-like Cl-H-C geometry rather than a conventional three-centre or four-centre transition state. Furthermore, access to this geometry is attained by roaming excursions of the Cl atom from the initially formed adduct. In effect, the alkene π cloud serves to capture the Cl atom and hold it, allowing many subsequent opportunities for the energized intermediate to find a suitable approach to the abstraction geometry. These bimolecular roaming reactions are closely related to the roaming radical dynamics recently discovered to play an important role in unimolecular reactions.

  16. Control-volume representation of molecular dynamics.

    PubMed

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2012-05-01

    A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑ(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.

  17. Control-volume representation of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Smith, E. R.; Heyes, D. M.; Dini, D.; Zaki, T. A.

    2012-05-01

    A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys.JCPSA60021-960610.1063/1.1747782 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds’ transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑi for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys.JAPIAU0021-897910.1063/1.341877 64, 1152 (1988)] techniques and the method of planes [Todd , Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.52.1627 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.

  18. A molecular dynamics study of polymer/graphene interfacial systems

    SciTech Connect

    Rissanou, Anastassia N.; Harmandaris, Vagelis

    2014-05-15

    Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

  19. Molecular dynamics modeling of a nanomaterials-water surface interaction

    NASA Astrophysics Data System (ADS)

    Nejat Pishkenari, Hossein; Keramati, Ramtin; Abdi, Ahmad; Minary-Jolandan, Majid

    2016-04-01

    In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements.

  20. Phase transitions of methane using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    El-Sheikh, S. M.; Barakat, K.; Salem, N. M.

    2006-03-01

    Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.

  1. Phase transitions of methane using molecular dynamics simulations.

    PubMed

    El-Sheikh, S M; Barakat, K; Salem, N M

    2006-03-28

    Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4 under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256 molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.

  2. Molecular dynamics simulation study of methanesulfonic acid.

    PubMed

    Canales, Manel; Alemán, Carlos

    2014-03-27

    A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hydrogen bonds in structural and dynamical properties has also been performed. The continuous and interrupted methodologies to compute hydrogen bonding lifetimes have been applied. The interrupted hydrogen bond lifetimes values are consistent with the diffusion and viscosity coefficients. The activation energies of the self-diffusion, the reorientational motions, and the hydrogen bonding lifetimes are coincident.

  3. Polymer Fluid Dynamics: Continuum and Molecular Approaches.

    PubMed

    Bird, R B; Giacomin, A J

    2016-06-01

    To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems. PMID:27276553

  4. Application of optimal prediction to molecular dynamics

    SciTech Connect

    Barber, IV, John Letherman

    2004-12-01

    Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is δ-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.

  5. Local Refinements in Classical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fackeldey, Konstantin; Weber, Marcus

    2014-03-01

    Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

  6. Molecular Dynamics in Self-Assembled Monolayers

    NASA Astrophysics Data System (ADS)

    Bochinski, Jason; Stevens, Derrick; Scott, Mary; Guy, Laura; Dedeugd, Casey; Clarke, Laura

    2007-03-01

    Silane self-assembled monolayers (SAMs) are an important tool for both scientific research and technological applications. Despite their widespread use, few experimental investigations have addressed molecular motion within these films, which offer a unique and useful physical system for fundamental scientific studies, such as observing dipolar and other glass transitions in two-dimensions. In addition, relaxations such as ``rotator'' phases where molecular groups rotate in a plane parallel to the surface have been correlated with film conductivity, adhesive, and wetting properties. We utilize surface-sensitive, dielectric relaxation spectroscopy to probe molecular motion as a function of temperature within silane chemistry-based monolayers formed upon interdigitated electrodes. Our latest results exploring a previously published motion as well as comparisons to linear polymer films will be discussed.

  7. Stochastic Event-Driven Molecular Dynamics

    SciTech Connect

    Donev, Aleksandar Garcia, Alejandro L.; Alder, Berni J.

    2008-02-01

    A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in EDMD, rather, the momentum and energy exchange in the solvent is determined stochastically using DSMC. The coupling between the solvent and the solute is consistently represented at the particle level retaining hydrodynamic interactions and thermodynamic fluctuations. However, unlike full MD simulations of both the solvent and the solute, in SEDMD the spatial structure of the solvent is ignored. The SEDMD algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard-wall subjected to uniform shear. SEDMD closely reproduces results obtained using traditional EDMD simulations with two orders of magnitude greater efficiency. Results question the existence of periodic (cycling) motion of the polymer chain.

  8. Molecular dynamics in high electric fields

    NASA Astrophysics Data System (ADS)

    Apostol, M.; Cune, L. C.

    2016-06-01

    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.

  9. Effects of molecular architectures and solvophobic additives on the aggregative properties of polymeric surfactants

    NASA Astrophysics Data System (ADS)

    Lin, Yung-Lung; Wu, Ming-Zher; Sheng, Yu-Jane; Tsao, Heng-Kwong

    2012-03-01

    The aggregative behavior of the polymeric surfactants with various molecular architectures in dilute solutions is studied by dissipative particle dynamics. The effects of the solvophobic/solvophilic length, polymeric architecture (linear, star, dendritic, and cyclic type), chain rigidity, and solvophobic additives on the critical micelle concentration (CMC) and the aggregative patterns are systematically investigated. It is found that molecular architectures have a noteworthy impact on the aggregative properties. For linear diblock copolymers, the CMC declines with increasing solvophobic length but rises with increasing solvophilic length. Nonetheless, the solvophobic group has comparatively greater influence on the CMC. Imposition of the star, dendritic, or cyclic structures onto the solvophobic or solvophilic parts of the polymeric surfactant leads to an increase in the CMC. On the contrary, polymers imposed with the greater degree of the rigidity on the solvophobic or solvophilic block have lower CMC. The addition of solvophobic additives results in a decrease of CMC as well. The effects of the concentration and length of the additives on the aggregative behaviors of polymer surfactants were investigated. Interesting supramolecular structures such as caterpillar and worm-like micelles were observed.

  10. Molecular Dynamics: New Frontier in Personalized Medicine.

    PubMed

    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. PMID:26827606

  11. Molecular Dynamics: New Frontier in Personalized Medicine.

    PubMed

    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.

  12. Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events

    SciTech Connect

    Voter, A.F.

    1997-05-01

    I derive a general method for accelerating the molecular-dynamics (MD) simulation of infrequent events in solids. A bias potential ({Delta}V{sub b}) raises the energy in regions other than the transition states between potential basins. Transitions occur at an accelerated rate and the elapsed time becomes a statistical property of the system. {Delta}V{sub b} can be constructed without knowing the location of the transition states and implementation requires only first derivatives. I examine the diffusion mechanisms of a 10-atom Ag cluster on the Ag(111) surface using a 220 {mu}s hyper-MD simulation. {copyright} {ital 1997} {ital The American Physical Society}

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

    PubMed

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

    2010-01-01

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

  14. Molecular dynamics simulation of ice XII

    NASA Astrophysics Data System (ADS)

    Borzsák, István; Cummings, Peter T.

    1999-02-01

    Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.

  15. Crystallization of nickel nanoclusters by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Chamati, H.; Gaminchev, K.

    2012-12-01

    We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.

  16. MDLab: a molecular dynamics simulation prototyping environment.

    PubMed

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

    2010-05-01

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

  17. Molecular dynamics of the excitatory synapse.

    PubMed

    Okabe, Shigeo

    2012-01-01

    Molecular dynamics of synapses are one of the most important factors that control the remodeling of synaptic connection and efficacy of transmission. This chapter focuses on the dynamics of postsynaptic molecular machinery and describes the imaging technologies important for quantitative analyses of synapses, their application to the postsynaptic molecules, and the insights obtained from these analyses. New visualization techniques, such as super-resolution microscopy, will become an indispensable approach to reveal submicron changes of synaptic molecules. New methods of monitoring protein interactions will also be integrated with experimental paradigms of synaptic plasticity. Cell biological analyses, together with cutting-edge imaging technologies, have been applied to the studies of nascent synapse formation, synapse maintenance, and activity-dependent synapse remodeling. From these studies, a variety of new concepts emerged, such as local assembly of postsynaptic scaffolds, presence of "transport packets" of postsynaptic receptors, heterogeneity of actin movement within spines, and activity-free fluctuation of PSD/spine sizes. These new concepts are useful in understanding specific properties of postsynaptic functions and should be integrated in future to build a realistic model of the postsynaptic organization that can explain its remarkable stability and tunability. PMID:22351054

  18. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  19. Dynamic transitions in molecular dynamics simulations of supercooled silicon

    NASA Astrophysics Data System (ADS)

    Mei, Xiaojun; Eapen, Jacob

    2013-04-01

    Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.

  20. Detecting Allosteric Networks Using Molecular Dynamics Simulation.

    PubMed

    Bowerman, S; Wereszczynski, J

    2016-01-01

    Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. PMID:27497176

  1. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    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..

  2. Fiber lubrication: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    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

  3. Development of semiclassical molecular dynamics simulation method.

    PubMed

    Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi

    2016-04-28

    Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383

  4. Nonequilibrium molecular dynamics: The first 25 years

    SciTech Connect

    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.

  5. Molecular Dynamics Studies of Gold Surfaces

    NASA Astrophysics Data System (ADS)

    Ercolessi, F.; Bartolini, A.; Garofalo, M.; Parrinello, M.; Tosatti, E.

    1987-01-01

    In the glue model the total cohesion of a metal is determined by a pairwise atom-atom effective interaction plus a many-body force (the "glue") which is introduced to ensure optimal coordination. Using parameters optimized for gold, we have studied the structural behaviour of the low index surfaces Au(100), Au(110) and Au(111). We have used a simulated annealing strategy based on molecular dynamics to search the lowest surface energy configuration. In all cases the optimal structures are found to be reconstructed, and remarkably similar to some experimentally suggested reconstruction models. The main driving mechanism is the formation of close-packed triangular surface layers favoured by the glue term.

  6. Extended Lagrangian free energy molecular dynamics.

    PubMed

    Niklasson, Anders M N; Steneteg, Peter; Bock, Nicolas

    2011-10-28

    Extended free energy Lagrangians are proposed for first principles molecular dynamics simulations at finite electronic temperatures for plane-wave pseudopotential and local orbital density matrix-based calculations. Thanks to the extended Lagrangian description, the electronic degrees of freedom can be integrated by stable geometric schemes that conserve the free energy. For the local orbital representations both the nuclear and electronic forces have simple and numerically efficient expressions that are well suited for reduced complexity calculations. A rapidly converging recursive Fermi operator expansion method that does not require the calculation of eigenvalues and eigenfunctions for the construction of the fractionally occupied density matrix is discussed. An efficient expression for the Pulay force that is valid also for density matrices with fractional occupation occurring at finite electronic temperatures is also demonstrated.

  7. Development of semiclassical molecular dynamics simulation method.

    PubMed

    Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi

    2016-04-28

    Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed.

  8. Nonequilibrium molecular dynamics of liquid crystals

    NASA Astrophysics Data System (ADS)

    Sarman, S. S.; Cummings, P. T.; Evans, D. J.

    1994-11-01

    During the last 15 years, noneyuilibrium molecular dynamics (NEMD) has been successfully applied to study transport phenomena in fluids that are isotropic at equilibrium. A natural extension is therefore to study liquid crystals, which are anisotropic al equilibrium. The lower symmetry of these systems means that the linear transport coefficients are considerably more complicated than in an isotropic system. Part of the reason for this is that there are crosscouplings between tensors of different rank and parity. Such couplings arc symmetry-forbidden in isotropic phases. In this paper. we review some of fundamental theoretical results we have derived concerning the rheology of liquid crystals. report NEMD simulations of thermal conductivity and shear viscosity of liquid crystals, and present NEMD simulations of shear cessation phenomena. All of the NEMD results are presented for a model liquid crystal fluid which is a modification of the Gay-Borne fluid. The results obtained are in qualitative agreement with experimental measurements on liquid crystal systems.

  9. Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.

    PubMed

    Schwabe, Tobias

    2015-08-20

    For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273

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

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

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

  11. Molecular dynamics studies of metallic glasses

    NASA Astrophysics Data System (ADS)

    Lee, Hyon-Jee

    The thermodynamic, structural, and mechanical properties of metallic glasses are studied using molecular dynamics simulations. Molecular dynamics provides a computational framework to simulate the movement of interacting atoms in response to external perturbations, such as changes in temperature or pressure. In this thesis, a Sutton-Chen potential was chosen to describe the many-body interactions in metals and alloys. Our first application for this approach is to develop a simple model to derive the thermodynamic properties of metallic alloys (Chapter 2). Based on this model, we demonstrate that the glass transition is thermodynamically sensitive to differences between atomic radii and that there is an optimal difference for glass formation. Next, we extend these simulations to elucidate the details of structural organization in the glass (Chapter 3). We find that the liquid phase is characterized by a local five-fold symmetry, which becomes more prominent as the glass phase forms. This five-fold symmetry is related to the formation of icosahedral structures. The mechanical properties of glasses are also investigated and it is found that shear localization, which accompanies a sharp drop in the stress-strain curve, occurs at 45 degree with respect to the loading axis (Chapter 4). The generation of free volume is found to be the dominant mechanism that leads to shear localization, rather than adiabatic heating. Finally, generic first principle potentials are constructed to guide the experimental development of AlTiNi based metallic glasses (Chapter 5). Together, the results from these simulations improve our understanding of the thermodynamic, structural, and mechanical properties of metallic glasses and will aid computer-driven materials design.

  12. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect

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

    1998-02-01

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

  13. Molecular dynamics simulations of supramolecular polymer rheology

    NASA Astrophysics Data System (ADS)

    Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.

    2010-11-01

    Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.

  14. Molecular Dynamics Simulation of Telomere and TRF1

    NASA Astrophysics Data System (ADS)

    Kaburagi, Masaaki; Fukuda, Masaki; Yamada, Hironao; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako; Kato, Takamitsu A.; Uesaka, Mitsuru

    Telomeres play a central role in determining longevity of a cell. Our study focuses on the interaction between telomeric guanines and TRF1 as a means to observe the telomeric based mechanism of the genome protection. In this research, we performed molecular dynamics simulations of a telomeric DNA and TRF1. Our results show a stable structure with a high affinity for the specific protein. Additionally, we calculated the distance between guanines and the protein in their complex state. From this comparison, we found the calculated values of distance to be very similar, and the angle of guanines in their complex states was larger than that in their single state.

  15. Molecular beam studies of reaction dynamics

    SciTech Connect

    Lee, Y.T.

    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.

  16. Molecular-dynamic study of liquid ethylenediamine

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  17. Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics

    PubMed Central

    2015-01-01

    Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406

  18. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    SciTech Connect

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  19. Recovering position-dependent diffusion from biased molecular dynamics simulations

    SciTech Connect

    Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

  20. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

    PubMed Central

    Chen, Rui; Mias, George I.; Li-Pook-Than, Jennifer; Jiang, Lihua; Lam, Hugo Y. K.; Chen, Rong; Miriami, Elana; Karczewski, Konrad J.; Hariharan, Manoj; Dewey, Frederick E.; Cheng, Yong; Clark, Michael J.; Im, Hogune; Habegger, Lukas; Balasubramanian, Suganthi; O'Huallachain, Maeve; Dudley, Joel T.; Hillenmeyer, Sara; Haraksingh, Rajini; Sharon, Donald; Euskirchen, Ghia; Lacroute, Phil; Bettinger, Keith; Boyle, Alan P.; Kasowski, Maya; Grubert, Fabian; Seki, Scott; Garcia, Marco; Whirl-Carrillo, Michelle; Gallardo, Mercedes; Blasco, Maria A.; Greenberg, Peter L.; Snyder, Phyllis; Klein, Teri E.; Altman, Russ B.; Butte, Atul; Ashley, Euan A.; Nadeau, Kari C.; Gerstein, Mark; Tang, Hua; Snyder, Michael

    2012-01-01

    SUMMARY Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here we present an integrative Personal Omics Profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14-month period. Our iPOP analysis revealed various medical risks, including Type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high coverage genomic and transcriptomic data, which provide the basis of our iPOP, discovered extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and disease states by connecting genomic information with additional dynamic omics activity. PMID:22424236

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

    SciTech Connect

    Vashishta, Priya; Kalia, Rajiv

    2005-02-24

    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.

  2. Thermal transpiration: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    T, Joe Francis; Sathian, Sarith P.

    2014-12-01

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

  3. Thermal transpiration: A molecular dynamics study

    SciTech Connect

    T, Joe Francis; Sathian, Sarith P.

    2014-12-09

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

  4. Nanoscale deicing by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

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

  5. How Dynamic Visualization Technology Can Support Molecular Reasoning

    ERIC Educational Resources Information Center

    Levy, Dalit

    2013-01-01

    This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

  6. Nitrogen Additions Affect Root Dynamics in a Boreal Forest Ecosystem

    NASA Astrophysics Data System (ADS)

    Turner, K. M.; Treseder, K. K.

    2004-12-01

    As with many ecosystems, North American boreal forests are increasingly subjected to anthropogenic nitrogen deposition. To examine potential effects on plant growth, we created nitrogen fertilization plots in three sites along an Alaskan fire chronosequence composed of forests aged 5, 17, and 80 years. Each site had been exposed to two years of nitrogen fertilization, with four control plots and four nitrogen plots per site. General observations indicate that aboveground net primary productivity appears to be nitrogen limited in each site. We hypothesized that nitrogen fertilization would positively influence root dynamics as well, with nitrogen additions resulting in an increase in standing root biomass and length. To test our hypothesis, we used a minirhizotron camera to collect sequential images of roots in the top 10 cm of soil in both nitrogen fertilized and control plots in each site. Images were collected monthly during the growing season, with a total of five sampling times between May 2003 and May 2004. We then analyzed the images with WinRhizotron root measurement software. Nitrogen fertilization had varying effects on root biomass among the three sites, with a significant site by N interaction (P = 0.039). A decrease in root biomass was observed in the 5 and 80 year old sites, dropping from 207 g/m2 to 79 g/m2 and from 230 g/m2 to 129 g/m2 for the youngest and oldest sites, respectively. In contrast, root biomass increased from 52 g/m2 to 107 g/m2 in the 17 year old site. (Values are for the top 10 cm of soil only, and likely underestimate total root stocks.) Patterns in standing root lengths diverged from those of root biomass, with a 2.5-fold overall increase under nitrogen fertilization across all sites (P = 0.004). There were no significant differences among sites in nitrogen response. Standing root biomass and length differed from one another in their responses to nitrogen fertilization because nitrogen additions decreased specific root weight (as g

  7. Nanochannel flow past permeable walls via molecular dynamics

    NASA Astrophysics Data System (ADS)

    Xie, Jian-Fei; Cao, Bing-Yang

    2016-07-01

    The nanochannel flow past permeable walls with nanopores is investigated by molecular dynamics (MD) simulations, including the density distribution, velocity field, molecular penetration mechanism and surface friction coefficient. A low density distribution has been found at the gas-wall interface demonstrating the low pressure region. In addition, there exists a jump of the gas density on the permeable surface, which indicates the discontinuity of the density distribution across the permeable surface. On the other hand, the nanoscale vortices are observed in nanopores of the permeable wall, and the reduced mass flux of the flow in nanopores results in a shifted hydrodynamic boundary above the permeable surface. Particularly the slip length of the gas flow on the permeable surface is pronounced a non-linear function of the molecular mean free path, which produces a large value of the tangential momentum accommodation coefficient (TMAC) and a big portion of the diffusive refection. Moreover, the gas-gas interaction and multi-collision among gas molecules may take place in nanopores, which contribute to large values of TMAC. Consequently the boundary friction coefficient on the permeable surface is increased because of the energy dissipation consumed by the nanoscale vortices in nanopores. The molecular boundary condition provides us with a new picture of the nanochannel flow past the permeable wall with nanopores.

  8. Rempi Studies of Molecular Reaction Dynamics.

    NASA Astrophysics Data System (ADS)

    Black, John Forbes

    Available from UMI in association with The British Library. Requires signed TDF. Resonance-Enhanced Multi-Photon Ionisation (REMPI qv.) is used to prepare and probe systems undergoing unimolecular decomposition. It is shown that the highly efficient state selective nature of the REMPI process is well suited to both highly dynamical situations such as the "A-Band" dissociation of MeI at around 280nm and to the slower "Quasi-statistical" dissociations of the mainifold of states of the MeI(+) cation. In the study of the neutral dissociation we attempt to extract the population distributions of the quantum states "by implication" as has been done previously. We demonstrate the failings of the time-of-flight technique in being unable to do this effectively. A comparison with previous studies is made. We report the first rotationally resolved spectrum of a polyatomic (N atoms > 2) photofragment (Me from the "A-Band" photodissociation of MeI) and propose a mechanism to account for the observed differences of the rotational populations in the different dissociation channels. Two-photon linestrength theory incorporating alignment effects is extended to symmetric tops to analyse the data. The pre-dissociation dynamics of a high lying Rydberg state of the methyl radical have been extracted as part of a spectroscopic study performed on CH _3 and CD_3. The dynamics are compared to existing studies on the near-neighbours NH_3 and ND_3 with some apparent correlation. In the dissociations of the A and B states of the MeI(+) cation we are able to provide some more evidence for existing ideas that the A state dissociates by rapid inter-conversion to highly excited levels of the ground state whereas the B state dissociates in a more direct manner. We identify two existing features in the REMPI spectrum of MeI in the "A-Band" region as molecular Rydberg resonances and show that an interesting competition exists between the direct photodissociation and the "virtual" state involved in

  9. Molecular dynamics simulations of unsaturated lipid bilayers

    NASA Astrophysics Data System (ADS)

    Rabinovich, Alexander L.; Balabaev, Nikolay K.

    2001-02-01

    Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.

  10. Molecular dynamics simulations of unsaturated lipid bilayers

    NASA Astrophysics Data System (ADS)

    Rabinovich, Alexander L.; Balabaev, Nikolay K.

    2000-02-01

    Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.

  11. Molecular chaperone-mediated nuclear protein dynamics.

    PubMed

    Echtenkamp, Frank J; Freeman, Brian C

    2014-05-01

    Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus. PMID:24694369

  12. Molecular chaperone-mediated nuclear protein dynamics.

    PubMed

    Echtenkamp, Frank J; Freeman, Brian C

    2014-05-01

    Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus.

  13. Nanoscale deicing by molecular dynamics simulation.

    PubMed

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-08-14

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion. PMID:27431975

  14. Integrating influenza antigenic dynamics with molecular evolution

    PubMed Central

    Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew

    2014-01-01

    Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547

  15. Molecular Dynamics Simulations of Coulomb Explosion

    SciTech Connect

    Bringa, E M

    2002-05-17

    A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.

  16. Molecular dynamics simulations of gold nanomaterials

    NASA Astrophysics Data System (ADS)

    Wang, Yanting

    We have carried out Molecular Dynamics simulations to study the thermal stability and melting behavior of gold nanoclusters and gold nanorods. The surface is found to play a very important role in both gold nanomaterials. Upon cooling from the liquid, we find that gold nanoclusters with 600-3000 atoms crystallize into a Mackay icosahedron. Upon heating, the {111} facets on the surface of the Mackay icosahedral gold nanoclusters soften but do not premelt below the bulk melting temperature. We attribute this surface softening to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size. Upon heating, our simulated gold nanorods undergo a shape transformation preceding the melting transition. The shape transformation is induced by a minimization of the surface free energy, and is accompanied by a complete reconstruction of the internal structure driven by the surface change. During the transformation, the atoms on the end caps of the rod move to the sides of the rods, leading the rods to be shorter and wider. After the transformation, the surface of the stable intermediate state rod is mostly covered by the more stable {111} facets, other than the less stable {110} and {100} facets covering the sides of the initial constructed rod.

