Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data
White, Andrew D; Hocky, Glen M; Voth, Gregory A
2016-01-01
Accounting for electrons and nuclei simultaneously is a key goal of computer simulation via ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce the properties of systems such as water due to inaccuracies in the underlying electronic density functionals, shortcomings that are often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy-based approach to directly incorporate limited experimental data via a minimal bias. The biased AIMD simulations of both water and of an excess proton in water are shown to give significantly improved properties for both the biased and unbiased observables.
Giorgino, Toni
2014-03-01
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED’s rich syntax to define collective variables (CVs) and VMD’s chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Script development takes place without leaving VMD, thus enabling an incremental try-see-modify development model for molecular metrics.
Giorgino, Toni
2013-01-01
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective variables (CVs) and VMD's chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Development of scripts takes place without leaving VMD, thus enabling an incremental try-see-modify development model for molecular metrics.
Bias in Dynamic Monte Carlo Alpha Calculations
Energy Technology Data Exchange (ETDEWEB)
Sweezy, Jeremy Ed [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nolen, Steven Douglas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Adams, Terry R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Trahan, Travis John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2015-02-06
A 1/N bias in the estimate of the neutron time-constant (commonly denoted as α) has been seen in dynamic neutronic calculations performed with MCATK. In this paper we show that the bias is most likely caused by taking the logarithm of a stochastic quantity. We also investigate the known bias due to the particle population control method used in MCATK. We conclude that this bias due to the particle population control method is negligible compared to other sources of bias.
Osamu Ichikawa; Kazushi Fujimoto; Atsushi Yamada; Susumu Okazaki; Kazuto Yamazaki
2016-01-01
The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism ...
Opinion Dynamics with Confirmation Bias
Allahverdyan, A E
2014-01-01
Background: Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. Methodology/Principal Findings: We formulate a (non-Bayesian) model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect|when consecutively exposed to two opinions, the preferenc...
Opinion Dynamics with Confirmation Bias
Allahverdyan, Armen E.; Aram Galstyan
2014-01-01
Background: Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. Methodology/Principal Findings: We formulate a (non-Bayesian) model for revising subjective proba...
Accelerating Fermionic Molecular Dynamics
Clark, M. A.; Kennedy, A. D.
2004-01-01
We consider how to accelerate fermionic molecular dynamics algorithms by introducing n pseudofermion fields coupled with the nth root of the fermionic kernel. This reduces the maximum pseudofermionic force, and thus allows a larger molecular dynamics integration step size without hitting an instability in the integrator.
Polymer friction Molecular Dynamics
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
2010-01-01
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to ...
Nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Assessing atmospheric bias correction for dynamical consistency using potential vorticity
International Nuclear Information System (INIS)
Correcting biases in atmospheric variables prior to impact studies or dynamical downscaling can lead to new biases as dynamical consistency between the ‘corrected’ fields is not maintained. Use of these bias corrected fields for subsequent impact studies and dynamical downscaling provides input conditions that do not appropriately represent intervariable relationships in atmospheric fields. Here we investigate the consequences of the lack of dynamical consistency in bias correction using a measure of model consistency—the potential vorticity (PV). This paper presents an assessment of the biases present in PV using two alternative correction techniques—an approach where bias correction is performed individually on each atmospheric variable, thereby ignoring the physical relationships that exists between the multiple variables that are corrected, and a second approach where bias correction is performed directly on the PV field, thereby keeping the system dynamically coherent throughout the correction process. In this paper we show that bias correcting variables independently results in increased errors above the tropopause in the mean and standard deviation of the PV field, which are improved when using the alternative proposed. Furthermore, patterns of spatial variability are improved over nearly all vertical levels when applying the alternative approach. Results point to a need for a dynamically consistent atmospheric bias correction technique which results in fields that can be used as dynamically consistent lateral boundaries in follow-up downscaling applications. (letter)
Polymer friction Molecular Dynamics
DEFF Research Database (Denmark)
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....
BÄRBEL M. R. STADLER; Stadler, Peter F
2003-01-01
Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability...
Substructured multibody molecular dynamics.
Energy Technology Data Exchange (ETDEWEB)
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Molecular dynamics for fermions
International Nuclear Information System (INIS)
The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)
Orbital free molecular dynamics
International Nuclear Information System (INIS)
The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)
Biased motion and molecular motor properties of bipedal spiders
Samii, Laleh; Linke, Heiner; Zuckermann, Martin J.; Forde, Nancy R.
2010-02-01
Molecular spiders are synthetic molecular motors featuring multiple legs that each can interact with a substrate through binding and cleavage. Experimental studies suggest the motion of the spider in a matrix is biased toward uncleaved substrates and that spider properties such as processivity can be altered by changing the binding strength of the legs to substrate [R. Pei, S. K. Taylor, D. Stefanovic, S. Rudchenko, T. E. Mitchell, and M. N. Stojanovic, J. Am. Chem. Soc. 128, 12693 (2006)]. We investigate the origin of biased motion and molecular motor properties of bipedal spiders using Monte Carlo simulations. Our simulations combine a realistic chemical kinetic model, hand-over-hand or inchworm modes of stepping, and the use of a one-dimensional track. We find that stronger binding to substrate, cleavage and spider detachment from the track are contributing mechanisms to population bias. We investigate the contributions of stepping mechanism to speed, randomness parameter, processivity, coupling, and efficiency, and comment on how these molecular motor properties can be altered by changing experimentally tunable kinetic parameters.
Open boundary molecular dynamics
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.
Molecular Dynamics of Acetylcholinesterase
Energy Technology Data Exchange (ETDEWEB)
Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy
2002-06-01
Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.
From Molecular Dynamics to Dissipative Particle Dynamics
Flekkoy, Eirik G.; Coveney, Peter V.
1999-01-01
A procedure is introduced for deriving a coarse-grained dissipative particle dynamics from molecular dynamics. The rules of the dissipative particle dynamics are derived from the underlying molecular interactions, and a Langevin equation is obtained that describes the forces experienced by the dissipative particles and specifies the associated canonical Gibbs distribution for the system.
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
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.
Unified nonequilibrium dynamical theory for exchange bias and training effects
Institute of Scientific and Technical Information of China (English)
Zhang Kai-Cheng; Liu Bang-Gui
2009-01-01
We have investigated the exchange bias and training effect in the ferromagnetie/antiferromagnetic (FM/AF)heterostructures using a unified Monte Carlo dynamical approach. The magnetization of the uncompensated AF layer is still open after the first field cycling is finished. Our simulated results show obvious shift of hysteresis loops (exchange bias) and cycling dependence of exchange bias (training effect) when the temperature is below 45 K. The exchange bias field decreases with decreasing cooling rate or increasing temperature and the number of the field cycling. Essentially,these two effects can be explained on the basis of the microscopical coexistence of both reversible and irreversible moment reversals of the AF domains. Our simulations are useful to understand the real magnetization dynamics of such magnetic heterostructures.
The nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments
Introduction to Accelerated Molecular Dynamics
Energy Technology Data Exchange (ETDEWEB)
Perez, Danny [Los Alamos National Laboratory
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.
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Fluctuating-bias controlled electron transport in molecular junctions
Ridley, Michael; MacKinnon, Angus; Kantorovich, Lev
2016-05-01
We consider the problem of transport through a multiterminal molecular junction in the presence of a stochastic bias, which can also be used to describe transport through fluctuating molecular energy levels. To describe these effects, we first make a simple extension of our previous work [Phys. Rev. B 91, 125433 (2015), 10.1103/PhysRevB.91.125433] to show that the problem of tunneling through noisy energy levels can be mapped onto the problem of a noisy driving bias, which appears in the Kadanoff-Baym equations for this system in an analogous manner to the driving term in the Langevin equation for a classical circuit. This formalism uses the nonequilibrium Green's function method to obtain analytically closed formulas for transport quantities within the wide-band limit approximation for an arbitrary time-dependent bias and it is automatically partition free. We obtain exact closed formulas for both the colored and white noise-averaged current at all times. In the long-time limit, these formulas possess a Landauer-Büttiker-type structure which enables the extraction of an effective transmission coefficient for the transport. Expanding the Fermi function into a series of simple poles, we find an exact formal relation between the parameters which characterize the bias fluctuations and the poles of the Fermi function. This enables us to describe the effect of the temperature and the strength of the fluctuations on the averaged current which we interpret as a quantum analog to the classical fluctuation-dissipation theorem. We use these results to convincingly refute some recent results on the multistability of the current through a fluctuating level, simultaneously verifying that our formalism satisfies some well-known theorems on the asymptotic current. Finally, we present numerical results for the current through a molecular chain which demonstrate a transition from nonlinear to linear I -V characteristics as the strength of fluctuations is increased, as well as a
Molecular dynamics simulations
International Nuclear Information System (INIS)
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs
Cameron Abrams; Giovanni Bussi
2013-01-01
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including u...
The response dynamics of recognition memory: Sensitivity and bias.