  17. Molecular dynamics studies of lanthanum chloride solutions

    SciTech Connect

    Meier, W.; Bopp, Ph. ); Probst, M.M. ); Spohr, E. ); Lin, J.L. )

    1990-05-31

    Molecular dynamics studies are reported for LaCl{sub 3} solutions at two different concentrations and temperatures, and for isolated aqueous La{sup 3+} ions. Ion-water clusters La(H{sub 2}O){sub n}{sup 3+} with n = 61 and n = 100 and systems consisting of one ion and 100 or 200 water molecules in the usual periodic box, as well as solutions of 7 (4) cations and 21 (12) anions in 190 (200) water molecules, corresponding to 2 and 1.1 m solutions, respectively, were investigated. The 2 m solution was investigated at two different temperatures. The results for the static structure, with special emphasis on the hydration structure of the La{sup 3+} ion, are discussed in terms of radial distribution functions and resulting hydration numbers, and various other correlations. These results are compared with X-ray data and discussed in light of the hydration numbers observed for aqueous ions in general.

  18. Efficient compression of molecular dynamics trajectory files.

    PubMed

    Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James

    2012-10-15

    We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases.

  19. Quantum molecular dynamics simulations of dense matter

    SciTech Connect

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  20. Molecular dynamics studies of protein folding and aggregation

    NASA Astrophysics Data System (ADS)

    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

  1. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  2. Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution

    SciTech Connect

    Bossis, Fabrizio; Palese, Luigi L.

    2011-01-07

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

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2014-09-01

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

  6. Molecular dynamics of biaxial nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Sarman, Sten

    1996-01-01

    We devise a constraint algorithm that makes the angular velocity of the director of a liquid crystal a constant of motion. When the angular velocity is set equal to zero, a director based coordinate system becomes an inertial frame. This is a great advantage because most thermodynamic properties and time correlation functions of a liquid crystal are best expressed relative to a director based coordinate system. One also prevents the director reorientation from interfering with the tails of the time correlation functions. When the angular velocity is forced to be zero the constraints do not do any work on the system. This makes it possible to prove that ensemble averages of phase functions and time correlation functions are unaffected by the director constraint torques. The constraint algorithm also facilitates generalization of nonequilibrium molecular dynamics algorithms to liquid crystal phases. In order to test the algorithm numerically we have simulated a biaxial nematic phase of a variant of the Gay-Berne fluid [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)]. The director constraint algorithm works very well. We have calculated the velocity autocorrelation functions and the self diffusion coefficients. In a biaxial nematic liquid crystal there are three independent components of the self-diffusion tensor. They have been found to be finite and different thus proving that we really simulate a liquid rather than a solid and that the symmetry is biaxial. Simulation of biaxial liquid crystals requires fairly large systems. We have therefore developed an algorithm that we run on a parallel computer instead of an ordinary work station.

  7. An Inside Look at Traube's Rule: A Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Dickey, Allison; Faller, Roland

    2006-03-01

    According to Traube's Rule [1], the alcohol concentration required to maintain the interfacial tension (γ) of a bilayer is reduced by a factor of three for each additional CH2 group that is added to the alkyl chain of the alcohol. Recent experimental work confirmed that Traube’s Rule applies to 1-stearoyl, 2-oleoyl phosphatidylcholine (SOPC) lipid bilayers that are exposed to alcohol solutions of methanol, ethanol, propanol, and butanol [2]. To examine the molecular mechanisms leading to Traube’s Rule, we use molecular dynamics simulations to study the interactions between a dipalmitoylphsphatidylcholine (DPPC) bilayer and ethanol, propanol, and butanol solutions. We first examine how the bilayer structure variation depends on alcohol chain length via the area per lipid headgroup, lipid chain disorder, and electron distribution functions. We also study the alcohol dynamics within the bilayer by monitoring the time length, number, and location of hydrogen bonds. Lipid mean squared displacements are also calculated to determine the extent to which lipid mobility is affected by alcohols. [1] I. Traube Liebigs Annalen (1891)[2] H. Ly, M. Longo Biophys J (2004)

  8. Implementation of Green's function molecular dynamics: An extension to LAMMPS

    NASA Astrophysics Data System (ADS)

    Kong, Ling Ti; Bartels, Guido; Campañá, Carlos; Denniston, Colin; Müser, Martin H.

    2009-06-01

    reducing the problem from three dimensions to two dimensions without compromising the physical essence of the problem. Solution method: See "Nature of problem". Restrictions: The mean equilibrium positions of the GFMD surface atoms must be in a plane and be periodic in the plane, so that the Born-von Karman boundary condition can be used. In addition, only deformation within the harmonic regime is expected in the surface layer during Green's function molecular dynamics. Running time: FixGFC varies from minutes to days, depending on the system size, the numbers of processors used, and the complexity of the force field. FixGFMD varies from seconds to days depending on the system size and numbers of processors used. References: [1] C. Campañá, M.H. Müser, Phys. Rev. B 74 (2006) 075420.

  9. Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation.

    PubMed

    Fang, Jiansong; Wu, Ping; Yang, Ranyao; Gao, Li; Li, Chao; Wang, Dongmei; Wu, Song; Liu, Ai-Lin; Du, Guan-Hua

    2014-12-01

    In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds. PMID:26579414

  10. Frontiers in molecular dynamics simulations of DNA.

    PubMed

    Pérez, Alberto; Luque, F Javier; Orozco, Modesto

    2012-02-21

    It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global

  11. Accelerated Molecular Dynamics Simulations of Reactive Hydrocarbon Systems

    SciTech Connect

    Stuart, Steven J.

    2014-02-25

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

  12. Molecular dynamics simulations of hydrogen diffusion in aluminum

    DOE PAGES

    Zhou, X. W.; El Gabaly, F.; Stavila, V.; Allendorf, M. D.

    2016-03-23

    In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

  13. CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS

    SciTech Connect

    Swanson, Jessica

    2011-08-31

    This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.

  14. Molecular Dynamics Simulations of Highly Charged Green Fluorescent Proteins

    SciTech Connect

    Lau, E Y; Phillips, J L; Colvin, M E

    2009-03-26

    A recent experimental study showed that green fluorescent protein (GFP) that has been mutated to have ultra-high positive or negative net charges, retain their native structure and fluorescent properties while gaining resistance to aggregation under denaturing conditions. These proteins also provide an ideal test case for studying the effects of surface charge on protein structure and dynamics. They have performed classical molecular dynamics (MD) simulations on the near-neutral wildtype GFP and mutants with net charges of -29 and +35. They analyzed the resulting trajectories to quantify differences in structure and dynamics between the three GFPs. This analyses shows that all three proteins are stable over the MD trajectory, with the near-neutral wild type GFP exhibiting somewhat more flexibility than the positive or negative GFP mutants, as measured by the order parameter and changes in phi-psi angles. There are more dramatic differences in the properties of the water and counter ions surrounding the proteins. The water diffusion constant near the protein surface is closer to the value for bulk water in the positively charged GFP than in the other two proteins. Additionally, the positively charged GFP shows a much greater clustering of the counter ions (CL-) near its surface than corresponding counter ions (Na+) near the negatively charged mutant.

  15. Masses, luminosities and dynamics of galactic molecular clouds

    NASA Technical Reports Server (NTRS)

    Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.

    1987-01-01

    Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.

  16. Exploring the free energy surface using ab initio molecular dynamics

    DOE PAGES

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-22

    Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method inmore » collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.« less

  17. Insights into Buforin II Membrane Translocation from Molecular Dynamics Simulations

    PubMed Central

    Elmore, Donald E.

    2012-01-01

    Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner through forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides. PMID:23022591

  18. Pasta Elasticity: Molecular dynamics simulations of nuclear pasta deformations

    NASA Astrophysics Data System (ADS)

    Caplan, M. E.; Horowitz, C. J.; Berry, D. K.

    2015-04-01

    Nuclear pasta is expected in the inner crust of neutron stars at densities near the nuclear saturation density. In this work, the elastic properties of pasta are calculated from large scale molecular dynamics simulations by deforming the simulation volume. Our model uses a semi-classical two-nucleon potential that reproduces nuclear saturation. We report the shear modulus and breaking strain of a variety of pasta phases for different temperatures, densities, and proton fractions. The presence of pasta in neutron stars could have significant effects on crustal oscillations and could be inferred from observations of soft-gamma repeaters. Additionally, these elastic parameters will enable us to improve estimates of the maximum size and lifetime of ``mountains'' on the crust, which could efficiently radiate gravitational waves.

  19. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    SciTech Connect

    Splettstoesser, Thomas; Holmes, Kenneth; Noe, Frank; Smith, Jeremy C

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

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

    NASA Astrophysics Data System (ADS)

    Abraham, J. W.; Strunskus, T.; Faupel, F.; Bonitz, M.

    2016-05-01

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

  1. Dynamical analysis of highly excited molecular spectra

    SciTech Connect

    Kellman, M.E.

    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.

  2. Systematic Coarse-graining of Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Voth, Gregory

    2015-03-01

    Coarse-grained (CG) models can provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms that are correlated over distance scales of many covalent bond lengths and at long time scales. Systematic variational coarse-graining methods based on information from molecular dynamics simulations of finer-grained (e.g., all-atom) models provide attractive tools for the systematic development of CG models. Examples include the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, and results from the former theory will be presented in this talk. In addition, a new approach will be presented that is appropriate for the ``ultra coarse-grained'' (UCG) regime, e.g., at a coarse-grained resolution that is much coarser than one amino acid residue per CG particle in a protein. At this level of coarse-graining, one is faced with the possible existence of multiple metastable states ``within'' the CG sites for a given UCG model configuration. I will therefore describe newer systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain aspects of this work connect back to single-state force matching and open up new avenues for method development. This general body of theory and algorithm provides a formal statistical mechanical basis for the coarse-graining of fine-grained molecular dynamics simulation data at various levels of CG resolution. Representative applications will be described as time allows.

  3. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.

    PubMed

    Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G

    2016-04-12

    Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features. PMID:26949976

  4. Elucidation of molecular dynamics of invasive species of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...

  5. Attosecond molecular dynamics: fact or fiction?

    NASA Astrophysics Data System (ADS)

    Lépine, Franck; Ivanov, Misha Y.; Vrakking, Marc J. J.

    2014-03-01

    The emerging application of attosecond techniques to molecular systems allows the role of electronic coherence in the control of chemical reactions to be investigated. Prompt ionization of molecules by an attosecond pulse may induce charge migration across a molecular structure on attosecond to few-femtosecond timescales, thereby possibly determining the subsequent relaxation pathways that a molecule may take. We discuss how proposals for this 'charge-directed reactivity' fit within the current understanding of quantum control and review the current state of the art of attosecond molecular science. Specifically, we review the role of electronic coherence and coupling of the electronic and nuclear degrees of freedom in high-harmonic spectroscopy and in the first attosecond pump-probe experiments on molecular systems.

  6. Molecular dynamics simulation of interfacial adhesion

    SciTech Connect

    Yarovsky, I.; Chaffee, A.L.

    1996-12-31

    Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.

  7. Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

    PubMed Central

    2013-01-01

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176

  8. The study of dynamics heterogeneity and slow down of silica by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    San, L. T.; Hung, P. K.; Hue, H. V.

    2016-06-01

    We have numerically studied the diffusion in silica liquids via the SiOx → SiOx±1, OSiy → OSiy±1 reactions and coordination cells (CC). Five models with temperatures from 1000 to 3500 K have been constructed by molecular dynamics simulation. We reveal that the reactions happen not randomly in the space. In addition, the reactions correlated strongly with the mobility of CC atom. Further we examine the clustering of atoms having unbroken bonds and restored bonds. The time evolution of these clusters under temperature is also considered. The simulation shows that both slow down and dynamic heterogeneity (DH) is related not only to the percolation of restored-rigid clusters near glass transition but also to their long lifetime.

  9. Tunable Interfacial Thermal Conductance by Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Shen, Meng

    We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1

  10. Tunable Interfacial Thermal Conductance by Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Shen, Meng

    We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1

  11. Molecular structure and dynamical properties of niosome bilayers with and without cholesterol incorporation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Ritwiset, Aksornnarong; Krongsuk, Sriprajak; Johns, Jeffrey Roy

    2016-09-01

    Niosomes are non-ionic surfactant vesicles having a bilayer structure formed by self-assembly of hydrated surfactants, usually with cholesterol incorporation. Stability and mechanical properties of niosomes strongly depend on type of non-ionic surfactants and compositions used. In this study we present the structural and dynamical properties of niosome bilayers composed of sorbitan monostearate (Span60) with 0% and 50% cholesterol compositions which are investigated by using molecular dynamics simulations. The simulations reveal that niosome bilayer without cholesterol prefer to form in the gel phase with a higher order structure, while in the presence of cholesterol the bilayer exhibits more fluidity having a less ordered structure. The niosome bilayer with 50% cholesterol inclusion shows an increase of area per lipid (∼11%) and thickness (∼39%) compared with the niosome bilayer without cholesterol. The Span60 tailgroup orientation of the niosome bilayers without cholesterol exhibits more tilt (34.5o ± 0.5) than that of the bilayer with 50% cholesterol (15.4o ± 0.8). Additionally, our results show that the addition of cholesterol to the bilayer causes the higher in lateral and transverse diffusion, as well as an increase in the hydrogen bond number between Span60 and water. Such characteristics not only enhance the niosome stability but also increase the fluidity, which are necessary for the niosomal drug delivery.

  12. The Computer Simulation of Liquids by Molecular Dynamics.

    ERIC Educational Resources Information Center

    Smith, W.

    1987-01-01

    Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)

  13. Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

    SciTech Connect

    Lau, E Y; Krishnan, V V

    2007-07-18

    The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.

  14. Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.

    1999-01-01

    A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.

  15. On electronic representations in molecular reaction dynamics

    NASA Astrophysics Data System (ADS)

    Killian, Benjamin J.

    For many decades, the field of chemical reaction dynamics has utilized computational methods that rely on potential energy surfaces that are constructed using stationary-state calculations. These methods are typically devoid of dynamical couplings between the electronic and nuclear degrees of freedom, a fact that can result in incorrect descriptions of dynamical processes. Often, non-adiabatic coupling expressions are included in these methodologies. The Electron-Nuclear Dynamics (END) formalism, in contrast, circumvents these deficiencies by calculating all intermolecular forces directly at each time step in the dynamics and by explicitly maintaining all electronic-nuclear couplings. The purpose of this work is to offer two new frameworks for implementing electronic representations in dynamical calculations. Firstly, a new schema is proposed for developing atomic basis sets that are consistent with dynamical calculations. Traditionally, basis sets have been designed for use in stationary-state calculations of the structures and properties of molecules in their ground states. As a consequence of common construction techniques that utilize energy optimization methods, the unoccupied orbitals bear little resemblance to physical virtual atomic orbitals. We develop and implement a method for basis set construction that relies upon physical properties of atomic orbitals and that results in meaningful virtual orbitals. These basis sets are shown to provide a significant improvement in the accuracy of calculated dynamical properties such as charge transfer probabilities. Secondly, the theoretical framework of END is expanded to incorporate a multi-configurational representation for electrons. This formalism, named Vector Hartree-Fock, is based in the theory of vector coherent states and utilizes a complete active space electronic representation. The Vector Hartree-Fock method is fully disclosed, with derivation of the equations of motion. The expressions for the equation

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

    NASA Astrophysics Data System (ADS)

    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.

  17. Single Molecule Spectroscopy Illuminating the Molecular Dynamics of Life

    NASA Astrophysics Data System (ADS)

    Webb, Watt W.

    This chapter summarizes a series of new single-molecule spectroscopy investigations in the life sciences at Cornell University that began with our invention of Fluorescence Correlation Spectroscopy (FCS) about 1970. Our invention of FCS became my first focus on the "Molecular Dynamics of Life." It motivated my transition from research on quantum fluctuations and transport in condensed matter physics including superconductivity and in the molecular dynamics of coherent fluctuations and nano-transport in inanimate physical and chemical systems subject to the nonlinear dynamics of continuous phase transitions. These interdisciplinary transitions exemplify the productivity of such interdisciplinary interactions in science.

  18. Interfacial Molecular Searching Using Forager Dynamics

    NASA Astrophysics Data System (ADS)

    Monserud, Jon H.; Schwartz, Daniel K.

    2016-03-01

    Many biological and technological systems employ efficient non-Brownian intermittent search strategies where localized searches alternate with long flights. Coincidentally, molecular species exhibit intermittent behavior at the solid-liquid interface, where periods of slow motion are punctuated by fast flights through the liquid phase. Single-molecule tracking was used here to observe the interfacial search process of DNA for complementary DNA. Measured search times were qualitatively consistent with an intermittent-flight model, and ˜10 times faster than equivalent Brownian searches, suggesting that molecular searches for reactive sites benefit from similar efficiencies as biological organisms.

  19. Dynamics of molecular superrotors in an external magnetic field

    NASA Astrophysics Data System (ADS)

    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.

  20. Molecular dynamics simulations of displacement cascades in GaAs.

    SciTech Connect

    Foiles, Stephen Martin

    2010-04-01

    The quantification of the production of primary defects via displacement cascades is an important ingredient in the prediction of the influence of radiation on the performance of electronic components in radiation environments. Molecular dynamics simulations of displacement cascades are performed for GaAs The interatomic interactions are described using a recently proposed Bond Order Potential, and a simple model of electronic stopping is incorporated. The production of point defects is quantified as a function of recoil energy and recoil species. Correlations in the point defects are examined. There are a large number of anti-site defects nearest-neighbor pairs as well as di-vacancies and larger order vacancy clusters. Radiation damage and ion implantation in materials have been studied via molecular dynamics for many years. A significant challenge in these simulations is the detailed identification and quantification of the primary defect production. For the present case of a compound semiconductor, GaAs, there are a larger number of possible point defects compared to elemental materials; two types of vacancies, two types of interstitials and antisite defects. This is further complicated by the fact that, in addition to the formation of point defects, amorphous zones may also be created. The goal of the current work is to quantify the production of primary defects in GaAs due to radiation exposures. This information will be used as part of an effort to predict the influence of radiation environments on the performance of electronic components and circuits. The data provide the initial state for continuum-level analysis of the temporal evolution of defect populations. For this initial state, it is important to know both the number of the various point defects that may be produced as well as the initial spatial correlations between the primary defects. The molecular dynamics simulations employ a recently developed Bond Order Potential (BOP) for GaAs. The analysis

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

    NASA Astrophysics Data System (ADS)

    Zobač, Vladmír; Lewis, James P.; Jelínek, Pavel

    2016-07-01

    We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.

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

    PubMed

    Zobač, Vladmír; Lewis, James P; Jelínek, Pavel

    2016-07-15

    We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules. PMID:27255903

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

    SciTech Connect

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-28

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    SciTech Connect

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

    2015-01-28

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

  6. VUV studies of molecular photofragmentation dynamics

    SciTech Connect

    White, M.G.

    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.

  7. Molecular dynamics, spin dynamics study of phonon-magnon interactions in BCC iron

    NASA Astrophysics Data System (ADS)

    Perera, Dilina; Landau, David P.; Stocks, G. Malcolm; Nicholson, Don; Eisenbach, Markus; Yin, Junqi

    2013-03-01

    By combining an atomistic many-body potential (Finnis-Sinclair) with a classical Heisenberg-like spin Hamiltonian, we perform combined molecular and spin dynamics simulations to investigate phonon-magnon interactions in BCC iron. The coupling between atomic and spin degrees of freedom is established via a distance dependent exchange interaction derived from first principles electronic structure calculations. Coupled equations of motion are integrated using a second order Suzuki-Trotter decomposition of the exponential time evolution operator. To investigate the effect of lattice vibrations on spin wave spectrum, we calculate spin-spin and density-density dynamic structure factors S(q, ω), and compare that to the results obtained from pure spin dynamics simulations performed on a rigid lattice. In the presence of lattice vibrations, we observe an additional peak in the longitudinal spin-spin dynamic structure factor which coincides with the peak position in density-density dynanmic structure factor. Research sponsored by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, ''Center for Defect Physics,'' an Energy Frontier Research Center

  8. Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations.

    PubMed

    Posokhov, Yevgen O; Kyrychenko, Alexander

    2013-10-01

    The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ~0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of -3.6 kcal/mol, located at 15-16Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8-5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and

  9. Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

    SciTech Connect

    Luchko, T.; Simmerling, C.; Gusarov, S.; Roe, D.R., Case, D.A.; Tuszynski, J.; Kovalenko, A.

    2010-02-01

    We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multiple time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package and is illustrated here on alanine-dipeptide and protein-G.

  10. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber

    PubMed Central

    Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy

    2010-01-01

    We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G. PMID:20440377

  11. [Physical modeling of sedimentary basins, magma mechanics, and molecular dynamics of aqueous solutions]. Technical progress report

    SciTech Connect

    Spera, F.J.

    1993-07-01

    Work at UCSB has been in four areas: (1) Convection in porous media, (2) Geochemical fluid dynamics, (3) Experimental rheometry of silicate melts and (4) Molecular dynamics of silicate solutions. In the past 18 months we have published, have in press or submitted 8 papers (see Appendix) and are currently at work on several others. Additionally, a number of abstracts have been published. A list of these works is presented in the Appendix.

  12. [Physical modeling of sedimentary basins, magma mechanics, and molecular dynamics of aqueous solutions

    SciTech Connect

    Spera, F.J.

    1993-01-01

    Work at UCSB has been in four areas: (1) Convection in porous media, (2) Geochemical fluid dynamics, (3) Experimental rheometry of silicate melts and (4) Molecular dynamics of silicate solutions. In the past 18 months we have published, have in press or submitted 8 papers (see Appendix) and are currently at work on several others. Additionally, a number of abstracts have been published. A list of these works is presented in the Appendix.

  13. Metascalable molecular dynamics simulation of nano-mechano-chemistry

    NASA Astrophysics Data System (ADS)

    Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.

    2008-07-01

    We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.

  14. From molecular dynamics to hydrodynamics: a novel Galilean invariant thermostat.

    PubMed

    Stoyanov, Simeon D; Groot, Robert D

    2005-03-15

    This paper proposes a novel thermostat applicable to any particle-based dynamic simulation. Each pair of particles is thermostated either (with probability P) with a pairwise Lowe-Andersen thermostat [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] or (with probability 1-P) with a thermostat that is introduced here, which is based on a pairwise interaction similar to the Nosé-Hoover thermostat. When the pairwise Nosé-Hoover thermostat dominates (low P), the liquid has a high diffusion coefficient and low viscosity, but when the Lowe-Andersen thermostat dominates, the diffusion coefficient is low and viscosity is high. This novel Nosé-Hoover-Lowe-Andersen thermostat is Galilean invariant and preserves both total linear and angular momentum of the system, due to the fact that the thermostatic forces between each pair of the particles are pairwise additive and central. We show by simulation that this thermostat also preserves hydrodynamics. For the (noninteracting) ideal gas at P = 0, the diffusion coefficient diverges and viscosity is zero, while for P > 0 it has a finite value. By adjusting probability P, the Schmidt number can be varied by orders of magnitude. The temperature deviation from the required value is at least an order of magnitude smaller than in dissipative particle dynamics (DPD), while the equilibrium properties of the system are very well reproduced. The thermostat is easy to implement and offers a computational efficiency better than (DPD), with better temperature control and greater flexibility in terms of adjusting the diffusion coefficient and viscosity of the simulated system. Applications of this thermostat include all standard molecular dynamic simulations of dense liquids and solids with any type of force field, as well as hydrodynamic simulation of multiphase systems with largely different bulk viscosities, including surface viscosity, and of dilute gases and plasmas.