Koop, Gregory J; Criss, Amy H
2016-05-01
Advances in theories of memory are hampered by insufficient metrics for measuring memory. The goal of this paper is to further the development of model-independent, sensitive empirical measures of the recognition decision process. We evaluate whether metrics from continuous mouse tracking, or response dynamics, uniquely identify response bias and mnemonic evidence, and demonstrate 1 application of these metrics to the strength-based mirror-effect paradigm. In 4 studies, we show that response dynamics can augment our current analytic repertoire in a way that speaks to the psychological mechanisms underlying recognition memory. We manipulated familiarity and response bias via encoding strength and the proportion of targets at test (Experiment 1) and found that the initial degree of deviation of the mouse movement toward a response is a robust indicator of response bias. In order to better isolate measures of memory strength, we next minimized response bias through the use of 2-alternative forced-choice tests (Experiments 2 and 3). Changes in the direction of movement along the x-axis provided an indication of encoding strength. We conclude by applying these metrics to the typical strength-based mirror effect design (Experiment 4) in an attempt to further discriminate between differentiation and criterion-shift accounts. (PsycINFO Database Record PMID:26595069
Physical adsorption and molecular dynamics
International Nuclear Information System (INIS)
Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.)
A Polynomial Prediction Filter Method for Estimating Multisensor Dynamically Varying Biases
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
The estimation of the sensor measurement biases in a multisensor system is vital for the sensor data fusion. A solution is provided for the estimation of dynamically varying multiple sensor biases without any knowledge of the dynamic bias model parameters. It is shown that the sensor bias pseudomeasurement can be dynamically obtained via a parity vector. This is accomplished by multiplying the sensor uncalibrated measurement equations by a projection matrix so that the measured variable is eliminated from the equations. Once the state equations of the dynamically varying sensor biases are modeled by a polynomial prediction filter, the dynamically varying multisensor biases can be obtained by Kalman filter. Simulation results validate that the proposed method can estimate the constant biases and dynamic biases of multisensors and outperforms the methods reported in literature.
Galilei invariant molecular dynamics
International Nuclear Information System (INIS)
We construct a C*-dynamical model for a chemical reaction. Galilei invariance of our nonrelativistic model is demonstrated by defining it directly on a Galilean space-time fibrebundle with C*-algebra valued fibre, i.e. without reference to any coordinate system. The existence of equilibrium states in this model is established and some of their properties are discussed. (orig.)
Psychological biases affecting human cognitive performance in dynamic operational environments
International Nuclear Information System (INIS)
In order to identify cognitive error mechanisms observed in the dynamic operational environment, the following materials were analyzed giving special attention to psychological biases, together with possible cognitive tasks and these location, and internal and external performance shaping factors: (a) 13 human factors analyses of US nuclear power plant accidents, (b) 14 cases of Japanese nuclear power plant incidents, and (c) 23 cases collected in simulator experiments. In the resulting analysis, the most frequently identified cognitive process associated with error productions was situation assessment, and following varieties were KB processes and response planning, all of that were the higher cognitive activities. Over 70% of human error cases, psychological bias was affecting to cognitive errors, especially those to higher cognitive activities. In addition, several error occurrence patterns, including relations between cognitive process, biases, and PSFs were identified by the multivariate analysis. According to the identified error patterns, functions that an operator support system have to equip were discussed and specified for design base considerations. (author)
Implied dynamics biases the visual perception of velocity.
Directory of Open Access Journals (Sweden)
Barbara La Scaleia
Full Text Available We expand the anecdotic report by Johansson that back-and-forth linear harmonic motions appear uniform. Six experiments explore the role of shape and spatial orientation of the trajectory of a point-light target in the perceptual judgment of uniform motion. In Experiment 1, the target oscillated back-and-forth along a circular arc around an invisible pivot. The imaginary segment from the pivot to the midpoint of the trajectory could be oriented vertically downward (consistent with an upright pendulum, horizontally leftward, or vertically upward (upside-down. In Experiments 2 to 5, the target moved uni-directionally. The effect of suppressing the alternation of movement directions was tested with curvilinear (Experiment 2 and 3 or rectilinear (Experiment 4 and 5 paths. Experiment 6 replicated the upright condition of Experiment 1, but participants were asked to hold the gaze on a fixation point. When some features of the trajectory evoked the motion of either a simple pendulum or a mass-spring system, observers identified as uniform the kinematic profiles close to harmonic motion. The bias towards harmonic motion was most consistent in the upright orientation of Experiment 1 and 6. The bias disappeared when the stimuli were incompatible with both pendulum and mass-spring models (Experiments 3 to 5. The results are compatible with the hypothesis that the perception of dynamic stimuli is biased by the laws of motion obeyed by natural events, so that only natural motions appear uniform.
Kühne, Thomas D
2012-01-01
Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.
State-Dependent Molecular Dynamics
Directory of Open Access Journals (Sweden)
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
A sampling of molecular dynamics
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
Energy Technology Data Exchange (ETDEWEB)
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
The Extracellular Surface of the GLP-1 Receptor Is a Molecular Trigger for Biased Agonism.
Wootten, Denise; Reynolds, Christopher A; Smith, Kevin J; Mobarec, Juan C; Koole, Cassandra; Savage, Emilia E; Pabreja, Kavita; Simms, John; Sridhar, Rohan; Furness, Sebastian G B; Liu, Mengjie; Thompson, Philip E; Miller, Laurence J; Christopoulos, Arthur; Sexton, Patrick M
2016-06-16
Ligand-directed signal bias offers opportunities for sculpting molecular events, with the promise of better, safer therapeutics. Critical to the exploitation of signal bias is an understanding of the molecular events coupling ligand binding to intracellular signaling. Activation of class B G protein-coupled receptors is driven by interaction of the peptide N terminus with the receptor core. To understand how this drives signaling, we have used advanced analytical methods that enable separation of effects on pathway-specific signaling from those that modify agonist affinity and mapped the functional consequence of receptor modification onto three-dimensional models of a receptor-ligand complex. This yields molecular insights into the initiation of receptor activation and the mechanistic basis for biased agonism. Our data reveal that peptide agonists can engage different elements of the receptor extracellular face to achieve effector coupling and biased signaling providing a foundation for rational design of biased agonists. PMID:27315480
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Progress in quantum molecular dynamics
International Nuclear Information System (INIS)
In this paper a microscopic simulation method of the quantum molecular dynamics (QMD) and its extensions to high- and low-energy regions are reported. Combined with the statistical decay calculation, QMD can reproduce experimental data with fixed and very few parameters. (J.P.N.)
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.
2015-01-01
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 disc...
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale 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.
Driving ordering processes in molecular-dynamics simulations.
Dittmar, Harro; Kusalik, Peter G
2014-05-16
Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized. PMID:24877946
Molecular Dynamics for Dense Matter
Maruyama, Toshiki; Chiba, Satoshi
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...
Rheology via nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference
Rheology via nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.
Laser Controlled Molecular Orientation Dynamics
International Nuclear Information System (INIS)
Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation
Better, Cheaper, Faster Molecular Dynamics
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.
Functional bias in molecular evolution rate of Arabidopsis thaliana
Directory of Open Access Journals (Sweden)
Anandakrishnan Ramu
2010-05-01
Full Text Available Abstract Background Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they are responsible for fundamental biological function, others are conserved for their unique functional characteristics. Therefore one would expect the rate of molecular evolution for individual genes to be dependent on their biological function. Whether this expectation holds for genes duplicated by whole genome duplication is not known. Results We empirically demonstrate here, using duplicated genes generated from the Arabidopsis thaliana α-duplication event, that the rate of molecular evolution of genes duplicated in this event depend on biological function. Using functional clustering based on gene ontology annotation of gene pairs, we show that some duplicated genes, such as defense response genes, are under weaker purifying selection or under stronger diversifying selection than other duplicated genes, such as protein translation genes, as measured by the ratio of nonsynonymous to synonymous divergence (dN/dS. Conclusions These results provide empirical evidence indicating that molecular evolution rate for genes duplicated in whole genome duplication, as measured by dN/dS, may depend on biological function, which we characterize using gene ontology annotation. Furthermore, the general approach used here provides a framework for comparative analysis of molecular evolution rate for genes based on their biological function.
Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup
Directory of Open Access Journals (Sweden)
Baines John F
2009-12-01
Full Text Available Abstract Background Genes with sex-biased expression often show rapid molecular evolution between species. Previous population genetic and comparative genomic studies of Drosophila melanogaster and D. simulans revealed that male-biased genes have especially high rates of adaptive evolution. To test if this is also the case for other lineages within the melanogaster group, we investigated gene expression in D. ananassae, a species that occurs in structured populations in tropical and subtropical regions. We used custom-made microarrays and published microarray data to characterize the sex-biased expression of 129 D. ananassae genes whose D. melanogaster orthologs had been classified previously as male-biased, female-biased, or unbiased in their expression and had been studied extensively at the population-genetic level. For 43 of these genes we surveyed DNA sequence polymorphism in a natural population of D. ananassae and determined divergence to the sister species D. atripex and D. phaeopleura. Results Sex-biased expression is generally conserved between D. melanogaster and D. ananassae, with the majority of genes exhibiting the same bias in the two species. However, about one-third of the genes have either gained or lost sex-biased expression in one of the species and a small proportion of genes (~4% have changed bias from one sex to the other. The male-biased genes of D. ananassae show evidence of positive selection acting at the protein level. However, the signal of adaptive protein evolution for male-biased genes is not as strong in D. ananassae as it is in D. melanogaster and is limited to genes with conserved male-biased expression in both species. Within D. ananassae, a significant signal of adaptive evolution is also detected for female-biased and unbiased genes. Conclusions Our findings extend previous observations of widespread adaptive protein evolution to an independent Drosophila lineage, the D. ananassae subgroup. However, the rate
Molecular dynamics investigation of dynamic crack stability
International Nuclear Information System (INIS)
A series of molecular-dynamics simulations has been performed in order to evaluate the effects of several physical factors on dynamic crack stability. These factors are the crystalline structure and the interatomic interaction modeled by various empirical potentials. For brittle crack propagation at low temperature we find that steady-state crack velocities are limited to a band of accessible values. Increasing the overload beyond KIc, the crack can propagate with a steady-state velocity, which quickly reaches the terminal velocity of about 0.4 of the Rayleigh wave speed. The magnitude of the terminal velocity can be related to the nonlinearity of the interatomic interaction. Further increasing the overload does not change the steady-state velocity dramatically, but significantly increases the amplitude of acoustic emission from the crack tip. Loading the crack even further leads to instabilities which take the form of cleavage steps, dislocation emission, or branching. The instability is closely related to the buildup of a localized coherent, phononlike field generated by the bond-breaking events. The form of the instability depends critically on crystal structure and on the crystallographic orientation of the crack system but can also be correlated with the relative ease of dislocation generation (and motion). copyright 1997 The American Physical Society
Molecular dynamics of interface rupture
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.
Molecular potentials and relaxation dynamics
International Nuclear Information System (INIS)
The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X1Σ+ and a3Σ+ states of LiH, NaH, KH, RbH, and CsH and the X2Σ+ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm-1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 5000K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Molecular dynamics studies of palladium
International Nuclear Information System (INIS)
Equilibrium bulk properties of Pd are examined using molecular dynamics technique based on the embedded atom potential. We calculate the total energy and the lattice parameter as a function of temperature. Melting temperature is determined from the discontinuous transition in the energy and lattice parameter. Specific heat and linear coefficient of thermal expansion are calculated from the energy and lattice parameters respectively and results show good agreement with experimental values. Finally the mean square displacements of thermal expansion are calculated form the energy and lattice parameters respectively and results show good agreement with the experimental values. Finally the mean square displacements of the atoms in bulk Pd are compared with the mean square displacements on the three low-index faces (100), (110) and (III). (author)
Theoretical Concepts in Molecular Photodissociation Dynamics
DEFF Research Database (Denmark)
Henriksen, Niels Engholm
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic Mole...
Theoretical Concepts in Molecular Photodissociation Dynamics
DEFF Research Database (Denmark)
Henriksen, Niels Engholm
1995-01-01
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
Molecular dynamics of membrane proteins.
Energy Technology Data Exchange (ETDEWEB)
Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); 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.
International Nuclear Information System (INIS)
Highlights: → There exists a universal G:C → A:T mutation bias in three domains of life. → This universal mutation bias has not been sufficiently explained. → A DNA mutation model proposed by Loewdin 40 years ago offers a common explanation. -- Abstract: Recently, numerous genome analyses revealed the existence of a universal G:C → A:T mutation bias in bacteria, fungi, plants and animals. To explore the molecular basis for this mutation bias, we examined the three well-known DNA mutation models, i.e., oxidative damage model, UV-radiation damage model and CpG hypermutation model. It was revealed that these models cannot provide a sufficient explanation to the universal mutation bias. Therefore, we resorted to a DNA mutation model proposed by Loewdin 40 years ago, which was based on inter-base double proton transfers (DPT). Since DPT is a fundamental and spontaneous chemical process and occurs much more frequently within GC pairs than AT pairs, Loewdin model offers a common explanation for the observed universal mutation bias and thus has broad biological implications.
Molecular dynamics simulation by atomic mass weighting
Mao, Boryeu; Friedman, Alan R.
1990-01-01
A molecular dynamics-based simulation method in which atomic masses are weighted is described. Results from this method showed that the capability for conformation search in molecular dynamics simulation of a short peptide (FMRF-amide) is significantly increased by mass weighting.
Jourdan, T.
2015-12-01
Sensitivity of microstructures under irradiation to absorption biases of dislocations and dislocation loops is investigated by rate equation cluster dynamics (RECD). Contrary to standard rate theory which is often used to estimate sensitivity of cavity growth to biases, it is possible with RECD to quantify the effect of biases on nucleation, growth and coarsening of loops and cavities. For this purpose simple and accurate expressions for dislocation and dislocation loop biases are derived, based on finite element calculations. They are used in a RECD code to quantify the effect of biases on microstructures of austenitic steels irradiated with electrons. It is shown that biases have a strong influence not only on the loop and dislocation network evolutions, but also on cavity nucleation. Sensitivity to some other parameters of the model is also discussed.
Thermally driven molecular linear motors - A molecular dynamics study
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence
2009-01-01
We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...
Inelastic effects in molecular transport junctions: The probe technique at high bias
Kilgour, Michael; Segal, Dvira
2016-03-01
We extend the Landauer-Büttiker probe formalism for conductances to the high bias regime and study the effects of environmentally induced elastic and inelastic scattering on charge current in single molecule junctions, focusing on high-bias effects. The probe technique phenomenologically incorporates incoherent elastic and inelastic effects to the fully coherent case, mimicking a rich physical environment at trivial cost. We further identify environmentally induced mechanisms which generate an asymmetry in the current, manifested as a weak diode behavior. This rectifying behavior, found in two types of molecular junction models, is absent in the coherent-elastic limit and is only active in the case with incoherent-inelastic scattering. Our work illustrates that in the low bias-linear response regime, the commonly used "dephasing probe" (mimicking only elastic decoherence effects) operates nearly indistinguishably from a "voltage probe" (admitting inelastic-dissipative effects). However, these probes realize fundamentally distinct I-V characteristics at high biases, reflecting the central roles of dissipation and inelastic scattering processes on molecular electronic transport far-from-equilibrium.
Yan WANG; Ruan, Xiulin; Roy, Ajit K.
2012-01-01
We have used a two-temperature nonequilibrium molecular dynamics method for predicting interfacial thermal resistance across metal-nonmetal interfaces. This method is an extension of the conventional nonequilibrium molecular dynamics for the dielectric-dielectric interface, where a temperature bias is imposed and the heat current is derived. We have included the electron degree of freedom for the interfacial thermal transport problem by treating the electron-phonon coupling with the two-tempe...
Nonlinear excitation kinetics of biased quantum wells. Coherent dynamical screening effect
DEFF Research Database (Denmark)
Turchinovich, Dmitry; Jepsen, Peter Uhd
2006-01-01
In this paper we describe a strongly nonlinear process of ultrafast photoexcitation of a biased quantum well. This process is governed by coherent dynamical screening, where the instantaneously polarized photoexcited carriers screen initial bias field. This results in a dynamic modification of the...... bandstructure of the quantum well, which is totally coherent with the temporal intensity distribution of the excitation laser pulse. We developed a time-resolved theoretical model of coherent dynamical screening, which predicts interesting fundamental consequences, such as nonlinear absorption and ultra...
The population dynamical implications of male-biased parasitism in different mating systems.
Directory of Open Access Journals (Sweden)
Martin R Miller
Full Text Available Although there is growing evidence that males tend to suffer higher levels of parasitism than females, the implications of this for the population dynamics of the host population are not yet understood. Here we build on an established 'two-sex' model and investigate how increased susceptibility to infection in males affects the dynamics, under different mating systems. We investigate the effect of pathogenic disease at different case mortalities, under both monogamous and polygynous mating systems. If the case mortality is low, then male-biased parasitism appears similar to unbiased parasitism in terms of its effect on the population dynamics. At higher case mortalities, we identified significant differences between male-biased and unbiased parasitism. A host population may therefore be differentially affected by male-biased and unbiased parasitism. The dynamical outcome is likely to depend on a complex interaction between the host's mating system and demography, and the parasite virulence.
International Nuclear Information System (INIS)
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
Quantum dynamics of complex molecular systems
Miller, William H.
2005-01-01
This Perspective presents a broad overview of the present status of theoretical capabilities for describing quantum dynamics in molecular systems with many degrees of freedom, e.g., chemical reactions in solution, clusters, solids, or biomolecular environments.
Dynamical processes in atomic and molecular physics
Ogurtsov, Gennadi
2012-01-01
Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece
Ab initio mass tensor molecular dynamics
Tsuchida, Eiji
2010-01-01
Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal ato...
Accelerated molecular dynamics simulations of protein folding
Miao, Y.; Feixas, F; Eun, C; McCammon, JA
2015-01-01
© 2015 Wiley Periodicals, Inc. Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native ...