  15. Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics

    NASA Astrophysics Data System (ADS)

    Ehrlicher, Allen

    2012-02-01

    Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.

  16. Combining Molecular Dynamics and Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Kaxiras, Efthimios

    2015-03-01

    The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.

  17. Pseudorotational Dynamics of Small Molecular Systems

    NASA Astrophysics Data System (ADS)

    Hagelberg, Frank

    2001-03-01

    A variety of dynamic effects related to the pseudorotation of triatomic singly charged species is explored using the Electron Nuclear Dynamics(END)Theory. The concepts relevant to the motion studied are developed through the analysis of the simplest polyatomic molecule, namely H3+. It is shown that the limiting situation of circular pseudorotation is unattainable for this case. This observation is explained by the anisotropy of the ground state potential energy surface caused by the interaction between the D3h ground state of the molecule and its twofold degenerate first excited state. Further, pseudorotational motion is demonstrated to induce a rotational mode which in turn couples the two shape oscillation modes by action of the Coriolis force. Analogous phenomena are found for Li3+. The Jahn-Teller system C3+ exhibits a range of new motional effects. Particularly, a characteristic frequency shift between the two shape oscillation modes is obtained, resulting from the anisotropy in the curvature of the C2v minimum of C3+. The Jahn-Teller parameters of the system are determined from Electron Nuclear Dynamics simulations.

  18. Hydrolysis of Al3+ from constrained molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

    2006-02-01

    We investigated the hydrolysis reactions of Al3+ in AlCl3 aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of ΔG0≃8.0kcalmol-1 the hydrolysis constant pKa1 is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al3+ in acidic conditions is at least 4kcalmol-1 higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH.

  19. Molecular dynamics insights into human aquaporin 2 water channel.

    PubMed

    Binesh, A R; Kamali, R

    2015-12-01

    In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney. PMID:26489820

  20. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors

    PubMed Central

    Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem

    2015-01-01

    Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. PMID:25688287

  1. Molecular dynamics insights into human aquaporin 2 water channel.

    PubMed

    Binesh, A R; Kamali, R

    2015-12-01

    In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney.

  2. Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

    NASA Astrophysics Data System (ADS)

    Elliott, William Dewey

    1995-01-01

    A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over

  3. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    PubMed Central

    Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro

    2012-01-01

    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. PMID:22500085

  4. Molecular dynamics simulations on the interactions of low molecular weight natural organic acids with C60.

    PubMed

    Sun, Qian; Xie, Hong-Bin; Chen, Jingwen; Li, Xuehua; Wang, Zhuang; Sheng, Lianxi

    2013-07-01

    As an important part of dissolved organic matter (DOM), low molecular weight organic acids (LOAs) may play a key role in the process for DOM stabilizing carbon nanomaterials (e.g. C60) suspensions in aquatic environment. In addition, both LOAs and C60 have been detected in the troposphere and therefore have a chance to interact with each other in the gaseous phase. However, the mechanism for LOAs-C60 interactions and their environmental implications need further investigations. In this study, molecular dynamics (MD) simulation was employed to investigate the interactions between both neutral and ionic LOAs with C60 in vacuum and water. The results showed that the adsorptions of all LOAs on C60 in energy are favorable, and the aromatic acids have stronger interactions with C60 than the aliphatic acids in vacuum and water. The interaction energies (Eint) of the LOA anions with C60 were weaker than those of their corresponding neutral LOA molecules. The models were also developed to predict and interpret Eint based on the results from MD simulations. Dispersion, induction and hydrophobic interactions were found to be the dominating factor in Eint. These findings indicate that cost-efficient MD simulation can be employed as an important tool to predict the adsorption behavior of LOAs on carbon nanomaterials.

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

    SciTech Connect

    Gentry, W.R.; Giese, C.F.

    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.

  6. AceCloud: Molecular Dynamics Simulations in the Cloud.

    PubMed

    Harvey, M J; De Fabritiis, G

    2015-05-26

    We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

  7. How Dynamic Visualization Technology can Support Molecular Reasoning

    NASA Astrophysics Data System (ADS)

    Levy, Dalit

    2012-11-01

    This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and gas. They interact with the visualizations and carry out inquiry activities to make and refine connections between observable phenomena and atomic level processes related to phase change. The explanations proposed by 300 pairs of students in response to pre/post-assessment items have been analyzed using a scale for measuring the level of molecular reasoning. Results indicate that from pretest to posttest, students make progress in their level of molecular reasoning and are better able to connect intermolecular forces and phase change in their explanations. The paper presents the results through the lens of improvement patterns and the metaphor of the "ladder of molecular reasoning," and discusses how this adds to our understanding of the benefits of interacting with dynamic molecular visualizations.

  8. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  9. Electron-phonon interaction within classical molecular dynamics

    DOE PAGES

    Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.

    2016-07-14

    Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

  10. Electron-phonon interaction within classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.

    2016-07-01

    We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.

  11. Numerical methods for molecular dynamics. Progress report

    SciTech Connect

    Skeel, R.D.

    1991-12-31

    This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.

  12. Molecular dynamics simulation studies of liquid crystalline materials

    NASA Astrophysics Data System (ADS)

    Tian, Pu

    Molecular dynamics (MD) simulation studies of the phase behavior, the response to an applied field of nematic liquid crystalline (LC) materials and interactions of nanoparticles in isotropic mesogenic materials are presented in this work. Molecular models used include the rigid bead-necklace model and soft spherocylinders. Free energy calculations applying thermodynamic integration and the Gibbs-Duhem integration method were used to establish the (T, P) phase diagram of the repulsive bead-necklace model, subsequently the Gibbs-Duhem integration method was further utilized to investigate the influence of attractive interactions on the phase behavior of the bead-necklace model. Analysis of order and thermodynamics of LC phase transitions (Isotropic-Nematic transition and Nematic-Smectic A transition) demonstrate that this simple model can capture the basic physics of liquid crystalline phases, and good agreement with experimental results is obtained. Further addition of chemical details to this multiple interaction sites model is much easier than to the idealized models (Gay-Berne, Spherocylinders) while the computation cost increase with respect to these idealized models is minimal. With a mean field representation of field-molecules interaction, MD simulation studies of the switching behavior of nematic LC, which is the basis of many LC devices, were performed. The switching mechanisms were explained in terms of the compromise between the elastic energy and field-molecules interactions. Qualitative agreement with experiments confirmed the validity of the mean field approximation. Finally, using the standard umbrella sampling technique and MD simulations, the potential of mean force between two nanoparticles in solvent of spherocylinders is calculated. It is found that while dispersed nanoparticles will delay the Isotropic-Nematics transition to higher density (lower temperature), they can induce local ordering fluctuations (within a few molecular lengths of the

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

    SciTech Connect

    Rudd, R E

    2001-12-21

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

  14. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    SciTech Connect

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-09-29

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition.

  15. Input File Creation for the Molecular Dynamics Program LAMMPS.

    2001-05-30

    The program creates an input data file for the molecular dynamics program LAMMPS. The input file created is a liquid mixture between two walls explicitly composed of particles. The liquid molecules are modeled as a bead-spring molecule. The input data file specifies the position and topology of the starting state. The data structure of input allows for dynamic bond creation (cross-linking) within the LAMMPS code.

  16. Imaging the molecular dynamics of dissociative electron attachment to water

    SciTech Connect

    Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali

    2009-10-19

    Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.

  17. Accelerating chemical reactions: Exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics

    PubMed Central

    Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.

    2011-01-01

    A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673

  18. Parallel Molecular Dynamics Stencil : a new parallel computing environment for a large-scale molecular dynamics simulation of solids

    NASA Astrophysics Data System (ADS)

    Shimizu, Futoshi; Kimizuka, Hajime; Kaburaki, Hideo

    2002-08-01

    A new parallel computing environment, called as ``Parallel Molecular Dynamics Stencil'', has been developed to carry out a large-scale short-range molecular dynamics simulation of solids. The stencil is written in C language using MPI for parallelization and designed successfully to separate and conceal parts of the programs describing cutoff schemes and parallel algorithms for data communication. This has been made possible by introducing the concept of image atoms. Therefore, only a sequential programming of the force calculation routine is required for executing the stencil in parallel environment. Typical molecular dynamics routines, such as various ensembles, time integration methods, and empirical potentials, have been implemented in the stencil. In the presentation, the performance of the stencil on parallel computers of Hitachi, IBM, SGI, and PC-cluster using the models of Lennard-Jones and the EAM type potentials for fracture problem will be reported.

  19. Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

    PubMed Central

    Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

    2014-01-01

    We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use 13C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc. PMID:23818175

  20. Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics

    SciTech Connect

    Holian, B.L.; Voter, A.F.; Ravelo, R.

    1995-09-01

    The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ``demon,`` which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations.

  1. Molecular circuits for dynamic noise filtering.

    PubMed

    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. PMID:27078094

  2. Quantum dynamics of light-driven chiral molecular motors.

    PubMed

    Yamaki, Masahiro; Nakayama, Shin-ichiro; Hoki, Kunihito; Kono, Hirohiko; Fujimura, Yuichi

    2009-03-21

    The results of theoretical studies on quantum dynamics of light-driven molecular motors with internal rotation are presented. Characteristic features of chiral motors driven by a non-helical, linearly polarized electric field of light are explained on the basis of symmetry argument. The rotational potential of the chiral motor is characterized by a ratchet form. The asymmetric potential determines the directional motion: the rotational direction is toward the gentle slope of the asymmetric potential. This direction is called the intuitive direction. To confirm the unidirectional rotational motion, results of quantum dynamical calculations of randomly-oriented molecular motors are presented. A theoretical design of the smallest light-driven molecular machine is presented. The smallest chiral molecular machine has an optically driven engine and a running propeller on its body. The mechanisms of transmission of driving forces from the engine to the propeller are elucidated by using a quantum dynamical treatment. The results provide a principle for control of optically-driven molecular bevel gears. Temperature effects are discussed using the density operator formalism. An effective method for ultrafast control of rotational motions in any desired direction is presented with the help of a quantum control theory. In this method, visible or UV light pulses are applied to drive the motor via an electronic excited state. A method for driving a large molecular motor consisting of an aromatic hydrocarbon is presented. The molecular motor is operated by interactions between the induced dipole of the molecular motor and the electric field of light pulses. PMID:19290336

  3. Molecular dynamics in polymers, polymer networks, and model compounds by dielectric relaxation spectroscopy

    NASA Astrophysics Data System (ADS)

    Fitz, Benjamin David

    Segmental dynamics are investigated in model compounds, polymers, and network-forming polymers. Two aspects of these materials are investigated: (1) the role of molecular structure and connectivity on determining the characteristics of the segmental relaxation, and (2) monitoring the variations in the segmental dynamics during network-forming chemical reactions. We quantify the most important aspects of the dynamics: the relaxation shape, the relaxation strength, the relaxation time, and the temperature dependencies of these properties. Additionally, two general segmental dynamics issues of interest are the length-scale and the homogeneous/heterogeneous aspects. A judicious choice of network-forming polymer provides for the determination of an upper bound on the length-scale. A comparison of relaxation characteristics between dynamic light scattering (measuring density fluctuations) and dielectric relaxation spectroscopy (measuring segmental dipolar reorientation) provides one evaluation of the heterogeneity issue. Dipole dynamics in small molecule model compounds show the influence of molecular connectivity on the cooperative molecular response associated with the glass transition. A rigid, nonpolar, cyanate ester network is shown to develop an anomalous relaxation process during crosslinking. A specific local mode of motion is assigned. Additionally, the main relaxation becomes extraordinarily broad during the course of the network formation, due to markedly increased segmental rigidity and loss of configurational entropy.

  4. Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Bebout, Brad M.; Visscher, Pieter T.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2

  5. Optimizing legacy molecular dynamics software with directive-based offload

    NASA Astrophysics Data System (ADS)

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

    2015-10-01

    Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.

  6. Open boundary molecular dynamics of sheared star-polymer melts.

    PubMed

    Sablić, Jurij; Praprotnik, Matej; Delgado-Buscalioni, Rafael

    2016-02-28

    Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution. PMID:26820315

  7. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    PubMed Central

    De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.

    2015-01-01

    Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

  8. Reasoning with Atomic-Scale Molecular Dynamic Models

    ERIC Educational Resources Information Center

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

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

  9. Molecular dynamics simulation of size segregation in three dimensions

    NASA Astrophysics Data System (ADS)

    Gallas, Jason A. C.; Herrmann, Hans J.; Pöschel, Thorsten; Sokołowski, Stefan

    1996-01-01

    We report the first three-dimensional molecular dynamics simulation of particle segregation by shaking. Two different containers are considered: one cylindrical and another with periodic boundary conditions. The dependence of the time evolution of a test particle inside the material is studied as a function of the shaking frequency and amplitude, damping coefficients, and dispersivity.

  10. Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

    NASA Technical Reports Server (NTRS)

    Menon, Madhu

    1998-01-01

    In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.

  11. Clustering molecular dynamics trajectories for optimizing docking experiments.

    PubMed

    De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

    2015-01-01

    Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

  12. Clustering molecular dynamics trajectories for optimizing docking experiments.

    PubMed

    De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

    2015-01-01

    Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

  13. Optimizing legacy molecular dynamics software with directive-based offload

    SciTech Connect

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

    2015-05-14

    The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.

  14. Optimizing legacy molecular dynamics software with directive-based offload

    DOE PAGES

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

    2015-05-14

    The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  16. Cellulose microfibril formation within a coarse grained molecular dynamics

    NASA Astrophysics Data System (ADS)

    Nili, Abdolmadjid; Shklyaev, Oleg; Crespi, Vincent; Zhao, Zhen; Zhong, Linghao; CLSF Collaboration

    2014-03-01

    Cellulose in biomass is mostly in the form of crystalline microfibrils composed of 18 to 36 parallel chains of polymerized glucose monomers. A single chain is produced by cellular machinery (CesA) located on the preliminary cell wall membrane. Information about the nucleation stage can address important questions about intermediate region between cell wall and the fully formed crystalline microfibrils. Very little is known about the transition from isolated chains to protofibrils up to a full microfibril, in contrast to a large body of studies on both CesA and the final crystalline microfibril. In addition to major experimental challenges in studying this transient regime, the length and time scales of microfibril nucleation are inaccessible to atomistic molecular dynamics. We have developed a novel coarse grained model for cellulose microfibrils which accounts for anisotropic interchain interactions. The model allows us to study nucleation, kinetics, and growth of cellulose chains/protofibrils/microfibrils. This work is supported by the US Department of Energy, Office of Basic Energy Sciences as part of The Center for LignoCellulose Structure and Formation, an Energy Frontier Research Center.

  17. Mechanical properties of irradiated nanowires - A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Figueroa, Emilio; Tramontina, Diego; Gutiérrez, Gonzalo; Bringa, Eduardo

    2015-12-01

    In this work we study, by means of molecular dynamics simulation, the change in the mechanical properties of a gold nanowire with pre-existing radiation damage. The gold nanowire is used as a simple model for a nanofoam, made of connected nanowires. Radiation damage by keV ions leads to the formation of a stacking fault tetrahedron (SFT), and this defect leads to a reduced plastic threshold, as expected, when the nanowire is subjected to tension. We quantify dislocation and twin density during the deformation, and find that the early activation of the SFT as a dislocation source leads to reduced dislocation densities compared to the case without radiation damage. In addition, we observed a total destruction of the SFT, as opposed to a recent simulation study where it was postulated that SFTs might act as self-generating dislocation sources. The flow stress at large deformation is also found to be slightly larger for the irradiated case, in agreement with recent experiments.

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

    PubMed

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

    2016-11-01

    The most recent experimental advances could provide ways for the fabrication of several atomic thick and planar forms of boron atoms. For the first time, we explore the mechanical properties of five types of boron films with various vacancy ratios ranging from 0.1-0.15, using molecular dynamics simulations with ReaxFF force field. It is found that the Young's modulus and tensile strength decrease with increasing the temperature. We found that boron sheets exhibit an anisotropic mechanical response due to the different arrangement of atoms along the armchair and zigzag directions. At room temperature, 2D Young's modulus and fracture stress of these five sheets appear in the range 63-136 N m(-1) and 12-19 N m(-1), respectively. In addition, the strains at tensile strength are in the ranges of 9%-14%, 11%-19%, and 10%-16% at 1, 300, and 600 K, respectively. This investigation not only reveals the remarkable stiffness of 2D boron, but establishes relations between the mechanical properties of the boron sheets to the loading direction, temperature and atomic structures. PMID:27678335

  19. Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A

    SciTech Connect

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

    1999-03-16

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

  20. Optimization of replica exchange molecular dynamics by fast mimicking.

    PubMed

    Hritz, Jozef; Oostenbrink, Chris

    2007-11-28

    We present an approach to mimic replica exchange molecular dynamics simulations (REMD) on a microsecond time scale within a few minutes rather than the years, which would be required for real REMD. The speed of mimicked REMD makes it a useful tool for "testing" the efficiency of different settings for REMD and then to select those settings, that give the highest efficiency. We present an optimization approach with the example of Hamiltonian REMD using soft-core interactions on two model systems, GTP and 8-Br-GTP. The optimization process using REMD mimicking is very fast. Optimization of Hamiltonian-REMD settings of GTP in explicit water took us less than one week. In our study we focus not only on finding the optimal distances between neighboring replicas, but also on finding the proper placement of the highest level of softness. In addition we suggest different REMD simulation settings at this softness level. We allow several replicas to be simulated at the same Hamiltonian simultaneously and reduce the frequency of switching attempts between them. This approach allows for more efficient conversions from one stable conformation to the other.

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

    PubMed

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

    2016-11-01

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

  2. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  3. Theoretical spectroscopy using molecular dynamics: theory and application to CH5(+) and its isotopologues.

    PubMed

    Ivanov, Sergei D; Witt, Alexander; Marx, Dominik

    2013-07-01

    Infrared spectroscopy is a powerful technique to unravel the structure and dynamics of molecular systems of ever increasing complexity. For isolated molecules in the gas phase theoretical approaches that directly rely on solving the Schrödinger equation, either approximately or quasi-exactly, are well established. A distinctly different approach to compute infrared spectra can be based on advanced molecular dynamics, itself being based on classical Newtonian dynamics, in conjunction with concurrent first principles electronic structure calculations. At variance with traditional methods, which are formulated in terms of the Schrödinger representation of quantum mechanics, the molecular dynamics approach stems from Heisenberg's representation and thus relies on computing thermal expectation values of time-correlation functions. Crucial in addition to generating the spectra themselves is their decomposition in terms of modes, which can be assigned to correlated atomic motion. This ab initio molecular dynamics route to compute infrared spectra, and its recent extension to quasiclassical techniques relying on approximate path integral dynamics, is covered in the review part of this Perspective. The usefulness of this unconventional approach, which can be generalized beyond infrared spectroscopy, is demonstrated in detail by applying the full machinery in computing and assigning the infrared spectra of protonated methane and its isotopologues. This particular molecule is often considered to be the most prominent member of the class of floppy or fluxional molecules. CH5(+) has been a longstanding challenge for theoretical infrared spectroscopy because it undergoes intricate large-amplitude motion, which is also reviewed. Molecular dynamics based infrared spectroscopy is general and can be applied to diverse systems such as molecular complexes in the gas phase, chromophores in biomolecular environments, and solute-solvent systems in the liquid phase.

  4. Properties and Microstructural Characteristic of Kaolin Geopolymer Ceramics with Addition of Ultra High Molecular Weight Polyethylene

    NASA Astrophysics Data System (ADS)

    Ahmad, Romisuhani; Bakri Abdullah, Mohd Mustafa Al; Hussin, Kamarudin; Sandu, Andrei Victor; Binhussain, Mohammed; Ain Jaya, Nur

    2016-06-01

    In this paper, the mechanical properties and microstructure of kaolin geopolymer ceramics with addition of Ultra High Molecular Weight Polyethylene were studied. Inorganic polymers based on alumina and silica polysialate units were synthesized at room temperature from kaolin and sodium silicate in a highly alkaline medium, followed by curing and drying at 80 °C. Alkaline activator was formed by mixing the 12 M NaOH solution with sodium silicate at a ratio of 0.24. Addition of Ultra High Molecular Weight Polyethylene to the kaolin geopolymer are fabricated with Ultra High Molecular Weight Polyethylene content of 2, 4, 6 and 8 (wt. %) by using powder metallurgy method. The samples were heated at 1200 °C and the strength and morphological were tested. It was found that the flexural strength for the kaolin geopolymer ceramics with addition of UHMWPE were improved and generally increased with the increasing of UHMWPE loading. The result revealed that the optimum flexural strength was obtained at UHMWPE loading of 4 wt. % (92.1 MPa) and the flexural strength started to decrease. Microstructural analysis showed the samples appeared to have more number of pores and connected of pores increased with the increasing of UHMWPE content.

  5. Rational Prediction with Molecular Dynamics for Hit Identification

    PubMed Central

    Nichols, Sara E; Swift, Robert V; Amaro, Rommie E

    2012-01-01

    Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline. PMID:23110535

  6. Diversity dynamics: molecular phylogenies need the fossil record.

    PubMed

    Quental, Tiago B; Marshall, Charles R

    2010-08-01

    Over the last two decades, new tools in the analysis of molecular phylogenies have enabled study of the diversification dynamics of living clades in the absence of information about extinct lineages. However, computer simulations and the fossil record show that the inability to access extinct lineages severely limits the inferences that can be drawn from molecular phylogenies. It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota. PMID:20646780

  7. Collisional dynamics in a gas of molecular super-rotors.

    PubMed

    Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh

    2015-01-01

    Recently, femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a metastable 'gyroscopic stage' in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational-translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the 'gyroscopic stage' is abruptly terminated by an explosive rotational-translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules. PMID:26160223

  8. Collisional dynamics in a gas of molecular super-rotors

    PubMed Central

    Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh.

    2015-01-01

    Recently, femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a metastable ‘gyroscopic stage' in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational–translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the ‘gyroscopic stage' is abruptly terminated by an explosive rotational–translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules. PMID:26160223

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

    PubMed

    Tavernelli, Ivano

    2015-03-17

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

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

    PubMed

    Tavernelli, Ivano

    2015-03-17

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

  11. Ab initio molecular dynamics: Concepts, recent developments, and future trends

    PubMed Central

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E.

    2005-01-01

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed “on the fly” from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  12. Molecular Dynamics Simulations of Lignin Peroxidase in Solution

    PubMed Central

    Francesca Gerini, M.; Roccatano, Danilo; Baciocchi, Enrico; Nola, Alfredo Di

    2003-01-01

    The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel. PMID:12770894

  13. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    PubMed

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  14. Structural and dynamic properties of vitreous and crystalline barium disilicate: molecular dynamics simulation and Raman scattering experiments

    NASA Astrophysics Data System (ADS)

    Rodrigues, A. M.; Rino, J. P.; Pizani, P. S.; Zanotto, E. D.

    2016-11-01

    In this paper, we use a molecular dynamics simulation and Raman scattering measurements to study the vibrational and structural characteristics of barium disilicate, BaSi2O5, in vitreous and crystalline states. Our proposed atomic interaction potential describes the structural and dynamic behaviour of this material very well and can also be used for further extended studies. In addition, Raman spectroscopy enabled validation of the predictions of the potential by comparing the simulated vibrational density of states with the spectrum of the material in its vitreous state. Furthermore, we characterized the kinetics of the crystallization process through in situ Raman measurements as a function of temperature.

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

    NASA Astrophysics Data System (ADS)

    Levine, Zachary Alan

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

  16. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    SciTech Connect

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  17. A random rotor molecule: Vibrational analysis and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.

    2012-12-01

    Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4″″-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2″-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.

  18. Laser-enhanced dynamics in molecular rate processes

    NASA Technical Reports Server (NTRS)

    George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.

    1978-01-01

    The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.

  19. Molecular dynamics computer simulation of permeation in solids

    SciTech Connect

    Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M.

    1997-12-31

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

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

    NASA Astrophysics Data System (ADS)

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

    PubMed Central

    Liu, Qixin; Cai, Zhiyong

    2014-01-01

    This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. 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 is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

  2. The effect of the molecular weight of additive on the properties of antimisting fuels

    SciTech Connect

    Hadermann, A.F.; Trippe, J.C.; Waters, P.F.

    1983-09-01

    Antimisting aircraft fuels, when ignited, do not produce the roaring fireball which often accompanies aircraft crashes. This result is attributable to the suppression of the aerosolization of the fuel by added macromolecules which alter the structure of the droplets of fuel emanating from rent fuel tanks after the crash. The first studies of the antimisting effect of macromolecules on aviation fuel were carried out in Great Britain in 1968. In that early work it was established that there was a qualitative relationship between the suppression of the atomization of the fuel and the molecular weight of the additive above a certain critical concentration; the latter being inverse to the molecular weight of the additive. Subsequent investigations have demonstrated a dependence of the antimisting effectiveness of polyisobutylene in diesel fuel on the viscosity average molecular weight to a power exceeding 2, and in jet-A fuel to the 2..cap alpha.. + 1 power, where ..cap alpha.. is the exponent in the Mark-Houwink equation. In their study Chao et al, were able to demonstrate a strong correlation between the extent of antimisting effectiveness and flammability reduction with the maximum ductless siphon height supported by the solution. They introduced the ductless siphon to the study of antimisting fuels as a measure of the elongational viscosity impaired by the macromolecules to the fuel.

  3. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Hardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.

    2016-03-01

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.

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

    NASA Astrophysics Data System (ADS)

    Rapaport, Dennis C.

    2009-03-01

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

  5. Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Garate, J.-A.; English, Niall J.; MacElroy, J. M. D.

    2011-02-01

    Water self-diffusion within human aquaporin 4 has been studied using molecular dynamics (MD) simulations in the absence and presence of external ac and dc electric fields. The computed diffusive (pd) and osmotic (pf) permeabilities under zero-field conditions are (0.718 ± 0.24) × 10-14 cm3 s-1 and (2.94 ± 0.47) × 10-14 cm3 s-1, respectively; our pf agrees with the experimental value of (1.50 ± 0.6) × 10-14 cm3 s-1. A gating mechanism has been proposed in which side-chain dynamics of residue H201, located in the selectivity filter, play an essential role. In addition, for nonequilibrium MD in external fields, it was found that water dipole orientation within the constriction region of the channel is affected by electric fields (e-fields) and that this governs the permeability. It was also found that the rate of side-chain flipping motion of residue H201 is increased in the presence of e-fields, which influences water conductivity further.

  6. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

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

    SciTech Connect

    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.

  8. Photochemical processes in laser ablation of organic solids: Molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Yingling, Yaroslava G.

    In this thesis, a comprehensive study of the effect of the photochemical processes on laser ablation mechanisms has been conducted using molecular dynamics simulations. We developed a new concept for modeling photochemical processes in laser ablation of organic films using a mesoscopic coarse-grain breathing sphere model for molecular dynamics simulations. The main advantage of our model is the ability to study the dynamics of the system at the mesoscopic length scale, a regime that is not accessible either with atomistic or continuum computational methods. The photodecomposition of the excited molecules and the chemical reaction patterns in our simulations are based on the photochemistry of chlorobenzene due to ease of its fragmentation and available experimental data. Interpretation of the experimental data is the main objective of our theoretical efforts. Molecular dynamics simulations are used to investigate the effect of photochemical processes on molecular ejection mechanisms in 248-nm laser irradiation of organic solids. Photochemical reactions are found to release additional energy into the irradiated sample and decrease the average cohesive energy, therefore decreasing the value of the ablation threshold. The yield of emitted fragments becomes significant only above the ablation threshold. Below the ablation threshold, only the most volatile photoproduct, HCl, is ejected in very small amounts, whereas the remainder of photoproducts are trapped inside the sample. The presence of photochemical decomposition processes and subsequent chemical reactions changes the temporal and spatial energy deposition profile from pure photothermal ablation. The chemical reactions create an additional local pressure build up and, as a result, generate a strong and broad acoustic pressure wave propagating toward the bottom of the computational cell. The strong pressure wave in conjunction with the temperature increase in the absorbing region causes the ejection of hot massive

  9. Accelerating ring-polymer molecular dynamics with parallel-replica dynamics

    NASA Astrophysics Data System (ADS)

    Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F.

    2016-06-01

    Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach.

  10. Accelerating ring-polymer molecular dynamics with parallel-replica dynamics.

    PubMed

    Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F

    2016-06-28

    Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach. PMID:27369499

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

    ERIC Educational Resources Information Center

    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,…

  12. Concise NMR approach for molecular dynamics characterizations in organic solids.

    PubMed

    Aliev, Abil E; Courtier-Murias, Denis

    2013-08-22

    Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.

  13. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

    SciTech Connect

    Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  14. Efficient molecular dynamics simulations of multiple radical center systems based on the fragment molecular orbital method.

    PubMed

    Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree-Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  15. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

  16. Molecular dynamical simulations of melting behaviors of metal clusters

    SciTech Connect

    Hamid, Ilyar; Fang, Meng; Duan, Haiming

    2015-04-15

    The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.

  17. Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms

    SciTech Connect

    Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R

    2005-02-02

    Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.

  18. Application of two dimensional periodic molecular dynamics to interfaces.

    NASA Astrophysics Data System (ADS)

    Gay, David H.; Slater, Ben; Catlow, C. Richard A.

    1997-08-01

    We have applied two-dimensional molecular dynamics to the surface of a crystalline aspartame and the interface between the crystal face and a solvent (water). This has allowed us to look at the dynamic processes at the surface. Understanding the surface structure and properties are important to controlling the crystal morphology. The thermodynamic ensemble was constant Number, surface Area and Temperature (NAT). The calculations have been carried out using a 2D Ewald summation and 2D periodic boundary conditions for the short range potentials. The equations of motion integration has been carried out using the standard velocity Verlet algorithm.

  19. Stochastic Vortex Dynamics in Two-Dimensional Easy Plane Ferromagnets: Multiplicative Versus Additive Noise

    SciTech Connect

    Kamppeter, T.; Mertens, F.G.; Moro, E.; Sanchez, A.; Bishop, A.R.

    1998-09-01

    We study how thermal fluctuations affect the dynamics of vortices in the two-dimensional anisotropic Heisenberg model depending on their additive or multiplicative character. Using a collective coordinate theory, we analytically show that multiplicative noise, arising from fluctuations in the local field term of the Landau-Lifshitz equations, and Langevin-like additive noise have the same effect on vortex dynamics (within a very plausible assumption consistent with the collective coordinate approach). This is a highly non-trivial result as multiplicative and additive noises usually modify the dynamics in very different ways. We also carry out numerical simulations of both versions of the model finding that they indeed give rise to very similar vortex dynamics.

  20. Visual verification and analysis of cluster detection for molecular dynamics.

    PubMed

    Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas

    2007-01-01

    A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented. PMID:17968118

  1. Visual verification and analysis of cluster detection for molecular dynamics.

    PubMed

    Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas

    2007-01-01

    A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented.

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.

    PubMed

    Omelyan, I P

    2006-09-01

    A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations. PMID:17025782

  4. Annihilation of craters: Molecular dynamic simulations on a silver surface

    SciTech Connect

    Henriksson, K. O. E.; Nordlund, K.; Keinonen, J.

    2007-12-15

    The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.

  5. Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.

    PubMed

    Omelyan, I P

    2006-09-01

    A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations.

  6. Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics

    PubMed Central

    Mücksch, Christian; Urbassek, Herbert M.

    2013-01-01

    The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ( s) and experiment (up to hours), and the accordingly different ‘final’ adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces. PMID:23755156

  7. Adiabatic molecular-dynamics-simulation-method studies of kinetic friction

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Sokoloff, J. B.

    2005-06-01

    An adiabatic molecular-dynamics method is developed and used to study the Muser-Robbins model for dry friction (i.e., nonzero kinetic friction in the slow sliding speed limit). In this model, dry friction between two crystalline surfaces rotated with respect to each other is due to mobile molecules (i.e., dirt particles) adsorbed at the interface. Our adiabatic method allows us to quickly locate interface potential-well minima, which become unstable during sliding of the surfaces. Since dissipation due to friction in the slow sliding speed limit results from mobile molecules dropping out of such unstable wells, our method provides a way to calculate dry friction, which agrees extremely well with results found by conventional molecular dynamics for the same system, but our method is more than a factor of 10 faster.

  8. Coherent Amplification of Ultrafast Molecular Dynamics in an Optical Oscillator.

    PubMed

    Aharonovich, Igal; Pe'er, Avi

    2016-02-19

    Optical oscillators present a powerful optimization mechanism. The inherent competition for the gain resources between possible modes of oscillation entails the prevalence of the most efficient single mode. We harness this "ultrafast" coherent feedback to optimize an optical field in time, and show that, when an optical oscillator based on a molecular gain medium is synchronously pumped by ultrashort pulses, a temporally coherent multimode field can develop that optimally dumps a general, dynamically evolving vibrational wave packet, into a single vibrational target state. Measuring the emitted field opens a new window to visualization and control of fast molecular dynamics. The realization of such a coherent oscillator with hot alkali dimers appears within experimental reach.

  9. An implicit divalent counterion force field for RNA molecular dynamics

    NASA Astrophysics Data System (ADS)

    Henke, Paul S.; Mak, Chi H.

    2016-03-01

    How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg2+ screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.

  10. Molecular dynamics studies of U1A-RNA complexes.

    PubMed Central

    Reyes, C M; Kollman, P A

    1999-01-01

    The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity. PMID:10024175

  11. Shock induced phase transition of water: Molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Neogi, Anupam; Mitra, Nilanjan

    2016-02-01

    Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.

  12. Molecular dynamic simulation of non-melt laser annealing process

    NASA Astrophysics Data System (ADS)

    Liren, Yan; Dai, Li; Wei, Zhang; Zhihong, Liu; Wei, Zhou; Quan, Wang

    2016-03-01

    Molecular dynamic simulation is performed to study the process of material annealing caused by a 266 nm pulsed laser. A micro-mechanism describing behaviors of silicon and impurity atoms during the laser annealing at a non-melt regime is proposed. After ion implantation, the surface of the Si wafer is acted by a high energy laser pulse, which loosens the material and partially frees both Si and impurity atoms. While the residual laser energy is absorbed by valence electrons, these atoms are recoiled and relocated to finally form a crystal. Energy-related movement behavior is observed by using the molecular dynamic method. The non-melt laser anneal appears to be quite sensitive to the energy density of the laser, as a small excess energy may causes a significant impurity diffusion. Such a result is also supported by our laser anneal experiment.

  13. Long Timestep Molecular Dynamics on the Graphical Processing Unit

    PubMed Central

    Sweet, James C.; Nowling, Ronald J.; Cickovski, Trevor; Sweet, Christopher R.; Pande, Vijay S.; Izaguirre, Jesús A.

    2013-01-01

    Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 μs/day using implicit solvent models. PMID:24436689

  14. Molecular dynamics analysis on impact behavior of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Seifoori, Sajjad

    2015-01-01

    Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler-Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.

  15. Thioredoxin from Escherichia coli as a Role Model of Molecular Recognition, Folding, Dynamics and Function.

    PubMed

    Vazquez, Diego S; Delfino, Jose Maria; Santos, Javier

    2015-01-01

    Thioredoxin (TRX) catalyzes redox reactions via the reversible oxidation of the conserved active center CGPC and it is involved in multiple biological processes, some of them linked to redox activity while others not. TRX is a globular, thermodynamically stable and monomeric alpha/beta protein with a structure characterized by a central beta-sheet surrounded by alpha-helices. In this review we discuss central aspects of folding, dynamics and function of Escherichia coli TRX (EcTRX), pointing to the characterization of the full-length protein and of relevant fragments. In addition, we focus on the critical role that the C-terminal alpha-helical element plays in a late event in the consolidation of the overall EcTRX fold. Furthermore, we address the characterization of internal molecular motions by NMR and molecular dynamics simulation techniques. Finally, we review important aspects of the relationship among structure, dynamics and enzymatic function of this key redox protein. PMID:26149400

  16. Polydimethylsiloxane as a Macromolecular Additive for Enhanced Performance of Molecular Bulk Heterojunction Organic Solar Cells

    SciTech Connect

    Graham, Kenneth R.; Mei, Jianguo; Stalder, Romain; Shim, Jae Won; Cheun, Hyeunseok; Steffy, Fred; So, Franky; Kippelen, Bernard; Reynolds, John R.

    2011-03-15

    The effect of the macromolecular additive, polydimethylsiloxane (PDMS), on the performance of solution processed molecular bulk heterojunction solar cells is investigated, and the addition of PDMS is shown to improve device power conversion efficiency by ~70% and significantly reduce cell-to-cell variation, from a power conversion efficiency of 1.25 ± 0.37% with no PDMS to 2.16 ± 0.09% upon the addition of 0.1 mg/mL PDMS to the casting solution. The cells are based on a thiophene and isoindigo containing oligomer as the electron donor and [6,6]-phenyl-C61 butyric acid methyl ester (PC61BM) as the electron acceptor. PDMS is shown to have a strong influence on film morphology, with a significant decrease in film roughness and feature size observed. The morphology change leads to improved performance parameters, most notably an increase in the short circuit current density from 4.3 to 6.8 mA/cm2 upon addition of 0.1 mg/mL PDMS. The use of PDMS is of particular interest, as this additive appears frequently as a lubricant in plastic syringes commonly used in device fabrication; therefore, PDMS may unintentionally be incorporated into device active layers.

  17. Quantum tunneling splittings from path-integral molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  18. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W. G.; Hoover, C. G.

    1993-08-01

    Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

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

    PubMed

    Rapaport, D C

    2009-04-01

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

  20. Molecular dynamics simulations of ordering of polydimethylsiloxane under uniaxial extension

    SciTech Connect

    Lacevic, N M; Gee, R H

    2005-03-11

    Molecular dynamics simulations of a bulk melts of polydimethylsiloxane (PDMS) are utilized to study chain conformation and ordering under constant uniaxial tension. We find that large extensions induce chain ordering in the direction of applied tension. We also find that voids are created via a cavitation mechanism. This study represents a validation of the current model for PDMS and benchmark for the future study of mechanical properties of PDMS melts enriched with fillers under tension.

  1. A molecular dynamics study on sI hydrogen hydrate.

    PubMed

    Mondal, S; Ghosh, S; Chattaraj, P K

    2013-07-01

    A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

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

    PubMed

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394

  3. Molecular dynamics simulation of shocks in porous TATB crystals

    SciTech Connect

    Fried, L.E.; Tarver, C.

    1995-08-01

    We report molecular dynamics results on the shock structure of 2-D crystals of triaminotrinitrobenzene (TATB). We find that the shock front broadens to approx. 30 nm in materials with a 20% random void distribution. As expected from bulk experiments, the shock velocity decreases with increasing porosity and the temperature behind the shock front increases with increasing porosity. Shock equilibration times increase from 1 ps to greater than 10 ps.

  4. Molecular Dynamics study of Pb overlayer on Cu(100)

    NASA Technical Reports Server (NTRS)

    Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.

    1991-01-01

    Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.

  5. Current Status of Protein Force Fields for Molecular Dynamics

    PubMed Central

    Lopes, Pedro E.M.; Guvench, Olgun

    2015-01-01

    Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

  6. Current status of protein force fields for molecular dynamics simulations.

    PubMed

    Lopes, Pedro E M; Guvench, Olgun; MacKerell, Alexander D

    2015-01-01

    The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

  7. Molecular dynamics averaging of Xe chemical shifts in liquids

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Sears, Devin N.; Murad, Sohail

    2004-11-01

    The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.

  8. Shapiro like steps reveals molecular nanomagnets’ spin dynamics

    SciTech Connect

    Abdollahipour, Babak; Abouie, Jahanfar Ebrahimi, Navid

    2015-09-15

    We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.

  9. Molecular Dynamics Simulation of a Microvillus in a Cross Flow

    NASA Astrophysics Data System (ADS)

    Chen, X. Y.; Liu, Y.; So, R. M. C.; Yang, J. M.

    One of the functions of microvilli in the microvessel endothelial glycocalyx is molecular filtering. The microvillus behaves as a mechanosensory system which may sense the fluid shear and drag forces. The permeability of small particles in microvessel is crucial for drug design and drug delivery. Therefore a better understanding of flow field around microvillus is important to simulate accurately the particle penetration in microvessel. Since the dimension of the microvilli is about ~10 nm, the conventional Navier-Stokes equation may not be good enough to simulate the fluid flow in such microscale and nanoscale structures. Molecular dynamics (MD) simulation is a powerful method to simulate the fluid flow at the molecular level. As a first attempt, the microvillus is reduced as a two-dimensional cylinder which is in a cross flow. The detailed drag and lift together with flow field are obtained and compared with available data.

  10. High-Flow, High-Molecular-Weight, Addition-Curing Polyimides

    NASA Technical Reports Server (NTRS)

    Chuang, Kathy C.; Vannucci, Raymond D.

    1993-01-01

    In developed series of high-flow PMR-type polyimide resins, 2, 2'-bis(trifluoromethyl)-4, 4'-diaminobiphenyl (BTDB) substituted for 1, 4-pheylenediamine in PMR-II formulation. Polyimides designated either as PMR-12F when nadic ester (NE) end caps used, or as V-CAP-12F when p-aminostyrene end caps used. High-molecular-weight, addition-curing polyimides based on BTBD and HFDE highly processable high-temperature matrix resins used to make composite materials with excellent retention of properties during long-term exposure to air at 650 degrees F or higher temperature. Furthermore, 12F addition-curing polyimides useful for electronic applications; fluorinated rigid-rod polyimides known to exhibit low thermal expansion coefficients as well as low absorption of moisture.

  11. Molecular dynamics simulations of solutions at constant chemical potential

    NASA Astrophysics Data System (ADS)

    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.

  12. Exploiting molecular dynamics in Nested Sampling simulations of small peptides

    NASA Astrophysics Data System (ADS)

    Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

    2016-04-01

    Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

  13. Ultrafast Molecular Dynamics probed by Vacuum Ultraviolet Pulses

    NASA Astrophysics Data System (ADS)

    Cryan, James; Champenois, Elio; Shivaram, Niranjan; Wright, Travis; Yang, Chan-Shan; Falcone, Roger; Belkacem, Ali

    2014-05-01

    We present time-resolved measurements of the relaxation dynamics in small molecular systems (CO2 and C2H4) following ultraviolet (UV) photo-excitation. We probe these excitations through photoionization and velocity map imaging (VMI) spectroscopy. Vacuum and extreme ultraviolet (VUV/XUV) pump and probe pulses are created by exploiting strong-field high harmonic generation (HHG) from our state-of-the-art 30 mJ, 1 kHz laser system. Three dimensional photoelectron and photoion momentum images recorded with our VMI spectrometer reveal non-Born Oppenheimer dynamics in the vicinity of a conical intersection, and allow us track the state of the system as a function of time. We also present initial experiments with the goal of controlling the dynamics near a conical intersection using a strong-field IR pulse. Finally, we will show progress towards measurements of time-resolved molecular frame photoelectron angular distributions (TRMFPADs) by applying our VUV/XUV pulse sequence to an aligned molecular ensemble. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  14. Molecular-level dynamics of refractory dissolved organic matter

    NASA Astrophysics Data System (ADS)

    Niggemann, J.; Gerdts, G.; Dittmar, T.

    2012-04-01

    Refractory dissolved organic matter (DOM) accounts for most of the global oceanic organic carbon inventory. Processes leading to its formation and factors determining its stability are still largely unknown. We hypothesize that refractory DOM carries a universal molecular signature. Characterizing spatial and temporal variability in this universal signature is a key to understanding dynamics of refractory DOM. We present results from a long-term study of the DOM geo-metabolome in the open North Sea. Geo-metabolomics considers the entity of DOM as a population of compounds, each characterized by a specific function and reactivity in the cycling of energy and elements. Ten-thousands of molecular formulae were identified in DOM by ultrahigh resolution mass spectrometry analysis (FT-ICR-MS, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry). The DOM pool in the North Sea was influenced by a complex interplay of processes that produced, transformed and degraded dissolved molecules. We identified a stable fraction in North Sea DOM with a molecular composition similar to deep ocean DOM. Molecular-level changes in this stable fraction provide novel information on dynamics and interactions of refractory DOM.

  15. Molecular-scale evidence of aerosol particle formation via sequential addition of HIO3

    NASA Astrophysics Data System (ADS)

    Sipilä, Mikko; Sarnela, Nina; Jokinen, Tuija; Henschel, Henning; Junninen, Heikki; Kontkanen, Jenni; Richters, Stefanie; Kangasluoma, Juha; Franchin, Alessandro; Peräkylä, Otso; Rissanen, Matti P.; Ehn, Mikael; Vehkamäki, Hanna; Kurten, Theo; Berndt, Torsten; Petäjä, Tuukka; Worsnop, Douglas; Ceburnis, Darius; Kerminen, Veli-Matti; Kulmala, Markku; O'Dowd, Colin

    2016-09-01

    Homogeneous nucleation and subsequent cluster growth leads to the formation of new aerosol particles in the atmosphere. The nucleation of sulfuric acid and organic vapours is thought to be responsible for the formation of new particles over continents, whereas iodine oxide vapours have been implicated in particle formation over coastal regions. The molecular clustering pathways that are involved in atmospheric particle formation have been elucidated in controlled laboratory studies of chemically simple systems, but direct molecular-level observations of nucleation in atmospheric field conditions that involve sulfuric acid, organic or iodine oxide vapours have yet to be reported. Here we present field data from Mace Head, Ireland, and supporting data from northern Greenland and Queen Maud Land, Antarctica, that enable us to identify the molecular steps involved in new particle formation in an iodine-rich, coastal atmospheric environment. We find that the formation and initial growth process is almost exclusively driven by iodine oxoacids and iodine oxide vapours, with average oxygen-to-iodine ratios of 2.4 found in the clusters. On the basis of this high ratio, together with the high concentrations of iodic acid (HIO3) observed, we suggest that cluster formation primarily proceeds by sequential addition of HIO3, followed by intracluster restructuring to I2O5 and recycling of water either in the atmosphere or on dehydration. Our study provides ambient atmospheric molecular-level observations of nucleation, supporting the previously suggested role of iodine-containing species in the formation of new aerosol particles, and identifies the key nucleating compound.