Molecular Dynamic Simulation on High Performance Infrastrucutres
Bergant, Anže
2016-01-01
This thesis covers comparison between different computer platforms of high performance computing while performing molecular dynamics simulations, which falls under very complex problems and needs lots of processing power. Our goal was to critically evaluate different platforms while solving molecular dynamics, so we used 1 to 16 processor cores on a computer cluster and one and two graphics processing units (GPU) for simulations. The results will be used while planning on buying new computer ...
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Jahn, S.; P. A. Madden
2008-01-01
The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q) from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω) from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the ...
Modeling the Hydrogen Bond within Molecular Dynamics
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.
Molecular Dynamics Simulations of Simple Liquids
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.
Fermionic Molecular Dynamics for nuclear dynamics and thermodynamics
Hasnaoui, K H O; Gulminelli, F
2008-01-01
A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented
Directory of Open Access Journals (Sweden)
Vallon-Christersson Johan
2004-11-01
Full Text Available Abstract Background Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarray process may introduce such offsets and in this article we study the biases introduced by the microarray scanner and the image analysis software. Results By scanning the same spotted oligonucleotide microarray at different photomultiplier tube (PMT gains, we have identified a channel-specific bias present in two-channel microarray data. For the scanners analyzed it was in the range of 15–25 (out of 65,535. The observed bias was very stable between subsequent scans of the same array although the PMT gain was greatly adjusted. This indicates that the bias does not originate from a step preceding the scanner detector parts. The bias varies slightly between arrays. When comparing estimates based on data from the same array, but from different scanners, we have found that different scanners introduce different amounts of bias. So do various image analysis methods. We propose a scanning protocol and a constrained affine model that allows us to identify and estimate the bias in each channel. Backward transformation removes the bias and brings the channels to the same scale. The result is that systematic effects such as intensity dependent log-ratios are removed, but also that signal densities become much more similar. The average scan, which has a larger dynamical range and greater signal-to-noise ratio than individual scans, can then be obtained. Conclusions The study shows that microarray scanners may introduce a significant bias in each channel. Such biases have to be calibrated for, otherwise systematic effects such as intensity dependent log-ratios will be observed. The proposed scanning protocol and calibration method is simple to use and is useful for evaluating scanner biases or for obtaining calibrated measurements
Conductance of Alkanedithiol Single-Molecule Junctions: A Molecular Dynamics Study
DEFF Research Database (Denmark)
Paulsson, Magnus; Krag, Casper; Frederiksen, Thomas;
2009-01-01
We study formation and conductance of alkanedithiol junctions using density functional based molecular dynamics. The formation involves straightening of the molecule, migration of thiol end-groups, and pulling out Au atoms. Plateaus are found in the low-bias conductance traces which decrease by 1...
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... statistical mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular...
Advances in molecular vibrations and collision dynamics molecular clusters
Bacic, Zatko
1998-01-01
This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...
Fast dynamics of molecular bridges
Czech Academy of Sciences Publication Activity Database
Špička, Václav; Kalvová, Anděla; Velický, B.
T151, č. 1 (2012), s. 1-17. ISSN 0031-8949 R&D Projects: GA ČR GAP204/12/0897 Institutional research plan: CEZ:AV0Z10100521; CEZ:AV0Z10100520 Keywords : time quantum dynamics * nonequilibrium Green-functions * Kadanoff-Baym equations * initial correlations * transportequations * mesoscopic systems Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.032, year: 2012
Scalable Molecular Dynamics for Large Biomolecular Systems
Directory of Open Access Journals (Sweden)
Robert K. Brunner
2000-01-01
Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.
Molecular Scale Dynamics of Large Ring Polymers
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
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.
Methane in carbon nanotube - molecular dynamics simulation
Bartuś, Katarzyna; Bródka, Aleksander
2011-01-01
Abstract The behaviour of methane molecules inside carbon nanotube at room temperature is studied using classical molecular dynamics simulations. A methane molecule is represented either by a shapeless super-atom or by rigid set of 5 interaction centres localised on atoms. Different loadings of methane molecules ranging from the dense gas density to the liquid density, and the influence of flexibility of the CNT on structural and dynamics properties of confined molecules are consid...
Neutron Star Crust and Molecular Dynamics Simulation
Horowitz, C J; Schneider, A; Berry, D K
2011-01-01
In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.
DEFF Research Database (Denmark)
Tafuri, Felice Francesco; Sira, Daniel; Jensen, Ole Kiel; Larsen, Torben
a dynamic minimization of the current consumption while imposing simultaneously a constant gain condition. In such a way we maximize the efficiency of the ET transmitter maintaining a considerable linearity. Bias and supply voltages are modulated applying specific waveforms obtained as a function of...... vector magnitude (EVM) of 1.2% and an adjacent channel power ratio (ACPR) of -39.4/-43.5 dBc. The presented transmitter architecture allowed an improvement of 12% PAE compared to a classical ET transmitter where the measured PA was biased in class-AB, maintaining the linearity indicators....
Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics.
Ramírez, C L; Martí, M A; Roitberg, A E
2016-01-01
One of the main goals of chemistry is to understand the underlying principles of chemical reactions, in terms of both its reaction mechanism and the thermodynamics that govern it. Using hybrid quantum mechanics/molecular mechanics (QM/MM)-based methods in combination with a biased sampling scheme, it is possible to simulate chemical reactions occurring inside complex environments such as an enzyme, or aqueous solution, and determining the corresponding free energy profile, which provides direct comparison with experimental determined kinetic and equilibrium parameters. Among the most promising biasing schemes is the multiple steered molecular dynamics method, which in combination with Jarzynski's Relationship (JR) allows obtaining the equilibrium free energy profile, from a finite set of nonequilibrium reactive trajectories by exponentially averaging the individual work profiles. However, obtaining statistically converged and accurate profiles is far from easy and may result in increased computational cost if the selected steering speed and number of trajectories are inappropriately chosen. In this small review, using the extensively studied chorismate to prephenate conversion reaction, we first present a systematic study of how key parameters such as pulling speed, number of trajectories, and reaction progress are related to the resulting work distributions and in turn the accuracy of the free energy obtained with JR. Second, and in the context of QM/MM strategies, we introduce the Hybrid Differential Relaxation Algorithm, and show how it allows obtaining more accurate free energy profiles using faster pulling speeds and smaller number of trajectories and thus smaller computational cost. PMID:27497165
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamic simulation of directional crystal growth
Costa, B. V.; Coura, P. Z.; Mesquita, O. N.
1999-01-01
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach experimentally, being an important tool for further experimental and theoretical developments in the area of crystal growth.
Molecular dynamics - NMR experiments and simulations
Czech Academy of Sciences Publication Activity Database
Dračínský, Martin; Hodgkinson, P.; Kessler, Jiří; Bouř, Petr
Brno : Masaryk University Press, 2015 - (Sklenář, V.). s. 277-278 ISBN 978-80-210-7890-1. [EUROMAR 2015. 05.07.2015-10.07.2015, Praha] Institutional support: RVO:61388963 Keywords : molecular dynamics * NMR spectroscopy * MD simulations Subject RIV: CF - Physical ; Theoretical Chemistry
Reaction dynamics in polyatomic molecular systems
Energy Technology Data Exchange (ETDEWEB)
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
International Nuclear Information System (INIS)
A long-probe technique was utilized to record the expansion and retreat of the dynamic sheath around a spherical substrate immersed in pulsed cathode arc metal plasma. Positively biased, long cylindrical probes were placed on the side and downstream of a negatively pulsed biased stainless steel sphere of 1 in. (25.4 mm) diameter. The amplitude and width of the negative high voltage pulses (HVPs) were 2 kV, 5 kV, 10 kV, and 2 μs, 4 μs, 10 μs, respectively. The variation of the probe (electron) current during the HVP is a direct measure for the sheath expansion and retreat. Maximum sheath sizes were determined for the different parameters of the HVP. The expected rarefaction zone behind the biased sphere (wake) due to the fast plasma flow was clearly established and quantified.
Energy Technology Data Exchange (ETDEWEB)
Anders, Andre; Wu, Hongchen; Anders, Andre
2008-06-13
A long-probe technique was utilized to record the expansion and retreat of the dynamic sheath around a spherical substrate immersed in pulsed cathode arc metal plasma. Positively biased, long cylindrical probes were placed on the side and downstream of a negatively pulsed biased stainless steel sphere of 1" (25.4 mm) diameter. The amplitude and width of the negative high voltage pulses (HVP) were 2 kV, 5 kV, 10 kV, and 2 mu s, 4 mu s, 10 mu s, respectively. The variation of the probe (electron) current during the HVP is a direct measure for the sheath expansion and retreat. Maximum sheath sizes were determined for the different parameters of the HVP. The expected rarefaction zone behind the biased sphere (wake) due to the fast plasma flow was clearly established and quantified.
Non-equilibrium two-level system dynamics probed with a biased bridge resonator
Khalil, Moe; Gladchenko, Sergiy; Stoutimore, M. J. A.; Wellstood, F. C.; Osborn, K. D.