  16. Molecular dynamics of protein kinase-inhibitor complexes: a valid structural information.

    PubMed

    Caballero, Julio; Alzate-Morales, Jans H

    2012-01-01

    Protein kinases (PKs) are key components of protein phosphorylation based signaling networks in eukaryotic cells. They have been identified as being implicated in many diseases. High-resolution X-ray crystallographic data exist for many PKs and, in many cases, these structures are co-complexed with inhibitors. Although this valuable information confirms the precise structure of PKs and their complexes, it ignores the dynamic movements of the structures which are relevant to explain the affinities and selectivity of the ligands, to characterize the thermodynamics of the solvated complexes, and to derive predictive models. Atomistic molecular dynamics (MD) simulations present a convenient way to study PK-inhibitor complexes and have been increasingly used in recent years in structure-based drug design. MD is a very useful computational method and a great counterpart for experimentalists, which helps them to derive important additional molecular information. That enables them to follow and understand structure and dynamics of protein-ligand systems with extreme molecular detail on scales where motion of individual atoms can be tracked. MD can be used to sample dynamic molecular processes, and can be complemented with more advanced computational methods (e.g., free energy calculations, structure-activity relationship analysis). This review focuses on the most commonly applications to study PK-inhibitor complexes using MD simulations. Our aim is that researchers working in the design of PK inhibitors be aware of the benefits of this powerful tool in the design of potent and selective PK inhibitors. PMID:22571663

  17. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall, G.E.

    2011-05-31

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  18. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall G. E.; Goncharov, V.

    2012-05-29

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  19. Molecular Dynamics Simulations of p53 DNA-Binding Domain

    PubMed Central

    Lu, Qiang; Tan, Yu-Hong; Luo, Ray

    2008-01-01

    We have studied room-temperature structural and dynamic properties of the p53 DNA-binding domain in both DNA-bound and DNA-free states. A cumulative 55ns of explicit solvent molecular dynamics simulations with the Particle Mesh Ewald treatment of electrostatics were performed. It is found that the mean structures in the production portions of the trajectories agree well with the crystal structure: backbone root-mean squared deviations are in the range of 1.6Å and 2.0Å. In both simulations, noticeable backbone deviations from the crystal structure are observed only in loop L6, due to the lack of crystal packing in the simulations. More deviations are observed in the DNA-free simulation, apparently due to the absence of DNA. Computed backbone B-factor is also in qualitative agreement with the crystal structure. Interestingly little backbone structural change was observed between the mean simulated DNA-bound and DNA-free structures. Notable difference is only observed at the DNA-binding interface. The correlation between native contacts and inactivation mechanisms of tumor mutations is also discussed. In the H2 region, tumor mutations at sites D281, R282, E285, and E286 may weaken five key interactions that stabilize H2, indicating that their inactivation mechanisms may be related to the loss of local structure around H2, which in turn may reduce the overall stability to a measurable amount. In the L2 region, tumor mutations at sites Y163, K164, E171, V173, L194, R249, I251 and E271 are likely to be responsible for the loss of stability in the protein. In addition to apparent DNA contacts that are related to DNA binding, interactions R175/S183, S183/R196, and E198/N235 are highly occupied only in the DNA-bound form, indicating that they are more likely to be responsible for DNA binding. PMID:17824689

  20. Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture.

    PubMed

    Matvienko, Sergey; Alemasov, Nikolay; Fomin, Eduard

    2015-02-01

    Molecular dynamics (MD) is widely used in computational biology for studying binding mechanisms of molecules, molecular transport, conformational transitions, protein folding, etc. The method is computationally expensive; thus, the demand for the development of novel, much more efficient algorithms is still high. Therefore, the new algorithm designed in 2007 and called interaction sorting (IS) clearly attracted interest, as it outperformed the most efficient MD algorithms. In this work, a new IS modification is proposed which allows the algorithm to utilize SIMD processor instructions. This paper shows that the improvement provides an additional gain in performance, 9% to 45% in comparison to the original IS method.

  1. Molecular Dynamics and Energy Minimization Based on Embedded Atom Method

    1995-03-01

    This program performs atomic scale computer simulations of the structure and dynamics of metallic system using energetices based on the Embedded Atom Method. The program performs two types of calculations. First, it performs local energy minimization of all atomic positions to determine ground state and saddle point energies and structures. Second, it performs molecular dynamics simulations to determine thermodynamics or miscroscopic dynamics of the system. In both cases, various constraints can be applied to themore » system. The volume of the system can be varied automatically to achieve any desired external pressure. The temperature in molecular dynamics simulations can be controlled by a variety of methods. Further, the temperature control can be applied either to the entire system or just a subset of the atoms that would act as a thermal source/sink. The motion of one or more of the atoms can be constrained to either simulate the effects of bulk boundary conditions or to facilitate the determination of saddle point configurations. The simulations are performed with periodic boundary conditions.« less

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

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

    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.

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

    PubMed

    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.

  4. Molecular View on Supramolecular Chain and Association Dynamics

    NASA Astrophysics Data System (ADS)

    Monkenbusch, M.; Krutyeva, M.; Pyckhout-Hintzen, W.; Antonius, W.; Hövelmann, C. H.; Allgaier, J.; Brás, A.; Farago, B.; Wischnewski, A.; Richter, D.

    2016-09-01

    The chain and association dynamics of supramolecular polymer ensembles decisively determines their properties. Using neutron spin echo (NSE) spectroscopy we present molecular insight into the space and time evolution of this dynamics. Studying a well characterized ensemble of linearly associating telechelic poly(ethylene glycol) melts carrying triple H-bonding end groups, we show that H-bond breaking significantly impacts the mode spectrum of the associates. The breaking affects the mode contributions and not the relaxation times as was assumed previously. NSE spectra directly reveal the so far intangible H-bond lifetimes in the supramolecular melt and demonstrate that for both the microscopic and the macroscopic dynamics of the supramolecular ensemble the instantaneous average of the Mw distribution governs the system response at least as long as the Rouse picture applies.

  5. The classical and quantum dynamics of molecular spins on graphene.

    PubMed

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2016-02-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices. PMID:26641019

  6. (Artificial intelligence and molecular dynamics simulations of polymers)

    SciTech Connect

    Noid, D.W.

    1990-08-27

    The traveler participated in planning a new methodology for performing molecular dynamics simulation of polymers. Current computer polymer dynamics programs are either capable of very general calculations and are extremely inefficient or are very efficiently written for a particular computer architecture to study a specific polymer system. Both of these approaches involve tremendous efforts in FORTRAN programming. A combined effort of computer scientists and myself hope to develop an expert system to produce efficient FORTRAN codes for any polymer and be optimized on computer architectures ranging from TRANSPUTERS to CRAY. The result of this collaboration will be an efficient way to model polymer dynamics for an arbitrary polymer structure. The subsidiary purpose was to present a seminar at the University of Newcastle and discussions with several other departments at Oxford University.

  7. Molecular dynamics studies of interfacial water at the alumina surface.

    SciTech Connect

    Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David

    2011-01-01

    Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.

  8. Acceleration of dynamic fluorescence molecular tomography with principal component analysis

    PubMed Central

    Zhang, Guanglei; He, Wei; Pu, Huangsheng; Liu, Fei; Chen, Maomao; Bai, Jing; Luo, Jianwen

    2015-01-01

    Dynamic fluorescence molecular tomography (FMT) is an attractive imaging technique for three-dimensionally resolving the metabolic process of fluorescent biomarkers in small animal. When combined with compartmental modeling, dynamic FMT can be used to obtain parametric images which can provide quantitative pharmacokinetic information for drug development and metabolic research. However, the computational burden of dynamic FMT is extremely huge due to its large data sets arising from the long measurement process and the densely sampling device. In this work, we propose to accelerate the reconstruction process of dynamic FMT based on principal component analysis (PCA). Taking advantage of the compression property of PCA, the dimension of the sub weight matrix used for solving the inverse problem is reduced by retaining only a few principal components which can retain most of the effective information of the sub weight matrix. Therefore, the reconstruction process of dynamic FMT can be accelerated by solving the smaller scale inverse problem. Numerical simulation and mouse experiment are performed to validate the performance of the proposed method. Results show that the proposed method can greatly accelerate the reconstruction of parametric images in dynamic FMT almost without degradation in image quality. PMID:26114027

  9. Confinement of conjugated polymers into soft nanoparticles: molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wijesinghe, Sidath; Perahia, Dvora; Grest, Gary S.

    2013-03-01

    The structure and dynamics of conjugated polymers confined into soft nanoparticles (SNPs) have been studies by molecular dynamic simulations. This new class of tunable luminescent SNPs exhibits an immense potential as bio-markers as well as targeted drug delivery agents where tethering specific groups to the surface particles offers a means to target specific applications. Of particular interest are SNPs that consist of non- crosslinked polymers, decorated with polar groups. These SNPs are potentially tunable through the dynamics of the polymer chains, whereas the polar entity serves as internal stabilizer and surface encore. Confinement of a polymer whose inherent conformation is extended impacts not only their dynamics and as a result their optical properties. Here we will present insight into the structure and dynamics of dialkyl poly para phenylene ethynylene (PPE), decorated by a carboxylate groups, confined into a soft particle. The conformation and dynamics of polymer within SNP will be discussed and compared with that of the linear chain in solution. This work in partially supported by DOE grant DE-FG02-12ER46843

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

    NASA Astrophysics Data System (ADS)

    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.

  11. Nonadiabatic excited-state molecular dynamics: numerical tests of convergence and parameters.

    PubMed

    Nelson, Tammie; Fernandez-Alberti, Sebastian; Chernyak, Vladimir; Roitberg, Adrian E; Tretiak, Sergei

    2012-02-01

    Nonadiabatic molecular dynamics simulations, involving multiple Born-Oppenheimer potential energy surfaces, often require a large number of independent trajectories in order to achieve the desired convergence of the results, and simulation relies on different parameters that should be tested and compared. In addition to influencing the speed of the simulation, the chosen parameters combined with the frequently reduced number of trajectories can sometimes lead to unanticipated changes in the accuracy of the simulated dynamics. We have previously developed a nonadiabatic excited state molecular dynamics methodology employing Tully's fewest switches surface hopping algorithm. In this study, we seek to investigate the impact of the number of trajectories and the various parameters on the simulation of the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene) within our developed framework. Various user-defined parameters are analyzed: classical and quantum integration time steps, the value of the friction coefficient for Langevin dynamics, and the initial seed used for stochastic thermostat and hopping algorithms. Common approximations such as reduced number of nonadiabatic coupling terms and the classical path approximation are also investigated. Our analysis shows that, at least for the considered molecular system, a minimum of ~400 independent trajectories should be calculated in order to achieve statistical averaging necessary for convergence of the calculated relaxation timescales. PMID:22320726

  12. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall,G.E.; Sears, T.J.

    2009-04-03

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.

  13. Extended Molecular Dynamics Methods for Vortex Dynamics in Nano-structured Superconductors

    NASA Astrophysics Data System (ADS)

    Kato, Masaru; Sato, Osamu

    Using improved molecular dynamics simulation method, we study vortex dynamics in nano-scaled superconductors. Heat generations during vortex motion, heat transfer in superconductors, and entropy forces to vortices are incorporated. Also quasi-particle relaxations after vortex motion, and their attractive "retarded" forces to other vortices are incorporated using the condensation-energy field. We show the time development of formation of vortex channel flow in a superconducting Corbino-disk.

  14. Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.

    PubMed

    Han, Haiming; Bai, Li; Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

    2014-01-01

    Agropyron cristatum (L.) Gaertn. (2n = 4x = 28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

  15. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets.

    PubMed

    Ono, Junichi; Ando, Koji

    2012-11-01

    A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many

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

    NASA Astrophysics Data System (ADS)

    St. John, Alexander; Wexler, Carlos

    2015-03-01

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

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

    PubMed Central

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210

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

    PubMed

    Papaleo, Elena

    2015-01-01

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

  19. Wetting kinetics of water nano-droplet containing non-surfactant nanoparticles: A molecular dynamics study

    SciTech Connect

    Lu, Gui; Hu, Han; Sun, Ying E-mail: ysun@coe.drexel.edu; Duan, Yuanyuan E-mail: ysun@coe.drexel.edu

    2013-12-16

    In this Letter, dynamic wetting of water nano-droplets containing non-surfactant gold nanoparticles on a gold substrate is examined via molecular dynamics simulations. The results show that the addition of non-surfactant nanoparticles hinders the nano-second droplet wetting process, attributed to the increases in both surface tension of the nanofluid and friction between nanofluid and substrate. The droplet wetting kinetics decreases with increasing nanoparticle loading and water-particle interaction energy. The observed wetting suppression and the absence of nanoparticle ordering near the contact line of nano-sized droplets differ from the wetting behaviors reported from nanofluid droplets of micron size or larger.

  20. Phonon-magnon interactions in body centered cubic iron: A combined molecular and spin dynamics study

    SciTech Connect

    Perera, Dilina Landau, David P.; Nicholson, Don M.; Malcolm Stocks, G.; Eisenbach, Markus; Yin, Junqi; Brown, Gregory

    2014-05-07

    Combining an atomistic many-body potential with a classical spin Hamiltonian parameterized by first principles calculations, molecular-spin dynamics computer simulations were performed to investigate phonon-magnon interactions in body centered cubic iron. Results obtained for spin-spin and density-density dynamic structure factors show that noticeable softening and damping of magnon modes occur due to the presence of lattice vibrations. Furthermore, as a result of the phonon-magnon coupling, additional longitudinal spin wave excitations are observed, with the same frequencies as the longitudinal phonon modes.

  1. Accelerated molecular dynamics methods: introduction and recent developments

    SciTech Connect

    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

  2. Formation and nonlinear dynamics of the squeezed state of a helical electron beam with additional deceleration

    SciTech Connect

    Egorov, E. N. Koronovskii, A. A.; Kurkin, S. A.; Hramov, A. E.

    2013-11-15

    Results of numerical simulations and analysis of the formation and nonlinear dynamics of the squeezed state of a helical electron beam in a vircator with a magnetron injection gun as an electron source and with additional electron deceleration are presented. The ranges of control parameters where the squeezed state can form in such a system are revealed, and specific features of the system dynamics are analyzed. It is shown that the formation of a squeezed state of a nonrelativistic helical electron beam in a system with electron deceleration is accompanied by low-frequency longitudinal dynamics of the space charge.

  3. Semiclassical Monte Carlo: a first principles approach to non-adiabatic molecular dynamics.

    PubMed

    White, Alexander J; Gorshkov, Vyacheslav N; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-11-14

    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.

  4. Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

    SciTech Connect

    White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-11-14

    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.

  5. Semiclassical Monte Carlo: a first principles approach to non-adiabatic molecular dynamics.

    PubMed

    White, Alexander J; Gorshkov, Vyacheslav N; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-11-14

    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. PMID:25399126

  6. Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

    NASA Astrophysics Data System (ADS)

    White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-11-01

    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.

  7. The addition of body armor diminishes dynamic postural stability in military soldiers.

    PubMed

    Sell, Timothy C; Pederson, Jonathan J; Abt, John P; Nagai, Takashi; Deluzio, Jennifer; Wirt, Michael D; McCord, Larry J; Lephart, Scott M

    2013-01-01

    Poor postural stability has been identified as a risk factor for lower extremity musculoskeletal injury. The additional weight of body armor carried by Soldiers alters static postural stability and may predispose Soldiers to lower extremity musculoskeletal injuries. However, static postural stability tasks poorly replicate the dynamic military environment, which places considerable stress on the postural control system during tactical training and combat. Therefore, the purpose of this study was to examine the effects of body armor on dynamic postural stability during single-leg jump landings. Thirty-six 101st Airborne Division (Air Assault) Soldiers performed single-leg jump landings in the anterior direction with and without wearing body armor. The dynamic postural stability index and the individual stability indices (medial-lateral stability index, anterior-posterior stability index, and vertical stability index) were calculated for each condition. Paired sample t-tests were performed to determine differences between conditions. Significant differences existed for the medial-lateral stability index, anterior-posterior stability index, vertical stability index, and dynamic postural stability index (p < 0.05). The addition of body armor resulted in diminished dynamic postural stability, which may result in increased lower extremity injuries. Training programs should address the altered dynamic postural stability while wearing body armor in attempts to promote adaptations that will result in safer performance during dynamic tasks.

  8. Computational Studies on the Anharmonic Dynamics of Molecular Clusters

    NASA Astrophysics Data System (ADS)

    Mancini, John S.

    Molecular nanoclusters present ideal systems to probe the physical forces and dynamics that drive the behavior of larger bulk systems. At the nanocluster limit the first instances of several phenomena can be observed including the breaking of hydrogen and molecular bonds. Advancements in experimental and theoretical techniques have made it possible to explore these phenomena in great detail. The most fruitful of these studies have involved the use of both experimental and theoretical techniques to leverage to strengths of the two approaches. This dissertation seeks to explore several important phenomena of molecular clusters using new and existing theoretical methodologies. Three specific systems are considered, hydrogen chloride clusters, mixed water and hydrogen chloride clusters and the first cluster where hydrogen chloride autoionization occurs. The focus of these studies remain as close as possible to experimentally observable phenomena with the intention of validating, simulating and expanding on experimental work. Specifically, the properties of interested are those related to the vibrational ground and excited state dynamics of these systems. Studies are performed using full and reduced dimensional potential energy surface alongside advanced quantum mechanical methods including diffusion Monte Carlo, vibrational configuration interaction theory and quasi-classical molecular dynamics. The insight gained from these studies are great and varied. A new on-they-fly ab initio method for studying molecular clusters is validated for (HCl)1--6. A landmark study of the dissociation energy and predissociation mechanism of (HCl)3 is reported. The ground states of mixed (HCl)n(H2O)m are found to be highly delocalized across multiple stationary point configurations. Furthermore, it is identified that the consideration of this delocalization is required in vibrational excited state calculations to achieve agreement with experimental measurements. Finally, the theoretical

  9. Study of critical dynamics in fluids via molecular dynamics in canonical ensemble.

    PubMed

    Roy, Sutapa; Das, Subir K

    2015-12-01

    With the objective of understanding the usefulness of thermostats in the study of dynamic critical phenomena in fluids, we present results for transport properties in a binary Lennard-Jones fluid that exhibits liquid-liquid phase transition. Various collective transport properties, calculated from the molecular dynamics (MD) simulations in canonical ensemble, with different thermostats, are compared with those obtained from MD simulations in microcanonical ensemble. It is observed that the Nosé-Hoover and dissipative particle dynamics thermostats are useful for the calculations of mutual diffusivity and shear viscosity. The Nosé-Hoover thermostat, however, as opposed to the latter, appears inadequate for the study of bulk viscosity. PMID:26687057

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

    SciTech Connect

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

    2012-05-29

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

  11. Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

    SciTech Connect

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

    2010-06-01

    The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

  12. Dynamical Simulations of Molecular Clouds in the Galactic Center

    NASA Astrophysics Data System (ADS)

    Salas, Jesus; Morris, Mark

    2016-06-01

    The formation of the central massive cluster of young stars orbiting the Galactic black hole, Sgr A*, has been modeled by several groups by invoking an almost radially infalling molecular cloud that interacts with the black hole and creates a dense, gaseous disk in which stars can then form. However, the dynamical origin of such a cloud remains an open question. We present simulations of the central 30-100 pc of the Milky Way, starting from a population of molecular clouds located in a disk with scale height of ~30 pc, using the N-body/smoothed-particle hydrodynamics code, Gadget2. We followed the dynamical evolution of clouds in a galactic potential that includes a bar to explore whether cloud collisions or a succession of cloud scatterings can remove sufficient angular momentum from a massive cloud to endow it with a predominantly radial orbit. Initial results illustrate the importance of tidal shear; while dense cloud cores remain identifiable for extended periods of time, much of the molecular mass ends up in tidal streams, so cannot be deflected onto low angular momentum orbits by their mutual interactions. At the completion of our ongoing computations, we will report on whether the cloud cores can undergo sufficient scattering to achieve low-angular-momentum orbits.

  13. Molecular Dynamics Simulation of Carbon Nanotube Based Gears

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  14. Molecular Imprinting of Silica Nanoparticle Surfaces via Reversible Addition-Fragmentation Polymerization for Optical Biosensing Applications

    NASA Astrophysics Data System (ADS)

    Oluz, Zehra; Nayab, Sana; Kursun, Talya Tugana; Caykara, Tuncer; Yameen, Basit; Duran, Hatice

    Azo initiator modified surface of silica nanoparticles were coated via reversible addition-fragmentation polymerization (RAFT) of methacrylic acid and ethylene glycol dimethacrylate using 2-phenylprop 2-yl dithobenzoate as chain transfer agent. Using L-phenylalanine anilide as template during polymerization led molecularly imprinted nanoparticles. RAFT polymerization offers an efficient control of grafting process, while molecularly imprinted polymers shows enhanced capacity as sensor. L-phenylalanine anilide imprinted silica particles were characterized by X-Ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM). Performances of the particles were followed by surface plasmon resonance spectroscopy (SPR) after coating the final product on gold deposited glass substrate against four different analogous of analyte molecules: D-henylalanine anilide, L-tyrosine, L-tryptophan and L-phenylalanine. Characterizations indicated that silica particles coated with polymer layer do contain binding sites for L-phenylalanine anilide, and are highly selective for the molecule of interest. This project was supported by TUBITAK (Project No:112M804).

  15. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lu, Yan; Salsbury, Freddie R.

    2015-01-01

    ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

  16. Power conversion efficiency enhancement in OPV devices using spin 1/2 molecular additives

    NASA Astrophysics Data System (ADS)

    Basel, Tek; Vardeny, Valy; Yu, Luping

    2014-03-01

    We investigated the power conversion efficiency of bulk heterojunction OPV cells based on the low bandgap polymer PTB7, blend with C61-PCBM. We also employed the technique of photo-induced absorption, PA; electrical and magneto-PA (MPA) techniques to understand the details of the photocurrent generation process in this blend. We found that spin 1/2 molecular additives, such as Galvinoxyl (Gxl) radicals dramatically enhance the cell efficiency; we obtained 20% increase in photocurrent upon Gxl doping with 2% weight. We explain our finding by the ability of the spin 1/2 radicals to interfere with the known major loss mechanism in the cell due to recombination of charge transfer exciton at the D-A interface via triplet excitons in the polymer donors. Supported by National Science Foundation-Material Science & Engineering Center (NSF-MRSEC), University of Utah.

  17. Optimal receiver design for diffusive molecular communication with flow and additive noise.

    PubMed

    Noel, Adam; Cheung, Karen C; Schober, Robert

    2014-09-01

    In this paper, we perform receiver design for a diffusive molecular communication environment. Our model includes flow in any direction, sources of information molecules in addition to the transmitter, and enzymes in the propagation environment to mitigate intersymbol interference. We characterize the mutual information between receiver observations to show how often independent observations can be made. We derive the maximum likelihood sequence detector to provide a lower bound on the bit error probability. We propose the family of weighted sum detectors for more practical implementation and derive their expected bit error probability. Under certain conditions, the performance of the optimal weighted sum detector is shown to be equivalent to a matched filter. Receiver simulation results show the tradeoff in detector complexity versus achievable bit error probability, and that a slow flow in any direction can improve the performance of a weighted sum detector.

  18. Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

    SciTech Connect

    White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry

    2015-07-07

    Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.

  19. Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo.

    PubMed

    White, Alexander J; Gorshkov, Vyacheslav N; Tretiak, Sergei; Mozyrsky, Dmitry

    2015-07-01

    Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems. PMID:26156473

  20. Quantum mechanical molecular dynamics studies of chemical systems

    NASA Astrophysics Data System (ADS)

    Pavese, Marc

    Methods for including quantum mechanical effects in molecular dynamics (MD) simulations are discussed in this thesis. The thesis focuses on the path integral centroid molecular dynamics (CMD) algorithm. This algorithm is first described and then used in simulations of low temperature para-hydrogen, and also in simulations of the excess proton in water clusters and in the bulk. The CMD method allows one to include the effects of nuclear quantization approximately while still maintaining a quasi-classical, trajectory based, description of the dynamics. The effects of quantization of the electronic degrees of freedom are also discussed. These effects are usually taken into account implicitly through parameterized potential functions. However, methods for including the quantum electronic degrees of freedom explicitly in a MD simulation are also discussed in this thesis. Most notably, the Car-Parrinello method, which combines density functional theory (DFT) with MD, is employed with the CMD algorithm. This yields a method which takes explicit account of the quantum electrons and nuclei. Thus, this work represents one feasible approach for considering the quantum nature of all the degrees of freedom of the system while still maintaining an MD framework. In the concluding remarks, future directions and possibilities for this type of approach are discussed.

  1. Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

    DOE PAGES

    White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry

    2015-07-07

    Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore » as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less

  2. Collisional deactivation of CF 3I - a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Svedung, Harald; Marković, Nikola; Nordholm, Sture

    1999-10-01

    The detailed mechanisms of ro-vibrational energy transfer in collisions between CF 3I and argon or propane are investigated. Molecular dynamics simulations of collisions between a reactant CF 3I molecule at energies from 50 to 200 kJ/mol with medium argon or propane at selected initial temperatures are interpreted in terms of ergodic collision limits. The intramolecular potential used for CF 3I is a Morse-stretch/harmonic-bend type function with parameters fitted to equilibrium structure, normal mode frequencies and dissociation energies. Simple generic Buckingham type pair-potentials are used for intermolecular atom-atom interactions. Energy transfer is related to (i) geometry of collision, (ii) impact parameter, (iii) number of atom-atom encounters, (iv) average dynamical hardness of interaction at atom-atom collisions, (v) number of minima in the center of mass separation and (vi) lifetime of the collisional complex. The energy transfer in our molecular dynamics calculations is compared with experimental results for the same colliders. The observed trends are interpreted in terms of detailed collisional mechanisms. Our results highlight the importance of rotational excitation and the repulsive part of the intermolecular potential.

  3. Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

    SciTech Connect

    White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry

    2015-07-07

    Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.

  4. Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo

    SciTech Connect

    Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.

    2000-10-10

    Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.

  5. Protons in polar media: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    von Rosenvinge, Tycho

    1998-10-01

    The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Overcoming the Barrier on Time Step Size in Multiscale Molecular Dynamics Simulation of Molecular Liquids.

    PubMed

    Omelyan, Igor P; Kovalenko, Andriy

    2012-01-10

    We propose and validate a new multiscale technique, the extrapolative isokinetic Nóse-Hoover chain orientational (EINO) motion multiple time step algorithm for rigid interaction site models of molecular liquids. It nontrivially combines the multiple time step decomposition operator method with a specific extrapolation of intermolecular interactions, complemented by an extended isokinetic Nosé-Hoover chain approach in the presence of translational and orientational degrees of freedom. The EINO algorithm obviates the limitations on time step size in molecular dynamics simulations. While the best existing multistep algorithms can advance from a 5 fs single step to a maximum 100 fs outer step, we show on the basis of molecular dynamics simulations of the TIP4P water that our EINO technique overcomes this barrier. Specifically, we have achieved giant time steps on the order of 500 fs up to 5 ps, which now become available in the study of equilibrium and conformational properties of molecular liquids without a loss of stability and accuracy.

  8. Molecular Dynamics Simulations of Fracture of Model Epoxies

    SciTech Connect

    STEVENS,MARK J.

    2000-01-18

    The failure of thermosetting polymer adhesives is an important problem which particularly lacks understanding from the molecular viewpoint. While linear elastic fracture mechanics works well for such polymers far from the crack tip, the method breaks down near the crack tip where large plastic deformation occurs and the molecular details become important [1]. Results of molecular dynamics simulations of highly crosslinked polymer networks bonded to a solid surface are presented here. Epoxies are used as the guide for modeling. The focus of the simulations is the network connectivity and the interfacial strength. In a random network, the bond stress is expected to vary, and the most stressed bonds will break first [2]. Crack initiation should occur where a cluster of highly constrained bonds exists. There is no reason to expect crack initiation to occur at the interface. The results to be presented show that the solid surface limits the interfacial bonding resulting in stressed interfacial bonds and interfacial fracture. The bonds in highly-crosslinked random networks do not become stressed as expected. The sequence of molecular structural deformations that lead to failure has been determined and found to be strongly dependent upon the network connectivity. The structure of these networks and its influence on the stress-strain behavior will be discussed in general. A set of ideal, ordered networks have been constructed to manipulate the deformation sequence to achieve different fracture modes (i.e. cohesive vs. adhesive).

  9. Quantum molecular dynamics simulations of thermophysical properties of fluid ethane

    NASA Astrophysics Data System (ADS)

    Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

    2012-12-01

    We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.

  10. Thermal Transport in Carbon Nanotubes using Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    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.

  11. Permeance of H2 through porous graphene from molecular dynamics

    NASA Astrophysics Data System (ADS)

    Liu, Hongjun; Dai, Sheng; Jiang, De-en

    2013-12-01

    A recent experiment (Koenig et al., 2012 [15]) demonstrated the capability of porous graphene as one-atom-thin membrane to separate gases by molecular sieving. A quantitative connection between the measured leak rate and the simulated gas permeance has yet to be established. Using H2 as a model gas, here we determine its permeance through porous graphene from molecular dynamics (MD) simulations. Trajectories are used to directly obtain H2 flux, pressure drop across the graphene membrane, and subsequently, H2 permeance. The permeance is determined to be on the order of 105 GPU (gas permeance unit) for pressure driving forces ranging from 2 to 163 atm. By relating to the experimental leak rate, we then use the permeation data to estimate the pore density in the experimentally created porous graphene.

  12. Spotting the difference in molecular dynamics simulations of biomolecules.

    PubMed

    Sakuraba, Shun; Kono, Hidetoshi

    2016-08-21

    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.

  13. Spotting the difference in molecular dynamics simulations of biomolecules.

    PubMed

    Sakuraba, Shun; Kono, Hidetoshi

    2016-08-21

    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. PMID:27544096

  14. Spotting the difference in molecular dynamics simulations of biomolecules

    NASA Astrophysics Data System (ADS)

    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.

  15. 3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors.

    PubMed

    Wang, Fangfang; Yang, Wei; Shi, Yonghui; Le, Guowei

    2015-09-01

    The discovery of clinically relevant inhibitors of retinoic acid receptor-related orphan receptor-gamma-t (RORγt) for autoimmune diseases therapy has proven to be a challenging task. In the present work, to find out the structural features required for the inhibitory activity, we show for the first time a three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations for a series of novel thiazole/thiophene ketone amides with inhibitory activity at the RORγt receptor. The optimum CoMFA and CoMSIA models, derived from ligand-based superimposition I, exhibit leave-one-out cross-validated correlation coefficient (R(2)cv) of .859 and .805, respectively. Furthermore, the external predictive abilities of the models were evaluated by a test set, producing the predicted correlation coefficient (R(2)pred) of .7317 and .7097, respectively. In addition, molecular docking analysis was applied to explore the binding modes between the inhibitors and the receptor. MD simulation and MM/PBSA method were also employed to study the stability and rationality of the derived conformations, and the binding free energies in detail. The QSAR models and the results of molecular docking, MD simulation, binding free energies corroborate well with each other and further provide insights regarding the development of novel RORγt inhibitors with better activity.

  16. Estimation of atomic hydrophobicities using molecular dynamics simulation of peptides

    NASA Astrophysics Data System (ADS)

    Held, Marie; Nicolau, Dan V.

    2007-12-01

    The hydrophobic force is one of the main driving forces in protein folding and binding. However, its nature is not yet well understood and consequently there are more than 80 different scales published trying to quantify it. Most of the hydrophobicity scales are amino acid-based, but the interaction between the molecular surface of the proteins (and DNA) and surfaces they are immobilized on, e.g., on biomedical micro/nanodevices, occurs on fractions of, rather than whole amino acids. This fragmented structure of the biomolecular surface requires the derivation of atom-level hydrophobicity. Most attempts for the evaluation of atomic hydrophobicities are derived from amino acid-based values, which ignore dynamic and steric factors. This contribution reports on the Molecular Dynamics simulations that aim to overcome this simplification. The calculations examine various tripeptides in an aqueous solution and the analysis focuses on the distance of the nearest water molecules to the individual atoms in the peptides. Different environments result in a variation of average distances for similar atoms in different tripeptides. Comparison with the atomic hydrophobicities derived from the amino acid-based hydrophobicity obtained from peptide partition in water-octanol (Dgoct) and transport through the membrane interface (Dgwif) shows a similar trend to the calculated distances. The variations are likely due to the steric differences of similar types of atoms in different geometric contexts. Therefore, Molecular Dynamics simulations proved convenient for the evaluation of atomic hydrophobicities and open new research avenues. The atomic hydrophobicities can be used to design surfaces that mimic the biomolecular surfaces and therefore elicit an expected biomolecular activity from the immobilized biomolecules.

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

    PubMed

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

    2016-05-01

    The results of atomistic molecular-dynamics simulations of mechanical properties of heterocyclic polymer subjected to uniaxial deformation are reported. A new amorphous thermoplastic polyimide R-BAPO with a repeat unit consisting of dianhydride 1,3-bis-(3',4,-dicarboxyphenoxy)diphenyl (dianhydride R) and diamine 4,4'-bis-(4''-aminophenoxy)diphenyloxide (diamine BAPO) was chosen for the simulations. Our primary goal was to establish the impact of various factors (sample preparation method, molecular mass, and cooling and deformation rates) on the elasticity modulus. In particular, we found that the elasticity modulus was only slightly affected by the degree of equilibration, the molecular mass and the size of the simulation box. This is most likely due to the fact that the main contribution to the elasticity modulus is from processes on scales smaller than the entanglement length. Essentially, our simulations reproduce the logarithmic dependence of the elasticity modulus on cooling and deformation rates, which is normally observed in experiments. With the use of the temperature dependence analysis of the elasticity modulus we determined the flow temperature of R-BAPO to be 580 K in line with the experimental data available. Furthermore, we found that the application of high external pressure to the polymer sample during uniaxial deformation can improve the mechanical properties of the polyimide. Overall, the results of our simulations clearly demonstrate that atomistic molecular-dynamics simulations represent a powerful and accurate tool for studying the mechanical properties of heterocyclic polymers and can therefore be useful for the virtual design of new materials, thereby supporting cost-effective synthesis and experimental research. PMID:27033967

  18. Lipid converter, a framework for lipid manipulations in molecular dynamics simulations.

    PubMed

    Larsson, Per; Kasson, Peter M

    2014-11-01

    Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce Lipid Converter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes.

  19. Lipid-converter, a framework for lipid manipulations in molecular dynamics simulations

    PubMed Central

    Larsson, Per; Kasson, Peter M.

    2014-01-01

    Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce lipidconverter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes. PMID:25081234

  20. Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

    SciTech Connect

    Rastogi, Monisha; Vaish, Rahul

    2015-05-15

    The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generated and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.

  1. Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

    NASA Astrophysics Data System (ADS)

    Rastogi, Monisha; Vaish, Rahul

    2015-05-01

    The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generated and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.

  2. Stable conformation of full-length amyloid-β (1-42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations

    NASA Astrophysics Data System (ADS)

    Okamoto, Akisumi; Yano, Atsushi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki

    2013-07-01

    Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer’s disease (AD). It is known that full-length Aβ(1-42) is more prone to aggregation than Aβ(1-40). We here search stable conformations of solvated Aβ(1-42) monomer by replica exchange molecular dynamics simulations based on classical force fields, and the most stable conformation is determined from the total energies evaluated by the ab initio fragment molecular orbital (FMO) calculations. In addition, based on the FMO results, the amino acid residues of Aβ(1-42) contributing to the stabilization of the monomer are highlighted.

  3. Molecular Dynamics Trajectory Compression with a Coarse-Grained Model

    PubMed Central

    Cheng, Yi-Ming; Gopal, Srinivasa Murthy; Law, Sean M.; Feig, Michael

    2012-01-01

    Molecular dynamics trajectories are very data-intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data is about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory. PMID:22025759

  4. Molecular dynamics simulation of hollow thick-walled cylinder collapse

    SciTech Connect

    Nikonov, A. Yu.

    2015-10-27

    The generation and evolution of plastic deformation in a hollow single-crystal cylinder under high-rate axisymmetric loading were studied. An advantage of the proposed loading scheme is that all loading modes are applied simultaneously within the chosen crystallographic plane of the cylinder base and different strain degrees are achieved along the specimen cross section. Molecular dynamics simulation was performed to show that the achievement of a certain strain causes the formation of structural defects on the inner surface of the specimen. The obtained results can be used to explain the main plastic deformation mechanisms of crystalline solids.

  5. Higher-order symplectic Born-Oppenheimer molecular dynamics

    SciTech Connect

    Niklasson, Anders; Bock, Nicolas; Challacombe, Matt; Odell, Anders; Delin, Anna; Johansson, Borje

    2009-01-01

    The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics (TR-BOMD) enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the 6th order have been adapted and optimized to TR-BOMD in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements.

  6. Simple posterior frequency correction for vibrational spectra from molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tikhonov, Denis S.

    2016-05-01

    Vibrational spectra computed from molecular dynamics simulations with large integration time steps suffer from nonphysical frequency shifts of signals [M. Praprotnik and D. Janežič, J. Chem. Phys. 122, 174103 (2005)]. A simple posterior correction technique was developed for compensation of this behavior. It performs through replacement of abscissa in the calculated spectra using following formula: ν corrected = /√{ 2 ṡ (" separators=" 1 - cos ( 2 π ṡ Δ t ṡ ν initial ) ) } 2 π ṡ Δ t , where ν are initial and corrected frequencies and Δt is the MD simulation time step. Applicability of this method was tested on gaseous infrared spectra of hydrogen fluoride and formic acid.

  7. A molecular dynamics study of freezing in a confined geometry

    NASA Technical Reports Server (NTRS)

    Ma, Wen-Jong; Banavar, Jayanth R.; Koplik, Joel

    1992-01-01

    The dynamics of freezing of a Lennard-Jones liquid in narrow channels bounded by molecular walls is studied by computer simulation. The time development of ordering is quantified and a novel freezing mechanism is observed. The liquid forms layers and subsequent in-plane ordering within a layer is accompanied by a sharpening of the layer in the transverse direction. The effects of channel size, the methods of quench, the liquid-wall interaction and the roughness of walls on the freezing mechanism are elucidated. Comparison with recent experiments on freezing in confined geometries is presented.

  8. Accelerating ab initio molecular dynamics simulations by linear prediction methods

    NASA Astrophysics Data System (ADS)

    Herr, Jonathan D.; Steele, Ryan P.

    2016-09-01

    Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.

  9. Moderate pressure phase diagram of methane by Molecular Dynamics simulations

    NASA Astrophysics Data System (ADS)

    Spanu, L.; Donadio, D.; Galli, G.

    2008-12-01

    By using classical and ab initio Molecular Dynamics simulations we have investigated the phase diagram of methane up to ~ 25 Gpa. The melting line of phase I (fcc) was computed in a range of pressure corresponding to the Earth's crust conditions by using classical potentials and three different approaches -free energy calculations, phase coexistence method and integration over the coexistence line. The three techniques consistently give a phase boundary in good agreement with known experimental values. The solid phases in a range of temperature between 100K and 300K were investigated using a metadynamics technique, our results providing a possible assignments of structure and explanation of existing, controversial experiments.

  10. Molecular dynamic study of pressure fluctuations spectrum in plasma

    NASA Astrophysics Data System (ADS)

    Bystryi, R. G.

    2015-11-01

    Pressure of plasma is calculated by using classical molecular dynamics method. The formula based on virial theorem was used. Spectrum pressure's fluctuations of singly ionized non-ideal plasma are studied. 1/f-like spectrum behavior is observed. In other words, flicker noise is observed in fluctuations of pressure equilibrium non-ideal plasma. Relations between the obtained result and pressure fluctuations within the Gibbs and Einstein approaches are discussed. Special attention is paid to features of calculating the pressure in strongly coupled systems.

  11. Easy creation of polymeric systems for molecular dynamics with Assemble!

    NASA Astrophysics Data System (ADS)

    Degiacomi, Matteo T.; Erastova, Valentina; Wilson, Mark R.

    2016-05-01

    We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with Gromacs. We illustrate the capabilities of Assemble! by demonstrating the easy preparation of a 300 monomers-long polyisoprene in hexane, and a heterogeneous mixture of polybutadiene.

  12. Melting of icosahedral gold nanoclusters from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Yanting; Teitel, S.; Dellago, Christoph

    2005-06-01

    Molecular dynamics simulations show that gold clusters with about 600-3000 atoms crystallize into a Mackay icosahedron upon cooling from the liquid. A detailed surface analysis shows that the facets on the surface of the Mackay icosahedral gold clusters soften but do not premelt below the bulk melting temperature. This softening is found to be due to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size, so that the average shape of the cluster is nearly spherical at melting.

  13. Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization.

    PubMed

    Kohagen, Miriam; Lepšík, Martin; Jungwirth, Pavel

    2014-11-20

    Calcium represents a key biological signaling ion with the EF-hand loops being its most prevalent binding motif in proteins. We show using molecular dynamics simulations with umbrella sampling that including electronic polarization effects via ionic charge rescaling dramatically improves agreements with experiment in terms of the strength of calcium binding and structures of the calmodulin binding sites. The present study thus opens way to accurate calculations of interactions of calcium and other computationally difficult high-charge-density ions in biological contexts.

  14. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    SciTech Connect

    Mugnai, Mauro L.; Elber, Ron

    2015-01-07

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.

  15. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

  16. Molecular dynamics simulations of calcium binding in gramicidin A

    NASA Astrophysics Data System (ADS)

    Baştuğ, Turgut; Kuyucak, Serdar

    2006-06-01

    An important issue in molecular dynamics (MD) simulations of biomolecules is whether membrane proteins can be described using nonpolarizable force fields. To shed further light into this question, we study calcium ion binding and blocking of the gramicidin A channel which has not been investigated in MD simulations before. Potential of mean force calculations for calcium and potassium ions using a nonpolarizable force field reveal that calcium binding to the channel is much weaker compared to potassium, and hence calcium block of potassium current cannot be described. Inclusion of polarization interaction in force fields may help to rectify this problem.

  17. Generalized extended Lagrangian Born-Oppenheimer molecular dynamics

    SciTech Connect

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

    2014-10-28

    Extended Lagrangian Born-Oppenheimer molecular dynamics based on Kohn-Sham density functional theory is generalized in the limit of vanishing self-consistent field optimization prior to the force evaluations. The equations of motion are derived directly from the extended Lagrangian under the condition of an adiabatic separation between the nuclear and the electronic degrees of freedom. We show how this separation is automatically fulfilled and system independent. The generalized equations of motion require only one diagonalization per time step and are applicable to a broader range of materials with improved accuracy and stability compared to previous formulations.

  18. Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

    PubMed Central

    Schreiner, Wolfgang; Karch, Rudolf; Knapp, Bernhard; Ilieva, Nevena

    2012-01-01

    Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged. PMID:23019425

  19. Large scale molecular dynamics modeling of materials fabrication processes

    SciTech Connect

    Belak, J.; Glosli, J.N.; Boercker, D.B.; Stowers, I.F.

    1994-02-01

    An atomistic molecular dynamics model of materials fabrication processes is presented. Several material removal processes are shown to be within the domain of this simulation method. Results are presented for orthogonal cutting of copper and silicon and for crack propagation in silica glass. Both copper and silicon show ductile behavior, but the atomistic mechanisms that allow this behavior are significantly different in the two cases. The copper chip remains crystalline while the silicon chip transforms into an amorphous state. The critical stress for crack propagation in silica glass was found to be in reasonable agreement with experiment and a novel stick-slip phenomenon was observed.

  20. Molecular dynamics simulation of bicrystalline metal surface treatment

    SciTech Connect

    Nikonov, A. Yu.

    2015-10-27

    The paper reports the molecular dynamics simulation results on the behavior of a copper crystallite in local frictional contact. The crystallite has a perfect defect-free structure and contains a high-angle grain boundary of type Σ5. The influence of the initial structure on the specimen behavior under loading was analyzed. It is shown that nanoblocks are formed in the subsurface layer. The atomic mechanism of nanofragmentation was studied. A detailed analysis of atomic displacements in the blocks showed that the displacements are rotational. Calculations revealed that the misorientation angle of formed nanoblocks along different directions does not exceed 2 degrees.

  1. Large-scale molecular dynamics simulations of fracture and deformation

    NASA Astrophysics Data System (ADS)

    Zhou, S. J.; Beazley, D. M.; Lomdahl, P. S.; Holian, B. L.

    1996-08-01

    We have discussed the prospects of applying massively parallel molecular dynamics simulation to investigate brittle versus ductile fracture behaviors and dislocation intersection. This idea is illustrated by simulating dislocation emission from a three-dimensional crack. Unprecedentedly, the dislocation loops emitted from the crack fronts have been observed. It is found that dislocation-emission modes, jogging or blunting, are very sensitive to boundary conditions and interatomic potentials. These 3D phenomena can be effectively visualized and analyzed by a new technique, namely, plotting only those atoms within the certain ranges of local potential energies.

  2. Parallel-in-time molecular-dynamics simulations.

    PubMed

    Baffico, L; Bernard, S; Maday, Y; Turinici, G; Zérah, G

    2002-11-01

    While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations. PMID:12513644

  3. Parallel-in-time molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Baffico, L.; Bernard, S.; Maday, Y.; Turinici, G.; Zérah, G.

    2002-11-01

    While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations.

  4. Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems.

    PubMed

    Ceotto, Michele; Ayton, Gary S; Voth, Gregory A

    2008-04-01

    An extension of superposition state molecular dynamics (SSMD) [Venkatnathan and Voth J. Chem. Theory Comput. 2005, 1, 36] is presented with the goal to accelerate timescales and enable the study of "long-time" phenomena for condensed phase systems. It does not require any a priori knowledge about final and transition state configurations, or specific topologies. The system is induced to explore new configurations by virtue of a fictitious (free-particle-like) accelerating potential. The acceleration method can be applied to all degrees of freedom in the system and can be applied to condensed phases and fluids. PMID:26620930

  5. Molecular Dynamics Simulations Of Nanometer-Scale Feature Etch

    SciTech Connect

    Vegh, J. J.; Graves, D. B.

    2008-09-23

    Molecular dynamics (MD) simulations have been carried out to examine fundamental etch limitations. Beams of Ar{sup +}, Ar{sup +}/F and CF{sub x}{sup +} (x = 2,3) with 2 nm diameter cylindrical confinement were utilized to mimic 'perfect' masks for small feature etching in silicon. The holes formed during etch exhibit sidewall damage and passivation as a result of ion-induced mixing. The MD results predict a minimum hole diameter of {approx}5 nm after post-etch cleaning of the sidewall.