2013-03-01
We have designed a biased bridge resonator (BBR), which allows us to probe amorphous dielectric films by simultaneously applying a quasi-static electric bias field in addition to a microwave electric field. The BBR is made with a bridge arrangement of capacitors using superconducting aluminum electrodes and operated at millikelvin temperatures. Measurements of a universal amorphous dielectric film at high microwave amplitudes and a sufficiently fast bias field ramp reveals a non-equilibrium dielectric loss equal to its intrinsic steady state value. This phenomenon is explained by a theory which uses the dynamics of charged two-level systems undergoing Landau-Zener transitions to remain in their ground state. We will compare the experimental data to Monte Carlo simulations of the theory which allow for the separate extraction of the dipole moment and the spectral density of two-level systems.
Effect of frequency of dynamic bias to total dose effect of X-rays
International Nuclear Information System (INIS)
Bias voltage applied to MOSFET during irradiation has a major impact on the device response because charge yield, transport, and trapping in oxide are all bias dependent. NMOSFET and PMOSFET under different frequency of dynamic bias were irradiated by 10 keV X-rays to study the total dose effect. The shifts of threshold voltage of the MOSFETs before and after irradiation and effects of the radiation-induced charge on the threshold voltage of MOSFETs are analyzed in this paper. The results showed that the higher the frequency of pulse signal is, the less threshold shift and concentration of the radiation-induced charge were observed at the same pulsed voltage. (authors)
Molecular dynamics simulations of weak detonations.
Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie
2011-12-01
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055
Analytical propagation of errors in dynamic SPECT: estimators, degrading factors, bias and noise
International Nuclear Information System (INIS)
Dynamic SPECT is a relatively new technique that may potentially benefit many imaging applications. Though similar to dynamic PET, the accuracy and precision of dynamic SPECT parameter estimates are degraded by factors that differ from those encountered in PET. In this work we formulate a methodology for analytically studying the propagation of errors from dynamic projection data to kinetic parameter estimates. This methodology is used to study the relationships between reconstruction estimators, image degrading factors, bias and statistical noise for the application of dynamic cardiac imaging with 99mTc-teboroxime. Dynamic data were simulated for a torso phantom, and the effects of attenuation, detector response and scatter were successively included to produce several data sets. The data were reconstructed to obtain both weighted and unweighted least squares solutions, and the kinetic rate parameters for a two- compartment model were estimated. The expected values and standard deviations describing the statistical distribution of parameters that would be estimated from noisy data were calculated analytically. The results of this analysis present several interesting implications for dynamic SPECT. Statistically weighted estimators performed only marginally better than unweighted ones, implying that more computationally efficient unweighted estimators may be appropriate. This also suggests that it may be beneficial to focus future research efforts upon regularization methods with beneficial bias-variance trade-offs. Other aspects of the study describe the fundamental limits of the bias-variance trade-off regarding physical degrading factors and their compensation. The results characterize the effects of attenuation, detector response and scatter, and they are intended to guide future research into dynamic SPECT reconstruction and compensation methods. (author)
Dynamical quenching of tunneling in molecular magnets
International Nuclear Information System (INIS)
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation
Dynamical quenching of tunneling in molecular magnets
Energy Technology Data Exchange (ETDEWEB)
José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)
2015-12-15
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.
DEFF Research Database (Denmark)
Turchinovich, Dmitry; Monozon, B. S.; Jepsen, Peter Uhd
2006-01-01
In this work we describe the ultrafast excitation kinetics of biased quantum well, arising from the optically induced dynamical screening of a bias electric field. The initial bia electric field inside the quantum well is screened by the optically excited polarized electron-hole pairs. This leads...... to a dynamical modification of the properties of the system within an excitation pulse duration. We calculate the excitation kinetics of a biased quantum well and the dependency of resulting electronic and optical properties on the excitation pulse fluence, quantum well width,and initial bias field...
Exciton dynamics in perturbed vibronic molecular aggregates.
Brüning, C; Wehner, J; Hausner, J; Wenzel, M; Engel, V
2016-07-01
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
Molecular dynamics simulations of oxide memory resistors (memristors)
Energy Technology Data Exchange (ETDEWEB)
Savel' ev, S E; Alexandrov, A S [Department of Physics, Loughborough University, Loughborough LE11 3TU (United Kingdom); Bratkovsky, A M; Stanley Williams, R [Hewlett-Packard Laboratories, 1501 Page Mill Road, Palo Alto, CA 94304 (United States)
2011-06-24
Reversible bipolar nanoswitches that can be set and read electronically in a solid-state two-terminal device are very promising for applications. We have performed molecular dynamics simulations that mimic systems with oxygen vacancies interacting via realistic potentials and driven by an external bias voltage. The competing short- and long-range interactions among charged mobile vacancies lead to density fluctuations and short-range ordering, while illustrating some aspects of observed experimental behavior, such as memristor polarity inversion. The simulations show that the 'localized conductive filaments' and 'uniform push/pull' models for memristive switching are actually two extremes of the one stochastic mechanism.
Novel procedure for thermal equilibration in molecular dynamics simulation.
Gallo, Marco T; Grant, Barry J; Teodoro, Miguel L; Melton, Julia; Cieplak, Piotr; Phillips, George N; Stec, Boguslaw
2009-04-01
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797
Rudzinski, Joseph F; Bereau, Tristan
2016-01-01
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and reference (e.g., from experiments or higher-level simulations) observables. To bound the microscopic information generated by computer simulations within reference measurements, we propose a method that reweights the microscopic transitions of the system to improve consistency with a set of coarse kinetic observables. The method employs the well-developed Markov state modeling framework to efficiently link microscopic dynamics with long-time scale constraints, thereby consistently addressing a wide range of time scales. To emphasize the robustness of the method, we consider two distinct coarse-grained models with significant kinetic inconsistencies. When applied to the simulated conformational dynamics of small peptides, the reweighting procedure systematically ...
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Towards the molecular bases of polymerase dynamics
International Nuclear Information System (INIS)
One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (rf) and RNA polymerase (rt). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking rf and rt suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin rt may depend on the length (λt) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs
Nonadiabatic Molecular Dynamics Based on Trajectories
Directory of Open Access Journals (Sweden)
Felipe Franco de Carvalho
2013-12-01
Full Text Available Performing molecular dynamics in electronically excited states requires the inclusion of nonadiabatic effects to properly describe phenomena beyond the Born-Oppenheimer approximation. This article provides a survey of selected nonadiabatic methods based on quantum or classical trajectories. Among these techniques, trajectory surface hopping constitutes an interesting compromise between accuracy and efficiency for the simulation of medium- to large-scale molecular systems. This approach is, however, based on non-rigorous approximations that could compromise, in some cases, the correct description of the nonadiabatic effects under consideration and hamper a systematic improvement of the theory. With the help of an in principle exact description of nonadiabatic dynamics based on Bohmian quantum trajectories, we will investigate the origin of the main approximations in trajectory surface hopping and illustrate some of the limits of this approach by means of a few simple examples.
Molecular dynamics study of cyclohexane interconversion
Wilson, Michael A.; Chandler, David
1990-12-01
Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.
Molecular dynamics at constant Cauchy stress
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.
Molecular dynamics simulation for modelling plasma spectroscopy
Talin, B; Calisti, A; Gigosos, M A; González, M A; Gaztelurrutia, T R; Dufty, J W
2003-01-01
The ion-electron coupling properties for an ion impurity in an electron gas and for a two-component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely motivated by the study of radiator dipole relaxation in plasmas which makes a real link between models and experiments. Current radiative property models for plasmas include single electron collisions neglecting charge-charge correlations within the classical quasi-particle approach commonly used in this field. The dipole relaxation simulation based on electron-ion molecular dynamics proposed here will provide a means to benchmark and improve model developments. Benefiting from a detailed study of a single ion embedded in an electron plasma, the challenging two-component ion-electron molecular dynamics simulations are proved accurate. They open new possibilities of obtaining reference lineshape data.
Molecular quantum dynamics. From theory to applications
International Nuclear Information System (INIS)
An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the
Simulation of Abrasive Machining Using Molecular Dynamics
Oluwajobi, Akinjide O.; Chen, Xun
2009-01-01
The development of ultra–precision processes which can achieve excellent surface finish and tolerance at nanometre level is now a critical requirement for many applications in medical, electronics and energy industry. Presently, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use of Molecular Dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis ...
Modelling abrasive machining techniques using molecular dynamics
Oluwajobi, Akinjide O.; Chen, Xun
2008-01-01
The development of ultra–precision processes which can achieve nanometre surface finishes and tolerances is now a critical requirement for many applications in medical, electronics and energy industry. Presently, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use Molecular Dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis of these processes at the nanometre scal...
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Molecular dynamics modelling of solidification in metals
Energy Technology Data Exchange (ETDEWEB)
Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)
1997-12-31
Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.