  6. Multiple Point Dynamic Gas Density Measurements Using Molecular Rayleigh Scattering

    NASA Technical Reports Server (NTRS)

    Seasholtz, Richard; Panda, Jayanta

    1999-01-01

    A nonintrusive technique for measuring dynamic gas density properties is described. Molecular Rayleigh scattering is used to measure the time-history of gas density simultaneously at eight spatial locations at a 50 kHz sampling rate. The data are analyzed using the Welch method of modified periodograms to reduce measurement uncertainty. Cross-correlations, power spectral density functions, cross-spectral density functions, and coherence functions may be obtained from the data. The technique is demonstrated using low speed co-flowing jets with a heated inner jet.

  7. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.

    PubMed

    Mugnai, Mauro L; Elber, Ron

    2015-01-01

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide.

  8. Molecular Dynamics Models of Shaped Particles Using Filling Solutions

    NASA Astrophysics Data System (ADS)

    Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.

    Algorithms such as molecular dynamics are useful computational methods for generating trajectories for studying kinetics and nonequilibrium, as well as equilibrium, problems involving ensembles of nano- and colloidal particles. Highly coarse-grained representations of complex particles can be created by rigidly connecting beads into a compos- ite particle. Here we show that by permitting the beads to vary in radii and to overlap, particles can be modeled with more complicated shapes, approaching perfect polygons and polyhedra in two and three dimensions, respectively. The positions and radii of the beads correspond to afilling solution of the very short-range repulsive shape of the modeled nanoparticle.

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

    SciTech Connect

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

    1994-12-31

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

  10. High temperature phonon dispersion in graphene using classical molecular dynamics

    SciTech Connect

    Anees, P. Panigrahi, B. K.; Valsakumar, M. C.

    2014-04-24

    Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 K the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.

  11. Molecular dynamics simulation of radiation damage cascades in diamond

    SciTech Connect

    Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.

    2015-06-28

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

  12. Molecular dynamics simulations of a lithium/sodium carbonate mixture.

    PubMed

    Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo

    2016-03-01

    The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519

  13. Molecular dynamics simulations of detonation on the roadrunner supercomputer

    NASA Astrophysics Data System (ADS)

    Mniszewski, Susan; Cawkwell, Marc; Germann, Timothy C.

    2012-03-01

    The temporal and spatial scales intrinsic to a real detonating explosive are extremely difficult to capture using molecular dynamics (MD) simulations. Nevertheless, MD remains very attractive since it allows for the resolution of dynamic phenomena at the atomic scale. Large-scale reactive MD simulations in three dimensions require immense computational resources even when simple reactive force fields are employed. We focus on the REBO force field for 'AB' since it has been shown to support a detonation while being simple, analytic, and short-ranged. The transition from two-to three- dimensional simulations is being facilitated by the port of the REBO force field in the parallel MD code SPaSM to LANL's petaflop supercomputer 'Roadrunner'. We provide a detailed discussion of the challenges associated with computing interatomic forces on a hybrid Opteron/Cell BE computational architecture.

  14. Clustering effects in ionic polymers: Molecular dynamics simulations

    DOE PAGES

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less

  15. Clustering effects in ionic polymers: Molecular dynamics simulations

    SciTech Connect

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.

  16. ProtoMD: A prototyping toolkit for multiscale molecular dynamics

    NASA Astrophysics Data System (ADS)

    Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

    2016-05-01

    ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

  17. Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

    NASA Astrophysics Data System (ADS)

    Kluber, Alexander; Hayre, Robert; Cox, Daniel

    2012-02-01

    Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

  18. Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation.

    PubMed

    Liang, Shih-Wei; Wang, Chih-Hao; Fang, Te-Hua

    2016-12-01

    Mechanical properties of copper (Cu) film under grinding process were accomplished by molecular dynamics simulation. A numerical calculation was carried out to understand the distributions of atomic and slip vector inside the Cu films. In this study, the roller rotation velocity, temperature, and roller rotation direction change are investigated to clarify their effect on the deformation mechanism. The simulation results showed that the destruction of materials was increased proportionally to the roller rotation velocity. The machining process at higher temperature results in larger kinetic energy of atoms than lower temperature during the grinding process of the Cu films. The result also shows that the roller rotation in the counterclockwise direction had the better stability than the roller rotation in the clockwise direction due to significantly increased backfill atoms in the groove of the Cu film surface. Additionally, the effects of the rolling resistances on the Cu film surfaces during the grinding process are studied by the molecular dynamics simulation method. PMID:27637893

  19. Clumpy molecular clouds - A dynamic model self-consistently regulated by T Tauri star formation

    NASA Technical Reports Server (NTRS)

    Norman, C.; Silk, J.

    1980-01-01

    A model is proposed which can account for the longevity, energetics, and dynamical structure of dark molecular clouds. Recent observations of a high space density of T Tauri stars in some dark clouds provide the basis for the assertion that high-velocity winds from these low mass pre-main-sequence stars provide a continuous dynamic input into molecular clouds. It is postulated that as clumps are driven above the Jeans mass, both by coalescence and the enhancement of ram pressure through continuing acceleration by protostellar winds, collapse is followed by the formation of low-mass stars that generate additional protostellar winds. Finally, it is found that star formation occurs on a relatively slow time scale, comparable to the cloud lifetime

  20. Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation.

    PubMed

    Liang, Shih-Wei; Wang, Chih-Hao; Fang, Te-Hua

    2016-12-01

    Mechanical properties of copper (Cu) film under grinding process were accomplished by molecular dynamics simulation. A numerical calculation was carried out to understand the distributions of atomic and slip vector inside the Cu films. In this study, the roller rotation velocity, temperature, and roller rotation direction change are investigated to clarify their effect on the deformation mechanism. The simulation results showed that the destruction of materials was increased proportionally to the roller rotation velocity. The machining process at higher temperature results in larger kinetic energy of atoms than lower temperature during the grinding process of the Cu films. The result also shows that the roller rotation in the counterclockwise direction had the better stability than the roller rotation in the clockwise direction due to significantly increased backfill atoms in the groove of the Cu film surface. Additionally, the effects of the rolling resistances on the Cu film surfaces during the grinding process are studied by the molecular dynamics simulation method.

  1. Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Liang, Shih-Wei; Wang, Chih-Hao; Fang, Te-Hua

    2016-09-01

    Mechanical properties of copper (Cu) film under grinding process were accomplished by molecular dynamics simulation. A numerical calculation was carried out to understand the distributions of atomic and slip vector inside the Cu films. In this study, the roller rotation velocity, temperature, and roller rotation direction change are investigated to clarify their effect on the deformation mechanism. The simulation results showed that the destruction of materials was increased proportionally to the roller rotation velocity. The machining process at higher temperature results in larger kinetic energy of atoms than lower temperature during the grinding process of the Cu films. The result also shows that the roller rotation in the counterclockwise direction had the better stability than the roller rotation in the clockwise direction due to significantly increased backfill atoms in the groove of the Cu film surface. Additionally, the effects of the rolling resistances on the Cu film surfaces during the grinding process are studied by the molecular dynamics simulation method.

  2. Thermal transport in porous Si nanowires from approach-to-equilibrium molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Cartoixà, Xavier; Dettori, Riccardo; Melis, Claudio; Colombo, Luciano; Rurali, Riccardo

    2016-07-01

    We study thermal transport in porous Si nanowires (SiNWs) by means of approach-to-equilibrium molecular dynamics simulations. We show that the presence of pores greatly reduces the thermal conductivity, κ, of the SiNWs as long mean free path phonons are suppressed. We address explicitly the dependence of κ on different features of the pore topology—such as the porosity and the pore diameter—and on the nanowire (NW) geometry—diameter and length. We use the results of the molecular dynamics calculations to tune an effective model, which is capable of capturing the dependence of κ on porosity and NW diameter. The model illustrates the failure of Matthiessen's rule to describe the coupling between boundary and pore scattering, which we account for by the inclusion of an additional empirical term.

  3. Molecular dynamics analysis of metal surface sputtering due to bombardment of high energy particles

    SciTech Connect

    Kumar, K. Kishore; Donbosco, Ferdin Sagai; Kumar, Rakesh

    2014-12-09

    Dependence of sputtering yield of Cu (100) and Ni (100) metal surface by bombardment of 200 Ar ions at various energies and angles of projections is investigated in this paper. The sputtering yield has been calculated by performing molecular dynamics simulation and the same is compared with experiments and theoretical predictions wherever possible. Additionally the kinetic energy, velocity and scattering angle distribution for sputtered and incident atoms are also observed. The results obtained from the present molecular dynamics simulations are found to be in good agreement with experimental data and theoretical estimates. It is observed that the sputtering yield increases as the energy of the bombarding ion increases. Furthermore as the incidence angle increases, the sputtering yield increases until a specific angle and then decreases as normal incidence is approached.

  4. Advanced techniques for constrained internal coordinate molecular dynamics.

    PubMed

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

    2013-04-30

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

  5. Thermostats and thermostat strategies for molecular dynamics simulations of nanofluidics.

    PubMed

    Yong, Xin; Zhang, Lucy T

    2013-02-28

    The thermostats in molecular dynamics (MD) simulations of highly confined channel flow may have significant influences on the fidelity of transport phenomena. In this study, we exploit non-equilibrium MD simulations to generate Couette flows with different combinations of thermostat algorithms and strategies. We provide a comprehensive analysis on the effectiveness of three thermostat algorithms Nosé-Hoover chain (NHC), Langevin (LGV) and dissipative particle dynamics (DPD) when applied in three thermostat strategies, thermostating either walls (TW) or fluid (TF), and thermostating both the wall and fluid (TWTF). Our results of thermal and mechanical properties show that the TW strategy more closely resembles experimental conditions. The TF and TWTF systems also produce considerably similar behaviors in weakly sheared systems, but deviate the dynamics in strongly sheared systems due to the isothermal condition. The LGV and DPD thermostats used in the TF and TWTF systems provide vital ways to yield correct dynamics in coarse-grained systems by tuning the fluid transport coefficients. Using conventional NHC thermostat to thermostat fluid only produces correct thermal behaviors in weakly sheared systems, and breaks down due to significant thermal inhomogeneity in strongly sheared systems.

  6. Molecular dynamics simulations of heme reorientational motions in myoglobin.

    PubMed Central

    Henry, E R

    1993-01-01

    Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes

  7. Electrolysis of water in the diffusion layer: first-principles molecular dynamics simulation.

    PubMed

    Hofbauer, Florian; Frank, Irmgard

    2012-01-01

    With Car-Parrinello molecular dynamics simulations the elementary reaction steps of the electrolysis of bulk water are investigated. To simulate the reactions occurring near the anode and near the cathode, electrons are removed or added, respectively. The study focuses on the reactions in pure water. Effects depending on a particular electrode surface or a particular electrolyte are ignored. Under anodic conditions, the reaction continues till molecular oxygen is formed, under cathodic conditions the formation of molecular hydrogen is observed. In addition the formation of hydrogen peroxide is observed as an intermediate of the anodic reaction. The simulations demonstrate that the electrochemistry of oxygen formation without direct electrode contact can be explained by radical reactions in a solvent. These reactions may involve the intermediate formation of ions. The hydrogen formation is governed by rapid proton transfers between water molecules. PMID:22162243

  8. Development of a model electronic Hamiltonian for understanding electronic relaxation dynamics of [Fe(bpy){sub 3}]{sup 2+} through molecular dynamics simulations

    SciTech Connect

    Iuchi, Satoru; Koga, Nobuaki

    2015-12-31

    A model electronic Hamiltonian of [Fe(bpy){sub 3}]{sup 2+}, which was recently refined for use in molecular dynamics simulations, is reviewed with some additional results. In particular, the quality of the refined model Hamiltonian is examined in terms of the vibrational frequencies and solvation structures of the lowest singlet and quintet states.

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

    PubMed

    Al-Jabour, Salih; Leibscher, Monika

    2015-01-15

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

  10. Molecular Docking and Molecular Dynamics to Identify a Novel Human Immunodeficiency Virus Inhibitor from Alkaloids of Toddalia asiatica

    PubMed Central

    Priya, R.; Sumitha, Rajendrarao; Doss, C. George Priya; Rajasekaran, C.; Babu, S.; Seenivasan, R.; Siva, R.

    2015-01-01

    Background: 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. Objective: For this reason, anti-HIV agents are imperative, and the search for the same from natural resources would assure the safety. Materials and Methods: 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). Results: 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. Conclusion: 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. SUMMARY 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

  11. Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

    DOE PAGES

    Borreguero Calvo, Jose M.; Lynch, Vickie E.

    2015-11-23

    Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less

  12. Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

    SciTech Connect

    Borreguero Calvo, Jose M.; Lynch, Vickie E.

    2015-11-23

    Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulation due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.

  13. Identification of Potential Herbal Inhibitor of Acetylcholinesterase Associated Alzheimer's Disorders Using Molecular Docking and Molecular Dynamics Simulation

    PubMed Central

    Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep

    2014-01-01

    Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000 ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000 ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential. PMID:25054066

  14. Ion motions in molecular dynamics simulations on DNA

    NASA Astrophysics Data System (ADS)

    Ponomarev, Sergei Y.; Thayer, Kelly M.; Beveridge, David L.

    2004-10-01

    Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na+ counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA-Na+ radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.

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

    PubMed

    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.

  16. Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Laghaei, Rozita; Mousseau, Normand

    2010-04-01

    Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35-40 Gln) is associated with several neurodegenerative diseases including Huntington's disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from α-helical structure to random coil, without indication of any significant β-strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel β-sheets and triangular and circular β-helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 μs). This ˜32 Å diameter structure reorganizes further into a tight antiparallel double-stranded ˜22 Å nanotube with 22 residues per turn close to Perutz' model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.

  17. Molecular-Dynamics Study Melting Aluminum at High Pressures

    NASA Astrophysics Data System (ADS)

    Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.; Kozlova, S. A.

    The dependence of the melting temperature versus the pressure under static conditions and under shock-wave compression of aluminum was calculated by molecular-dynamic modeling technique. The Morse potential and EAM potential (embedded atom method) was used for the interatomic interaction for the solid and liquid phases of aluminum. The calculations show a change of crystal structure of aluminum close to the melting range static compression and compression in the shock wave. Melting point was determined by analysis of the radial distribution function and the standard deviation of the atoms with the visualization of crystal structure. The results of molecular dynamics calculations are consistent with experimental data on the compressibility of the shock wave up to 200 GPa. Static melting results are consistent across the field of experimental data up to 30 GPa. A short-term compression in the shock wave, accompanied by the increase of entropy can be leads to overheating nonequilibrium substances. Under these conditions, the melting temperature under static and shock compression may be different from each other. However, the calculations showed on pressure in the shock wave 122 GPa aluminum melting occurs at temperatures close to the melting temperature in static conditions.

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

    PubMed

    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. PMID:26909573

  19. Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution

    PubMed Central

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

    2016-01-01

    Sex and recombination are pervasive throughout nature despite their substantial costs1. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology2,3. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation4. Theory has proposed a number of 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)5,6 or by separating them from deleterious load (the ruby in the rubbish effect)7,8. Previous experiments confirm that sex can increase the rate of adaptation9–17, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here, we present the first comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual 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. PMID:26909573

  20. Rigid-body molecular dynamics of DNA inside a nucleosome.

    PubMed

    Fathizadeh, Arman; Berdy Besya, Azim; Reza Ejtehadi, Mohammad; Schiessel, Helmut

    2013-03-01

    The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use Kramers theory to calculate nucleosome sliding caused by such defects. It is shown that the twist defect scenario together with the sequence-dependent elasticity of DNA can explain the slow time scales observed for nucleosome mobility along DNA. With this method we also show how the twist defect mechanism leads to a higher mobility of DNA in the presence of sin mutations near the dyad axis. Finally, by performing simulations on 5s rDNA, 601, and telomeric base pair sequences, it is demonstrated that the current model is a powerful tool to predict nucleosome positioning. PMID:23475204

  1. Molecular Dynamics Study of Polyethylene under Extreme Confinement

    NASA Astrophysics Data System (ADS)

    Kritikos, G.; Sgouros, A.; Vogiatzis, G. G.; Theodorou, D. N.

    2016-08-01

    We present results concerning the dynamics and the structure of adsorbed layers of molten polyethylene (PE) between two graphite surfaces. The molecular weight of the monodisperse PE chains reaches the entanglement regime. We study three cases of interwall distances, equal to two, three and four times the unperturbed radius of gyration (Rg ) of PE chains. The confined system is equilibrated by use of efficient Monte Carlo (MC) algorithms. Conducting molecular dynamics (MD) simulations, we reveal the distribution of relaxation times as a function of distance from the graphite walls at the temperature of 450 K. From the atomic-level stresses we calculate a realistic estimate of the adhesion tension, which is not affected significantly by the width of the pore. Although the distance between the two walls is comparable to the width of the adsorbed layer, we do not record the formation of ‘glassy bridges’ under the studied conditions. The diffusion of polymer chains in the middle layer is not inhibited by the existence of the two adsorbed layers. Extreme confinement conditions imposed by the long range wall potentials bring about an increase in both the adsorption and desorption rates of chains. The presented results seem to cohere with a reduction in the calorimetric (heat capacity step) glass transition temperature (Tg ).

  2. Molecular dynamics modeling of ultrathin amorphous carbon films

    SciTech Connect

    Glosli, J.N.; Belak, J.; Philpott, M.R.

    1995-05-01

    Amorphous carbon films about 20 mn thick are used by the computer industry as protective coatings on magnetic disks. The structure and function of this family of materials at the atomic level is poorly understood. The growth and properties of a:C and a:CH films 1 to 5 nm thick has been simulated using classical molecular dynamics and a bond-order potential with torsional terms. Studies of quenched melts that verify the ability of this potential to reproduce known features of extended structures of carbon in two and three dimensions are briefly described. In molecular dynamics calculations the incident species were neutral atoms C, or C and H with energies up to 100 eV. The stoichiometry, chemical bonding and distribution functions within the films were analyzed using IBM`s Power Visualization System for different incident gas energies. Microscopic features such as multiple ring structures, including planar graphitic structures, were easily identified. Some preliminary studies of the nanotribology of the a:C films are described, including nano-indentation and sliding in contact with a rigid probe.

  3. Diffusion in liquid Germanium using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

    1996-03-01

    We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

  4. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

    The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)

  5. Accelerated Molecular Dynamics studies of He Bubble Growth in Tungsten

    NASA Astrophysics Data System (ADS)

    Uberuaga, Blas; Sandoval, Luis; Perez, Danny; Voter, Arthur

    2015-11-01

    Understanding how materials respond to extreme environments is critical for predicting and improving performance. In materials such as tungsten exposed to plasmas for nuclear fusion applications, novel nanoscale fuzzes, comprised of tendrils of tungsten, form as a consequence of the implantation of He into the near surface. However, the detailed mechanisms that link He bubble formation to the ultimate development of fuzz are unclear. Molecular dynamics simulations provide insight into the He implantation process, but are necessarily performed at implantation rates that are orders of magnitudes faster than experiment. Here, using accelerated molecular dynamics methods, we examine the role of He implantation rates on the physical evolution of He bubbles in tungsten. We find that, as the He rate is reduced, new types of events involving the response of the tungsten matrix to the pressure in the bubble become competitive and change the overall evolution of the bubble as well as the subsequent morphology of the tungsten surface. We have also examined how bubble growth differs at various microstructural features. These results highlight the importance of performing simulations at experimentally relevant conditions in order to correctly capture the contributions of the various significant kinetic processes and predict the overall response of the material.

  6. TIREX: Replica-exchange molecular dynamics using TINKER

    NASA Astrophysics Data System (ADS)

    Penev, Evgeni S.; Lampoudi, Sotiria; Shea, Joan-Emma

    2009-10-01

    We present a driver program for performing replica-exchange molecular dynamics simulations with the TINKER package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program output. Program summaryProgram title: TiReX Catalogue identifier: AEEK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEK_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.: 43 385 No. of bytes in distributed program, including test data, etc.: 502 262 Distribution format: tar.gz Programming language: Fortran 90/95 Computer: Most UNIX machines Operating system: Linux Has the code been vectorized or parallelized?: parallelized with MPI Classification: 16.13 External routines: TINKER version 4.2 or 5.0, built as a library Nature of problem: Replica-exchange molecular dynamics. Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals. Running time: The sample run may take up to a few minutes.

  7. Molecular dynamics simulations through GPU video games technologies

    PubMed Central

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

    2016-01-01

    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. PMID:27525251

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

    PubMed

    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.

  9. Attosecond vacuum UV coherent control of molecular dynamics

    PubMed Central

    Ranitovic, Predrag; Hogle, Craig W.; Rivière, Paula; Palacios, Alicia; Tong, Xiao-Ming; Toshima, Nobuyuki; González-Castrillo, Alberto; Martin, Leigh; Martín, Fernando; Murnane, Margaret M.; Kapteyn, Henry

    2014-01-01

    High harmonic light sources make it possible to access attosecond timescales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized; this is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep UV, which have not yet been synthesized. Here, we present a unique approach using attosecond vacuum UV pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born–Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipulate the ionization and dissociation channels. Furthermore, through advanced theory, we succeed in rigorously modeling multiscale electron and nuclear quantum control in a molecule. The observed richness and complexity of the dynamics, even in this very simplest of molecules, is both remarkable and daunting, and presents intriguing new possibilities for bridging the gap between attosecond physics and attochemistry. PMID:24395768

  10. Molecular dynamic simulations of the water absorbency of hydrogels.

    PubMed

    Ou, Xiang; Han, Qiang; Dai, Hui-Hui; Wang, Jiong

    2015-09-01

    A polymer gel can imbibe solvent molecules through surface tension effect. When the solvent happens to be water, the gel can swell to a large extent and forms an aggregate called hydrogel. The large deformation caused by such swelling makes it difficult to study the behaviors of hydrogels. Currently, few molecular dynamic simulation works have been reported on the water absorbing mechanism of hydrogels. In this paper, we first use molecular dynamic simulation to study the water absorbing mechanism of hydrogels and propose a hydrogel-water interface model to study the water absorbency of the hydrogel surface. Also, the saturated water content and volume expansion rate of the hydrogel are investigated by building a hydrogel model with different cross-linking degree and by comparing the water absorption curves under different temperatures. The sample hydrogel model used consists of Polyethylene glycol diglycidyl ether (PEGDGE) as epoxy and the Jeffamine, poly-oxy-alkylene-amines, as curing agent. The conclusions obtained are useful for further investigation on PEGDGE/Jeffamine hydrogel. Moreover, the simulation methods, including hydrogel-water interface modeling, we first propose are also suitable to study the water absorbing mechanism of other hydrogels. PMID:26271733

  11. Quantum Thermal Bath for Path Integral Molecular Dynamics Simulation.

    PubMed

    Brieuc, Fabien; Dammak, Hichem; Hayoun, Marc

    2016-03-01

    The quantum thermal bath (QTB) method has been recently developed to account for the quantum nature of the nuclei by using standard molecular dynamics (MD) simulation. QTB-MD is an efficient but approximate method when dealing with strongly anharmonic systems, while path integral molecular dynamics (PIMD) gives exact results but in a huge amount of computation time. The QTB and PIMD methods have been combined in order to improve the PIMD convergence or correct the failures of the QTB-MD technique. Therefore, a new power spectral density of the random force within the QTB has been developed. A modified centroid-virial estimator of the kinetic energy, especially adapted to QTB-PIMD, has also been proposed. The method is applied to selected systems: a one-dimensional double-well system, a ferroelectric phase transition, and the position distribution of an hydrogen atom in a fuel cell material. The advantage of the QTB-PIMD method is its ability to give exact results with a more reasonable computation time for strongly anharmonic systems.

  12. GPU-enabled molecular dynamics simulations of ankyrin kinase complex

    NASA Astrophysics Data System (ADS)

    Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran

    2014-10-01

    The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.

  13. Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

    SciTech Connect

    Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.

    2011-12-12

    This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12{sigma}, 14{sigma} and 16{sigma} and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.

  14. Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces

    NASA Technical Reports Server (NTRS)

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

    2008-01-01

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

  15. Dissecting the molecular origins of specific protein-nucleic acid recognition: hydrostatic pressure and molecular dynamics.

    PubMed Central

    Lynch, Thomas W; Kosztin, Dorina; McLean, Mark A; Schulten, Klaus; Sligar, Stephen G

    2002-01-01

    The fundamental processes by which proteins recognize and bind to nucleic acids are critical to understanding cellular function. To explore the factors involved in protein-DNA recognition, we used hydrostatic pressure to perturb the binding of the BamHI endonuclease to cognate DNA, both in experiment and in molecular dynamic simulations. A new technique of high-pressure gel mobility shift analysis was used to test the effects of elevated hydrostatic pressure on the binding of BamHI to its cognate recognition sequence. Upon application of a pressure of 500 bar, the equilibrium dissociation constant of BamHI binding to the cognate site was found to increase nearly 10-fold. A challenge has been to link this type of pure thermodynamic measurement to functional events occurring at the molecular level. Thus, we used molecular dynamic simulations at both ambient and elevated pressures to reveal details of the direct and water-mediated interactions between BamHI and cognate DNA, which allow explanation of the effects of pressure on site-specific protein-DNA binding and complex stability. PMID:11751298

  16. Molecular dynamics simulations of carbon nanotube-based gears

    NASA Astrophysics Data System (ADS)

    Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn

    1997-09-01

    We use a molecular dynamics simulation to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with 0957-4484/8/3/001/img1. Brenner's reactive hydrocarbon potential is used to model interatomic forces within each molecular gear. A Lennard - Jones 6 - 12 potential or the Buckingham 0957-4484/8/3/001/img2 potential plus electrostatic interaction terms are used for intermolecular interactions between gears. A number of gear and gear/shaft configurations are simulated on parallel computers. One gear is powered by forcing the atoms near the end of the nanotube to rotate, and a second gear is allowed to rotate by keeping the atoms near the end of its nanotube constrained to a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. Results suggest that these gears can operate at up to 50 - 100 GHz in a vacuum at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering the temperature and/or rotation rate.

  17. Molecular dynamics simulations of alkyl substituted nanographene crystals

    NASA Astrophysics Data System (ADS)

    Ziogos, Orestis George; Theodorou, Doros Nicolas

    2015-09-01

    Discotic polyaromatic molecules, similar to nanometric graphene flakes, constitute an interesting class of materials for organic electronic applications. Grafting flexible side chains around the periphery of such molecules enhances their processability and gives rise to diverse behaviours, such as the manifestation of liquid-crystalline character and anisotropic mechanical response. In this work, we examine by means of molecular dynamics simulations the properties of molecular crystals comprised of alkyl-substituted hexa-peri-hexabenzocoronene mesogens. Pristine and mono-substituted systems by hydrogen or iodine atoms are modelled, with variable side chain length. A general structural and mechanical robustness to peripheral substitution is reported, with the mesogens forming tightly packed molecular wires even at elevated temperature and pressure. In their discotic ordering, the molecules present relatively low translational mobility, a beneficial phenomenon for charge transport. A thermotropic dependence of the mechanical response is identified, with the systems behaving differently in their room-temperature crystalline phase and in their liquid-crystalline phase at elevated temperatures. The melting process is also examined, elucidating an initial negative expansion along a high symmetry direction and the existence of a metastable state, before falling into the final liquid-crystalline state. Dedicated to Professor Jean-Pierre Hansen, with deepest appreciation of his outstanding contributions to liquid and soft matter theory.

  18. Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?

    SciTech Connect

    Jang, Seogjoo; Sinitskiy, Anton V.; Voth, Gregory A.

    2014-04-21

    The ring polymer molecular dynamics (RPMD) method has gained popularity in recent years as a simple approximation for calculating real time quantum correlation functions in condensed media. However, the extent to which RPMD captures real dynamical quantum effects and why it fails under certain situations have not been clearly understood. Addressing this issue has been difficult in the absence of a genuine justification for the RPMD algorithm starting from the quantum Liouville equation. To this end, a new and exact path integral formalism for the calculation of real time quantum correlation functions is presented in this work, which can serve as a rigorous foundation for the analysis of the RPMD method as well as providing an alternative derivation of the well established centroid molecular dynamics method. The new formalism utilizes the cyclic symmetry of the imaginary time path integral in the most general sense and enables the expression of Kubo-transformed quantum time correlation functions as that of physical observables pre-averaged over the imaginary time path. Upon filtering with a centroid constraint function, the formulation results in the centroid dynamics formalism. Upon filtering with the position representation of the imaginary time path integral, we obtain an exact quantum dynamics formalism involving the same variables as the RPMD method. The analysis of the RPMD approximation based on this approach clarifies that an explicit quantum dynamical justification does not exist for the use of the ring polymer harmonic potential term (imaginary time kinetic energy) as implemented in the RPMD method. It is analyzed why this can cause substantial errors in nonlinear correlation functions of harmonic oscillators. Such errors can be significant for general correlation functions of anharmonic systems. We also demonstrate that the short time accuracy of the exact path integral limit of RPMD is of lower order than those for finite discretization of path. The

  19. Influence of annealing on chain entanglement and molecular dynamics in weak dynamic asymmetry polymer blends.

    PubMed

    Lin, Yu; Tan, Yeqiang; Qiu, Biwei; Shangguan, Yonggang; Harkin-Jones, Eileen; Zheng, Qiang

    2013-01-17

    The influence of annealing above the glass transition temperature (T(g)) on chain entanglement and molecular dynamics of solution-cast poly(methyl methacrylate)/poly(styrene-co-maleic anhydride) (PMMA/SMA) blends was investigated via a combination of dynamic rheological measurement and broadband dielectric spectroscopy. Chain entanglement density increases when the annealing temperature and/or time increases, resulting from the increased efficiency of chain packing and entanglement recovery. The results of the annealing treatment without cooling revealed that the increase of the entanglement density occurred during the annealing process instead of the subsequent cooling procedure. Annealing above T(g) exerts a profound effect on segmental motion, including the transition temperature and dynamics. Namely, T(g) shifts to higher temperatures and the relaxation time (τ(max)) increases due to the increased entanglement density and decreased molecular mobility. Either T(g) or τ(max) approaches an equilibrium value gradually, corresponding to the equilibrium entanglement density that might be obtained through the theoretical predictions. However, no obvious distribution broadening is observed due to the unchanged heterogeneous dynamics. Furthermore, side group rotational motion could be freely achieved without overcoming the chain entanglement resistance. Hence, neither the dynamics nor the distribution width of the subglass relaxation (β- and γ-relaxation) processes is affected by chain entanglement resulting from annealing, indicating that the local environment of the segments is unchanged.

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

    NASA Astrophysics Data System (ADS)

    Varandas, A. J. C.

    2011-08-01

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

  1. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid–vapor interface

    SciTech Connect

    Nagayama, Gyoko Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-07

    The structure and thermodynamic properties of the liquid–vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid–vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid–vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid–vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid–vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  2. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface

    NASA Astrophysics Data System (ADS)

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-01

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  3. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

    PubMed

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-01

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  4. Dewetting dynamics of nickel thin film on alpha-quartz substrate: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Maekawa, Yuki; Shibuta, Yasushi

    2016-08-01

    Dewetting dynamics of the nickel thin film on the alpha-quartz substrate is closely investigated by molecular dynamics simulation. Morphology after the spontaneous dewetting of thin films changes from multi-droplets, single-droplet and cylindrical structure as the film thickness increases. In the thin cylindrical structure, a neck is induced to break into the droplet due to the Plateau-Rayleigh instability whereas the thick cylindrical structure does not break. Nucleation and subsequent solidification happen only in the large droplet after the dewetting due to the size effect, which is dominated by the kinetic factor of nucleation in the small system.

  5. Structural and dynamical properties of hot dense matter by a Thomas-Fermi-Dirac molecular dynamics

    NASA Astrophysics Data System (ADS)

    Lambert, F.; Clérouin, J.; Mazevet, S.

    2006-09-01

    We use a model combining, in a consistent way, orbital-free density functional theory (OF-DFT) and molecular dynamics (MD), to compute the thermodynamical, structural and dynamical properties of Fe and Au plasmas at conditions relevant to astrophysics and inertial confinement fusion (ICF). The newly developed parallel numerical scheme presented here allows to propagate hundreds of particles and to obtain accurate transport properties. This allows us to investigate the validity of the commonly used one-component plasma (OCP) model in predicting the pair correlation, the diffusion and viscosity coefficients for these two high-temperature high-density plasmas.

  6. Spatially resolved dynamic structure factor of finite systems from molecular dynamics simulations

    SciTech Connect

    Raitza, Thomas; Roepke, Gerd; Reinholz, Heidi; Morozov, Igor

    2011-09-15

    The dynamical response of metallic clusters up to 10{sup 3} atoms is investigated using the restricted molecular dynamics simulations scheme. Exemplarily, a sodium like material is considered. Correlation functions are evaluated to investigate the spatial structure of collective electron excitations and the optical response of laser-excited clusters. In particular, the spectrum of bilocal correlation functions shows resonances representing different modes of collective excitations inside the nano plasma. The spatial structure, the resonance energy, and the width of the eigenmodes have been investigated for various values of electron density, temperature, cluster size, and ionization degree. Comparison with bulk properties is performed and the dispersion relation of collective excitations is discussed.

  7. The director and molecular dynamics of the field-induced alignment of a Gay-Berne nematic phase: An isothermal-isobaric nonequilibrium molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Luckhurst, Geoffrey R.; Satoh, Katsuhiko

    2010-05-01

    Isothermal-isobaric molecular dynamics simulations have been performed for the generic Gay-Berne (GB) mesogen, GB(4.4, 20.0, 1, 1), to investigate director and molecular rotational motion during the field-induced alignment of a nematic. The alignment process for the director is discussed within the context of a hydrodynamic analysis based on the Ericksen-Leslie theory and this is found to predict the simulated behavior well. The dependence of the relaxation time for the alignment on the field strength is also in good accord with the theory. The rotational viscosity coefficient estimated from the simulation is smaller than that typically observed for real nematics and the possible reasons for this are discussed. However, the simulation results are found to follow not only the theory but also the experiments, at least qualitatively. No significant variation in the local and long-range structure of the nematic phase is found during the field-induced alignment process. In addition, we have explored the molecular dynamics in the nematic phase in the presence of the field using the first- and second-rank time autocorrelation functions. More importantly we are able to show that the director relaxation time is longer than that for molecular rotation. It is also possible to use the two orientational correlation times to explore the relationship between the rotational viscosity coefficient and the rotational diffusion constant. The diffusion constants determined from the orientational correlation times, based on the short-time expansion of the autocorrelation functions, are found to be significantly different. In consequence it is not possible to test, unambiguously, the relationship between the rotational viscosity coefficient and the rotational diffusion constant. However, it would seem that the second-rank rotational correlation time provides the most reliable route to the rotational viscosity coefficient.

  8. Evaluating Molecular Interactions in Polycaprolactone-Biomineralized Hydroxyapatite Nanocomposites using Steered Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Sharma, Anurag; Payne, Scott; Katti, Kalpana S.; Katti, Dinesh R.

    2015-04-01

    An experimental and modeling study of a complex nanoclay-based polymeric scaffold system is presented here. A representative molecular model of polymeric nanocomposite scaffold system for bone tissue engineering applications was developed. Polymeric scaffolds were synthesized using organically modified montmorillonite clay (OMMT) with biomineralized hydroxyapatite and polycaprolactone (OMMT-HAP-PCL). The OMMT-HAP-PCL representative model was constructed and validated using transmission electron microscopy, x-ray diffraction and material density results. We observed strong molecular interactions between OMMT, hydroxyapatite (HAP) and polycaprolactone (PCL) in the OMMT-HAP-PCL system. Attractive and repulsive interactions between PCL and different constituents of OMMT and HAP indicate influence of OMMT-HAP on PCL. Polymeric scaffolds were found to have improved nanomechanical properties as compared to pristine PCL due to the introduction of OMMT-HAP. Stress-strain response for the representative OMMT-HAP-PCL model was evaluated using constant force steered molecular dynamics (SMD) simulations. Two distinct stress-strain responses observed in the system indicate a two-phase nanomechanical behavior of OMMT-HAP-PCL obtained at low and high applied stresses. The results obtained from the MD and SMD simulations provide quantitative understanding of molecular interactions between different constituents of OMMT, HAP and PCL and mechanical response in the OMMT-HAP-PCL system.

  9. Understanding anisotropic growth behavior of hexagonal ice on a molecular scale: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Seo, Myungjoo; Jang, Eunseon; Kim, Kyeongjin; Choi, Saehyun; Kim, Jun Soo

    2012-10-01

    Although distinct growth behaviors on different faces of hexagonal ice have long been suggested, their understanding on a molecular scale has been hampered due to experimental difficulties near interfaces. We present a molecular dynamics simulation study to unravel the molecular origin of anisotropy in the growth kinetics of hexagonal ice by visualizing the formation of transient water structures in the growing ice interface. During ice growth, the formation of transient structures and their rearrangement to the final ice configuration are observed irrespective of growth direction. However, we find that their structure and duration differ significantly depending on growth direction. In the direction perpendicular to the basal face of hexagonal ice along which growth occurs most slowly, a two-dimensional transient structure, which is formed by competing hexagonal and cubic arrangements within the same layer, persists for a significant period of time, contrasted with short-lived transient structures in other directions. This observation of such transient water structures and their rearrangement during ice growth provides a clear explanation of different growth rates on each face of hexagonal ice on a molecular scale.

  10. Molecular energetics in the capsomere of virus-like particle revealed by molecular dynamics simulations.

    PubMed

    Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan

    2013-05-01

    Virus-like particles (VLPs) are highly organized nanoparticles that have great potential in vaccinology, gene therapy, drug delivery, and materials science. However, the application of VLPs is hindered by obstacles in their design and production due to low efficiency of self-assembly. In the present study, all-atom (AA) molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method are utilized to examine the molecular interactions in the capsomere of a murine polyomavirus (MPV) VLP. It is found that both low ionic strength and the intracapsomere disulfide bonds are favorable for maintaining a stable capsomere. Simulation results examining the effects of solution conditions on the stabilization of a capsomere were verified by calorimetry experiments. Simulation results of free energy decomposition indicate that hydrophobic interaction is favorable for the formation of a capsomere, whereas electrostatic interaction is unfavorable. With increasing ionic strength, the dominant interaction for the stabilization of a capsomere changes from hydrophobic to electrostatic. By comprehensive analyses, the key amino acid residues (hot spots) in VP1 protein aiding formation of a capsomere in different solution conditions have been identified. These results provide molecular insights into the stabilization of building blocks for VLP and are expected to have implications in their partitioning between the correct and off-pathway reactions in VLP assembly. PMID:23586433

  11. Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    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-dynamics simulation of crystallization in helical polymers.

    PubMed

    Yamamoto, Takashi; Sawada, Kaoru

    2005-12-15

    The molecular mechanism of crystallization in helical polymers is a fascinating but very difficult subject of research. We here report our recent efforts toward better understanding of the crystallization in helical polymers by use of molecular-dynamics simulation. With straightforward approaches to the problem being quite difficult, we adopt a different strategy of categorizing the helical polymers into two distinct types: one type is a simple bare helix which is essentially made of backbone atomic groups only and has smoother molecular contours, and the other is a more general helix having large side groups that would considerably hamper molecular motion and crystallization. Both types of helical polymers are here constructed by use of the united atom model, but they show quite distinct crystallization behavior; the crystallization of the former-type polymer is rather fast, while that of the latter-type polymer is extremely slow. We find that the bare helix, when rapidly cooled in free three-dimensional space, freezes into partially ordered state with limited intramolecular and intermolecular orders, and that remarkable improvement of order and growth of an ordered chain-folded crystallite occurs by very long-time annealing of the partially ordered state around the apparent freezing temperature. We also study crystallization of the bare helix upon a growth surface; the crystallization in this case proceeds much faster through highly cooperative process of the intermolecular and the intramolecular degrees of freedom. On the other hand, crystallization of the realistic model of isotactic polypropylene (iPP) having pendant methylene groups is found to be extremely sluggish. By restricting the spatial dimension of the system thereby fully disentangling the chain, we observe that the molecule of iPP crystallizes very quickly onto the crystal substrate made of the same iPP chain. Quite remarkable is that the molecule of iPP strictly recognizes the helical sense of the

  13. Molecular Dynamics Simulations from SNL's Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)

    DOE Data Explorer

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

    LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.

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

    PubMed

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

    2015-01-01

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

  15. Ribosomal Dynamics: Intrinsic Instability of a Molecular Machine

    NASA Astrophysics Data System (ADS)

    Gao, Haixiao; Le Barron, Jamie; Frank, Joachim

    Ribosomes are molecular machines that translate genetic message into nascent peptides, through a complex dynamics interplay with mRNAs, tRNAs, and various protein factors. A prominent example of ribosomal dynamics is the rotation of small ribosomal subunit with respect to a large subunit, characterized as the "ratchet motion," which is triggered by the binding of several translation factors. Here, we analyze two kinds of ribosomal ratchet motions, induced by the binding of EF-G and RF3, respectively, as previously observed by cryo-electron microscopy. Using the flexible fitting technique (real-space refinement) and an RNA secondary structure display tool (coloRNA), we obtained quasi-atomic models of the ribosome in these ratchet-motion-related functional states and mapped the observed differences onto the highly conserved RNA secondary structure. Comparisons between two sets of ratchet motions revealed that, while the overall patterns of the RNA displacement are very similar, several local regions stand out in their differential behavior, including the highly conserved GAC (GTPase-associated-center) region. We postulate that these regions are important in modulating general ratchet motion and bestowing it with the dynamic characteristics required for the specific function.

  16. The classical and quantum dynamics of molecular spins on graphene

    PubMed Central

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2015-01-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019

  17. Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling

    PubMed Central

    Wu, Hulin; Lu, Tao; Xue, Hongqi; Liang, Hua

    2014-01-01

    Summary The gene regulation network (GRN) is a high-dimensional complex system, which can be represented by various mathematical or statistical models. The ordinary differential equation (ODE) model is one of the popular dynamic GRN models. High-dimensional linear ODE models have been proposed to identify GRNs, but with a limitation of the linear regulation effect assumption. In this article, we propose a sparse additive ODE (SA-ODE) model, coupled with ODE estimation methods and adaptive group LASSO techniques, to model dynamic GRNs that could flexibly deal with nonlinear regulation effects. The asymptotic properties of the proposed method are established and simulation studies are performed to validate the proposed approach. An application example for identifying the nonlinear dynamic GRN of T-cell activation is used to illustrate the usefulness of the proposed method. PMID:25061254

  18. Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling.

    PubMed

    Wu, Hulin; Lu, Tao; Xue, Hongqi; Liang, Hua

    2014-04-01

    The gene regulation network (GRN) is a high-dimensional complex system, which can be represented by various mathematical or statistical models. The ordinary differential equation (ODE) model is one of the popular dynamic GRN models. High-dimensional linear ODE models have been proposed to identify GRNs, but with a limitation of the linear regulation effect assumption. In this article, we propose a sparse additive ODE (SA-ODE) model, coupled with ODE estimation methods and adaptive group LASSO techniques, to model dynamic GRNs that could flexibly deal with nonlinear regulation effects. The asymptotic properties of the proposed method are established and simulation studies are performed to validate the proposed approach. An application example for identifying the nonlinear dynamic GRN of T-cell activation is used to illustrate the usefulness of the proposed method. PMID:25061254

  19. Molecular dynamics studies on the buffalo prion protein.

    PubMed

    Zhang, Jiapu; Wang, Feng; Chatterjee, Subhojyoti

    2016-01-01

    It was reported that buffalo is a low susceptibility species resisting to transmissible spongiform encephalopathies (TSEs) (same as rabbits, horses, and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (except for rabbits, dogs, horses, and buffalo), manifesting as scrapie in sheep and goats; bovine spongiform encephalopathy (BSE or "mad-cow" disease) in cattle; chronic wasting disease in deer and elk; and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and Kulu in humans etc. In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)), predominantly with α-helices, into insoluble abnormally folded infectious prions (PrP(Sc)), rich in β-sheets. In this article, we studied the molecular structure and structural dynamics of buffalo PrP(C) (BufPrP(C)), in order to understand the reason why buffalo is resistant to prion diseases. We first did molecular modeling of a homology structure constructed by one mutation at residue 143 from the NMR structure of bovine and cattle PrP(124-227); immediately we found that for BufPrP(C)(124-227), there are five hydrogen bonds (HBs) at Asn143, but at this position, bovine/cattle do not have such HBs. Same as that of rabbits, dogs, or horses, our molecular dynamics studies also revealed there is a strong salt bridge (SB) ASP178-ARG164 (O-N) keeping the β2-α2 loop linked in buffalo. We also found there is a very strong HB SER170-TYR218 linking this loop with the C-terminal end of α-helix H3. Other information, such as (i) there is a very strong SB HIS187-ARG156 (N-O) linking α-helices H2 and H1 (if mutation H187R is made at position 187, then the hydrophobic core of PrP(C) will be exposed (L.H. Zhong (2010). Exposure of hydrophobic core in human prion protein pathogenic mutant H187R. Journal of

  20. Molecular dynamics studies on the buffalo prion protein.

    PubMed

    Zhang, Jiapu; Wang, Feng; Chatterjee, Subhojyoti

    2016-01-01

    It was reported that buffalo is a low susceptibility species resisting to transmissible spongiform encephalopathies (TSEs) (same as rabbits, horses, and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (except for rabbits, dogs, horses, and buffalo), manifesting as scrapie in sheep and goats; bovine spongiform encephalopathy (BSE or "mad-cow" disease) in cattle; chronic wasting disease in deer and elk; and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and Kulu in humans etc. In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)), predominantly with α-helices, into insoluble abnormally folded infectious prions (PrP(Sc)), rich in β-sheets. In this article, we studied the molecular structure and structural dynamics of buffalo PrP(C) (BufPrP(C)), in order to understand the reason why buffalo is resistant to prion diseases. We first did molecular modeling of a homology structure constructed by one mutation at residue 143 from the NMR structure of bovine and cattle PrP(124-227); immediately we found that for BufPrP(C)(124-227), there are five hydrogen bonds (HBs) at Asn143, but at this position, bovine/cattle do not have such HBs. Same as that of rabbits, dogs, or horses, our molecular dynamics studies also revealed there is a strong salt bridge (SB) ASP178-ARG164 (O-N) keeping the β2-α2 loop linked in buffalo. We also found there is a very strong HB SER170-TYR218 linking this loop with the C-terminal end of α-helix H3. Other information, such as (i) there is a very strong SB HIS187-ARG156 (N-O) linking α-helices H2 and H1 (if mutation H187R is made at position 187, then the hydrophobic core of PrP(C) will be exposed (L.H. Zhong (2010). Exposure of hydrophobic core in human prion protein pathogenic mutant H187R. Journal of