Molecular dynamics simulation of expanding infinite matter
International Nuclear Information System (INIS)
Multi-fragmentation occurred in an expanding infinite system is studied by using molecular dynamics simulation. To evaluate the secondary decay effect, the time evolution of expanding system is proceeded till all fragments are stabilized completely. The fragment mass distribution from the expansion is compared with a percolation model and the cause of the exponential shape is clarified. The cause of small critical temperature is also discussed. (author)
Molecular Dynamics with Helical Periodic Boundary Conditions
Czech Academy of Sciences Publication Activity Database
Kessler, Jiří; Bouř, Petr
2014-01-01
Roč. 35, č. 21 (2014), s. 1552-1559. ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant ostatní: GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014
Implementation of Accelerated Molecular Dynamics in NAMD
Wang, Yi; Harrison, Christopher B.; Schulten, Klaus; McCammon, J. Andrew
2011-01-01
Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Here we present the implementation of aMD in the parallel simulation program NAMD. We show that aMD simulations performed with NAMD have only a small overhead compared with classical MD simulations. Through example applications to the alanine dipeptide, we discuss the choice of acceleration parameters, the inte...
Temperature Dependent Molecular Dynamic Simulation of Friction
Dias, R A; Coura, P Z; Costa, B V
2006-01-01
In this work we present a molecular dynamics simulation of a FFM experiment. The tip-sample interaction is studied by varying the normal force in the tip and the temperature of the surface. The friction force, cA, at zero load and the friction coefficient, $\\mu$, were obtained. Our results strongly support the idea that the effective contact area, A, decreases with increasing temperature and the friction coefficient presents a clear signature of the premelting process of the surface.
Simulating granular flow with molecular dynamics
Ristow, Gerald
1992-01-01
We investigate by means of Molecular Dynamics simulations an assembly of spheres to model a granular medium flowing from an upper rectangular chamber through a hole into a lower chamber. Two different two dimensional models are discussed one of them including rotations of the individual spheres. The outflow properties are investigated and compared to experimental data. The qualitative agreement suggests that our models contain the necessary ingredients to describe the outflow properties of gr...
Molecular dynamics simulations using graphics processing units
Baker, J.A.; Hirst, J.D.
2011-01-01
It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation com...
Molecular Dynamics Studies of Nanofluidic Devices
DEFF Research Database (Denmark)
Zambrano Rodriguez, Harvey Alexander
of transport mechanism to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe...... the molecular dynamics methodology. In the second part of this thesis, we present the results of three different research projects. Fristly, we present a computational study of thermophoresis as a suitable mechanism to drive water droplets confined in different types of carbon nanotubes. We observe a...... motion of the water droplet in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The...
Optimally designed fields for controlling molecular dynamics
Rabitz, Herschel
1991-10-01
This research concerns the development of molecular control theory techniques for designing optical fields capable of manipulating molecular dynamic phenomena. Although is has been long recognized that lasers should be capable of manipulating dynamic events, many frustrating years of intuitively driven laboratory studies only serve to illustrate the point that the task is complex and defies intuition. The principal new component in the present research is the recognition that this problem falls into the category of control theory and its inherent complexities require the use of modern control theory tools largely developed in the engineering disciplines. Thus, the research has initiated a transfer of the control theory concepts to the molecular scale. Although much contained effort will be needed to fully develop these concepts, the research in this grant set forth the basic components of the theory and carried out illustrative studies involving the design of optical fields capable of controlling rotational, vibrational and electronic degrees of freedom. Optimal control within the quantum mechanical molecular realm represents a frontier area with many possible ultimate applications. At this stage, the theoretical tools need to be joined with merging laboratory optical pulse shaping capabilities to illustrate the power of the concepts.
Control Volume Representation of Molecular Dynamics
Smith, E R; Dini, D; Zaki, T A
2012-01-01
A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of [1] 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 \\vartheta_{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 (VA, [2] Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, [3] Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges natu...
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Directory of Open Access Journals (Sweden)
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
The Specific Bias in Dynamic Monte Carlo Simulations of Nuclear Reactor
Yamamoto, Toshihisa; Endo, Hiroshi; Ishizu, Tomoko; Tatewaki, Isao
2014-06-01
During the development of Monte-Carlo-based dynamic code system, we have encountered two major Monte-Carlo-specific problems. One is the break down due to "false super-criticality" which is caused by an accidentally large eigenvalue due to statistical error in spite of the fact that the reactor is actually not. The other problem, which is the main topic in this paper, is that the statistical error in power level using the reactivity calculated with Monte Carlo code is not symmetric about its mean but always positively biased. This signifies that the bias is accumulated as the calculation proceeds and consequently results in over-estimation of the final power level. It should be noted that the bias will not eliminated by refining time step as long as the variance is not zero. A preliminary investigation on this matter using the one-group-precursor point kinetic equations was made and it was concluded that the bias in power level is approximately proportional to the product of variance in Monte Carlo calculation and elapsed time. This conclusion was verified with some numerical experiments. This outcome is important in quantifying the required precision of the Monte-Carlo-based reactivity calculations.
A Concurrent Multiscale Micromorphic Molecular Dynamics. Part I. Theoretical Formulation
Li, Shaofan
2014-01-01
Based on a novel concept of multiplicative multiscale decomposition, we have derived a multiscale micromorphic molecular dynamics (MMMD)to extent the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and macroscale. The multiscale micromorphic molecular dynamics is a con-current three-scale particle dynamics that couples a fine scale molecular dynamics, a mesoscale particle dynamics of micromorphic medium, and a coarse scale nonlocal particle dynamics of nonlinear continuum. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and it is a special case of the proposed multiscale micromorphic molecular dynamics. The discovered mutiscale structure and the corresponding multiscale dynamics reveal a seamless transition channel from atomistic scale to continuum scale and the intrinsic coupling relation among them, and it can be used to solve finite size nanoscale sc...
Molecular Dynamics Studies of Initiation in Energetic Materials
Haskins, P.
1995-01-01
In this paper an overview of Molecular Dynamics simulations of chemically reacting systems is described. In particular, molecular dynamics simulations of shock initiation in a model energetic material are reported. The use of Molecular Dynamics to model thermal initiation and determine reactions rates in energetic materials is also discussed. Finally, the future potential of MD techniques for energetic materials applications is considered.
Dynamical structure of fluid mercury: Molecular-dynamics simulations
Hoshino, Kozo; Tanaka, Shunichiro; Shimojo, Fuyuki
2007-01-01
We have carried out molecular-dynamics simulations for nonmetallic fluid mercury in liquid and vapor phases using a Lennard-Jones type effective potential and shown that the structure factors S(Q) and the dynamic structure factors S(Q, omega) of nonmetallic fluid mercury obtained by our MD simulations are in good agreement with recent X-ray diffraction and inelastic X-ray scattering experiments. We conclude from these results that, though the fluid mercury which shows a metal-nonmetal transit...
Application of optimal prediction to molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
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 {delta}-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.
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
WANG; Hui(
2001-01-01
［1］Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.［2］Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.［3］Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.［4］Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.［5］Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.［6］Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.［7］Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.［8］Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.［9］Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.［10］Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.［11］Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.［12］Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.［13］Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.
De-Biasing the Dynamic Mode Decomposition for Applied Koopman Spectral Analysis
Hemati, Maziar S
2015-01-01
The Dynamic Mode Decomposition (DMD)---a popular method for performing Koopman spectral analysis in numerous application areas---processes snapshot measurements sampled from a time-evolving system to extract dynamically meaningful spatio-temporal descriptions of the underlying process. Often times, DMD descriptions can be used for predictive purposes as well, which enables informed decision-making based on DMD model-forecasts. Despite its widespread use and utility, DMD regularly fails to yield accurate dynamical descriptions when the measured snapshot data are even slightly imprecise due to, e.g., sensor noise. Here, we express DMD as a two-stage algorithm in order to isolate a source of systematic error. We show that DMD's first stage, a subspace projection step, systematically introduces bias errors by processing snapshots asymmetrically. In order to remove this systematic error, we propose utilizing an augmented snapshot matrix in a subspace projection step, as in problems of total least-squares, in order...
Molecular dynamic results on transport properties
Energy Technology Data Exchange (ETDEWEB)
Alder, B.J.; Alley, W.E.
1978-06-01
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so.
Molecular dynamic results on transport properties
International Nuclear Information System (INIS)
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so
Electronic continuum model for molecular dynamics simulations.
Leontyev, I V; Stuchebrukhov, A A
2009-02-28
A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627
Molecular dynamics studies of aromatic hydrocarbon liquids
International Nuclear Information System (INIS)
This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules
Continuous Finite Element Methods of Molecular Dynamics Simulations
Qiong Tang; Luohua Liu; Yujun Zheng
2015-01-01
Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite elemen...
Parallelization of quantum molecular dynamics simulation code
International Nuclear Information System (INIS)
A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)
Ab Initio Molecular Dynamics: A Virtual Laboratory
Hobbi Mobarhan, Milad
2014-01-01
In this thesis, we perform ab initio molecular dynamics (MD) simulations at the Hartree-Fock level, where the forces are computed on-the-fly using the Born-Oppenheimer approximation. The theory behind the Hartree-Fock method is discussed in detail and an implementation of this method based on Gaussian basis functions is explained. We also demonstrate how to calculate the analytic energy derivatives needed for obtaining the forces acting on the nuclei. Hartree-Fock calculations on the ground s...
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
Electrostatic Energy Calculations for Molecular Dynamics
Love, M J; Comment, Henri J.F. Jansen; Love, Michael J.
1995-01-01
The evaluation of Coulomb forces is a difficult task. The summations that are involved converge only conditionally and care has to be taken in selecting the appropriate procedure to define the limits. The Ewald method is a standard method for obtaining Coulomb forces, but this method is rather slow, since it depends on the square of the number of atoms in a unit cell. In this paper we have adapted the plane-wise summation method for the evaluation of Coulomb forces. The use of this method allows for larger computational cells in molecular dynamics calculations.
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
Molecular dynamics at constant temperature and pressure
Toxvaerd, S.
1993-01-01
Algorithms for molecular dynamics (MD) at constant temperature and pressure are investigated. The ability to remain in a regular orbit in an intermittent chaotic regime is used as a criterion for long-time stability. A simple time-centered algorithm (leap frog) is found to be the most stable of the commonly used algorithms in MD. A model of N one-dimensional dimers with a double-well intermolecular potential, for which the distribution functions at constant temperature T and pressure P can be calculated, is used to investigate MD-NPT dynamics. A time-centered NPT algorithm is found to sample correctly and to be very robust with respect to volume scaling.
Fermionic Molecular Dynamics and short range correlations
Feldmeier, H; Roth, R S; Schnack, J
1998-01-01
Fermionic Molecular Dynamics (FMD) models a system of fermions by means of many-body states which are composed of antisymmetrized products of single-particle states. These consist of one or several Gaussians localized in coordinate and momentum space. The parameters specifying them are the dynamical variables of the model. As the repulsive core of the nucleon-nucleon interaction induces short range correlations which cannot be accommodated by a Slater determinant, a novel approach, the unitary correlation operator method (UCOM), is applied. The unitary correlator moves two particles away from each other whenever their relative distance is within the repulsive core. The time-dependent variational principle yields the equations of motion for the variables. Energies of the stationary ground states are calculated and compared to exact many-body results for nuclei up to Ca 48. Time-dependent solutions are shown for collisions between nuclei.
Combining optimal control theory and molecular dynamics for protein folding.
Directory of Open Access Journals (Sweden)
Yaman Arkun
Full Text Available A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD. In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.
Rudzinski, Joseph F.; Kremer, Kurt; Bereau, Tristan
2016-02-01
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and reference (e.g., from experiments or higher-level simulations) observables. To bound the microscopic information generated by computer simulations within reference measurements, we propose a method that reweights the microscopic transitions of the system to improve consistency with a set of coarse kinetic observables. The method employs the well-developed Markov state modeling framework to efficiently link microscopic dynamics with long-time scale constraints, thereby consistently addressing a wide range of time scales. To emphasize the robustness of the method, we consider two distinct coarse-grained models with significant kinetic inconsistencies. When applied to the simulated conformational dynamics of small peptides, the reweighting procedure systematically improves the time scale separation of the slowest processes. Additionally, constraining the forward and backward rates between metastable states leads to slight improvement of their relative stabilities and, thus, refined equilibrium properties of the resulting model. Finally, we find that difficulties in simultaneously describing both the simulated data and the provided constraints can help identify specific limitations of the underlying simulation approach.
Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity
Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.
2012-01-01
Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of
Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations
Byutner, Oleksiy; Smith, Grant
2001-03-01
In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.
Multiple branched adaptive steered molecular dynamics
Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
2014-08-01
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient "multiple branching" (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.
Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations
Alkis, S.; Krause, J. L.; Fry, J. N.; Cheng, H.-P.
2009-03-01
We study the diffusion of silver nanoparticles on self-assembled monolayers (SAMs). Silver clusters Agn of sizes n=55 , 147, and 1289 were evolved in contact with an alkanethiol (12 carbon, dodecanethiol) SAM deposited on a gold (111) surface. Analysis based on classical molecular dynamics simulations reveals that these systems exhibit a rich variety of behaviors, from superdiffusive for the lightest cluster to pinned for the heaviest, evolution self-similar in lengths and times for the lightest cluster but with characteristic time scales and directional anisotropies emerging for the heavier clusters.
Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow
Archereau, Aurelien Y M; Willmott, Geoff R
2016-01-01
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
A dynamic-biased dual-loop-feedback CMOS LDO regulator with fast transient response
Han, Wang; Maomao, Sun
2014-04-01
This paper presents a low-dropout regulator (LDO) for portable applications with dual-loop feedback and a dynamic bias circuit. The dual-loop feedback structure is adopted to reduce the output voltage spike and the response time of the LDO. The dynamic bias circuit enhances the slew rate at the gate of the power transistor. In addition, an adaptive miller compensation technique is employed, from which a single pole system is realized and over a 59° phase margin is achieved under the full range of the load current. The proposed LDO has been implemented in a 0.6-μm CMOS process. From the experimental results, the regulator can operate with a minimum dropout voltage of 200 mV at a maximum 300 mA load and IQ of 113 μA. The line regulation and load regulation are improved to 0.1 mV/V and 3.4 μV/mA due to the sufficient loop gain provided by the dual feedback loops. Under a full range load current step, the voltage spikes and the recovery time of the proposed LDO is reduced to 97 mV and 0.142 μs respectively.
The 2011 Dynamics of Molecular Collisions Conference
Energy Technology Data Exchange (ETDEWEB)
Nesbitt, David J. [JILA, NIST
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
A scheme to combine molecular dynamics and dislocation dynamics
International Nuclear Information System (INIS)
Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake. (paper)
Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.
2009-01-01
Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and mu...
Color Molecular-Dynamics for High Density Matter
Maruyama, Toshiki; Hatsuda, Tetsuo
1999-01-01
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Statistical feature and the dynamical change between confinement and deconfinement phases are studied with this molecular dynamics simulation.
Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS
Astuti, A. D.; Mutiara, A. B.
2009-01-01
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example of molecular dynamics application developed by Groningen University. This application is a non-commercial and able to work in the operating system Linux. The main ability of Gromacs is to perform molecular dynamics simulation and minimization energy. In this...
Development of semiclassical molecular dynamics simulation method.
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
DMS: A Package for Multiscale Molecular Dynamics
Somogyi, Endre; Ortoleva, Peter J
2013-01-01
Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables...
Molecular dynamics simulations of shock compressed graphite
International Nuclear Information System (INIS)
We present molecular dynamic simulations of the shock compression of graphite with the LCBOPII potential. The range of shock intensities covers the full range of available experimental data, including near-tera-pascal pressures. The results are in excellent agreement with the available DFT data and point to a graphite-diamond transition for shock pressures above 65 GPa, a value larger than the experimental data (20 to 50 GPa). The transition mechanism leads preferentially to hexagonal diamond through a diffusion-less process but is submitted to irreversible re-graphitization upon release: this result is in good agreement with the lack of highly ordered diamond observed in post-mortem experimental samples. Melting is found for shock pressures ranging from 200 to 300 GPa, close to the approximate LCBOPII diamond melting line. A good overall agreement is found between the calculated and experimental Hugoniot data up to 46% compression rate. (authors)
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
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
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
Molecular dynamics simulation of laser shock phenomena
Energy Technology Data Exchange (ETDEWEB)
Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).
2001-10-01
Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)
Statistical mechanics and dynamics of molecular fragmentation
Energy Technology Data Exchange (ETDEWEB)
Quack, M. (Goettingen Univ. (Germany, F.R.). Inst. fuer Physikalische Chemie)
1981-05-11
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored.
Statistical mechanics and dynamics of molecular fragmentation
International Nuclear Information System (INIS)
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored. (author)
Cell list algorithms for nonequilibrium molecular dynamics
Dobson, Matthew; Fox, Ian; Saracino, Alexandra
2016-06-01
We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.
Superdeformed $\\Lambda$ hypernuclei with antisymmetrized molecular dynamics
Isaka, Masahiro; Kimura, Masaaki; Hiyama, Emiko; Sagawa, Hiroyuki; Yamamoto, Yasuo
2014-01-01
The response to the addition of a $\\Lambda$ hyperon is investigated for the deformed states such as superdeformation in $^{41}_\\Lambda$Ca, $^{46}_\\Lambda $Sc and $^{48}_\\Lambda$Sc. In the present study, we use the antisymmetrized molecular dynamics (AMD) model. It is pointed out that many kinds of deformed bands appear in $^{45}$Sc and $^{47}$Sc. Especially, it is found that there exists superdeformed states in $^{45}$Sc. By the addition of a $\\Lambda$ particle to $^{40}$Ca, $^{45}$Sc and $^{47}$Sc, it is predicted, for the first time, that the superdeformed states exist in the hypernuclei $^{41}_\\Lambda$Ca and $^{46}_\\Lambda$Sc. The manifestation of the dependence of the $\\Lambda$-separation energy on nuclear deformation such as spherical, normal deformation and superdeformation is shown in the energy spectra of $^{41}_\\Lambda$Ca, $^{46}_\\Lambda $Sc and $^{48}_\\Lambda$Sc hypernuclei.
Molecular Dynamics Simulations for Predicting Surface Wetting
Directory of Open Access Journals (Sweden)
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Nonequilibrium molecular dynamics: The first 25 years
International Nuclear Information System (INIS)
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
Dynamics of dewetting at the nanoscale using molecular dynamics.
Bertrand, E; Blake, T D; Ledauphin, V; Ogonowski, G; Coninck, J De; Fornasiero, D; Ralston, J
2007-03-27
Large-scale molecular dynamics simulations are used to model the dewetting of solid surfaces by partially wetting thin liquid films. Two levels of solid-liquid interaction are considered that give rise to large equilibrium contact angles. The initial length and thickness of the films are varied over a wide range at the nanoscale. Spontaneous dewetting is initiated by removing a band of molecules either from each end of the film or from its center. As observed experimentally and in previous simulations, the films recede at an initially constant speed, creating a growing rim of liquid with a constant receding dynamic contact angle. Consistent with the current understanding of wetting dynamics, film recession is faster on the more poorly wetted surface to an extent that cannot be explained solely by the increase in the surface tension driving force. In addition, the rates of recession of the thinnest films are found to increase with decreasing film thickness. These new results imply not only that the mobility of the liquid molecules adjacent to the solid increases with decreasing solid-liquid interactions, but also that the mobility adjacent to the free surface of the film is higher than in the bulk, so that the effective viscosity of the film decreases with thickness. PMID:17328565
Continuous Finite Element Methods of Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Qiong Tang
2015-01-01
Full Text Available Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite element method is also a reliable method to simulate long-time classical trajectory of molecular systems.
Molecular Dynamic Simulation of Failure of Ettringite
International Nuclear Information System (INIS)
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
Molecular Dynamic Simulation of Failure of Ettringite
Sun, W.; Wang, D.; Wang, L.
2013-03-01
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Directory of Open Access Journals (Sweden)
Ryo Kanada
Full Text Available Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."
Molecular dynamics studies on nanoscale gas transport
Barisik, Murat
Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the
Junghans, Christoph; Perez, Danny; Vogel, Thomas
2014-01-01
We show direct formal relationship between the Wang-Landau iteration [PRL 86, 2050 (2001)], metadynamics [PNAS 99, 12562 (2002)] and statistical temperature molecular dynamics [PRL 97, 050601 (2006)], the major Monte Carlo and molecular dynamics work-horses for sampling from a generalized, multicanonical ensemble. We demonstrate that statistical temperature molecular dynamics (which is formally derived from the Wang-Landau method), augmented by the introduction of kernel updates of the statis...
Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules
International Nuclear Information System (INIS)
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wave packet calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics
Coarsening dynamics in condensing zero-range processes and size-biased birth death chains
International Nuclear Information System (INIS)
Zero-range processes with decreasing jump rates are well known to exhibit a condensation transition under certain conditions on the jump rates, and the dynamics of this transition continues to be a subject of current research interest. Starting from homogeneous initial conditions, the time evolution of the condensed phase exhibits an interesting coarsening phenomenon of mass transport between cluster sites characterized by a power law. We revisit the approach in Godrèche (2003 J. Phys. A: Math. Gen. 36 6313) to derive effective single site dynamics which form a nonlinear birth death chain describing the coarsening behavior. We extend these results to a larger class of parameter values, and introduce a size-biased version of the single site process, which provides an effective tool to analyze the dynamics of the condensed phase without finite size effects and is the main novelty of this paper. Our results are based on a few heuristic assumptions and exact computations, and are corroborated by detailed simulation data. (paper)
Coarsening dynamics in condensing zero-range processes and size-biased birth death chains
Jatuviriyapornchai, Watthanan; Grosskinsky, Stefan
2016-05-01
Zero-range processes with decreasing jump rates are well known to exhibit a condensation transition under certain conditions on the jump rates, and the dynamics of this transition continues to be a subject of current research interest. Starting from homogeneous initial conditions, the time evolution of the condensed phase exhibits an interesting coarsening phenomenon of mass transport between cluster sites characterized by a power law. We revisit the approach in Godrèche (2003 J. Phys. A: Math. Gen. 36 6313) to derive effective single site dynamics which form a nonlinear birth death chain describing the coarsening behavior. We extend these results to a larger class of parameter values, and introduce a size-biased version of the single site process, which provides an effective tool to analyze the dynamics of the condensed phase without finite size effects and is the main novelty of this paper. Our results are based on a few heuristic assumptions and exact computations, and are corroborated by detailed simulation data.
Thermostat artifacts in replica exchange molecular dynamics simulations.
Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard
2009-01-01
We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980
Lokshin, B
2008-01-01
This paper extends the LSDV bias-corrected estimator in [Bun, M., Carree, M.A. 2005. Bias-corrected estimation in dynamic panel data models, Journal of Business and Economic Statistics, 23(2): 200-10] to unbalanced panels and discusses the analytic method of obtaining the solution. Using a Monte Carlo approach the paper compares the performance of this estimator with three other available techniques for dynamic panel data models. Simulation reveals that LSDV-bc estimator is a good choice exce...
Molecular Dynamics Investigated by Neutron Scattering
International Nuclear Information System (INIS)
A short review of the present state of the problem of applicability of the Krieger-Nelkin theory as well as of the Griffing theory to gases is made. Then, on the basis of experiments with liquid methane, the applicability of the mass-tensor concept to molecules in condensed states is criticized. Strong arguments against the application of the Krieger-Nelkin theory to condensed states are: a shift of neutron energy distribution after scattering towards higher energies and the lack of dependence of the Inelastic part on the scattering angle. Further sections deal with the rotational dynamics of ammonium groups in ammonium compounds. Most of the experimental material is discussed in connection with ammonium halides on the basis of experiments by different authors. For some substances a freedom of rotation of NH4 groups was obtained from neutron measurements, whereas for some others the rotation goes over into torsional vibration. In this case, frequencies of torsional vibrations obtained by various authors from neutron experiments were compared with those obtained from infrared spectroscopy and specific heat measurements. The barrier-to-rotation evaluation from total neutron cross-section measurements is also discussed. Further a comparison is made of the rotational dynamics of NH4 groups in NH4CIO4 and H3O groups in H3OCIO4 on the basis of neutron inelastic scattering experiments. A free rotation of the NH4 group in ammonium perchlorate was obtained even at temperatures as low as liquid nitrogen temperature. For H3OCIO4 a torsional vibration of the H3O group with a frequency of 497 cm-1 was obtained. So in spite of the identity of the crystal lattices of NH4CIO4 and H3OCIO4 the dynamics of the NH4 and H3O groups are different. The results are compared with those known from Raman spectroscopy and nuclear magnetic resonance. Finally, a number of other substances is discussed from the point of view of molecular dynamics. (author)
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
International Nuclear Information System (INIS)
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
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
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
Nanoscale deicing by molecular dynamics simulation
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
How Dynamic Visualization Technology Can Support Molecular Reasoning
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…
DEFF Research Database (Denmark)
Thorson, James T.; Kristensen, Kasper
2016-01-01
Statistical models play an important role in fisheries science when reconciling ecological theory with available data for wild populations or experimental studies. Ecological models increasingly include both fixed and random effects, and are often estimated using maximum likelihood techniques...... is calculated as a nonlinear function of random effects. We therefore describe and evaluate a new "epsilon" estimator as a generic bias-correction estimator for derived quantities. We use simulated data to compare the epsilon-method with an existing bias-correction algorithm for estimating...... recruitment in four configurations of an age-structured population dynamics model. This simulation experiment shows that the epsilon-method and the existing bias-correction method perform equally well in data-rich contexts, but the epsilon-method is slightly less biased in data-poor contexts. We then apply...
Imaging the Breakdown of Molecular Frame Dynamics through Rotational Uncoupling
Zipp, Lucas J; Bucksbaum, Philip H
2016-01-01
We have observed directly in the time domain the uncoupling of electron motion from the molecular frame due to rotational-electronic coupling in a molecular Rydberg system. In contrast to Born- Oppenheimer dynamics, in which the electron is firmly fixed to the molecular frame, there exists a regime of molecular dynamics known as $l$-uncoupling where the motion of a non-penetrating Rydberg electron decouples from the instantaneous alignment of the molecular frame. We have imaged this unusual regime in time-dependent photoelectron angular distributions of a coherently prepared electron wave packet in the 4$f$ manifold of $N_2$.
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
International Nuclear Information System (INIS)
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed. (c) 1999 American Institute of Physics
A molecular dynamics simulation code ISIS
International Nuclear Information System (INIS)
Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)
Quantum molecular dynamics simulations of dense matter
Energy Technology Data Exchange (ETDEWEB)
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Biases in the determination of dynamical parameters of star clusters: today and in the Gaia era
Sollima, A; Zocchi, A; Balbinot, E; Gieles, M; Henault-Brunet, V; Varri, A L
2015-01-01
The structural and dynamical properties of star clusters are generally derived by means of the comparison between steady-state analytic models and the available observables. With the aim of studying the biases of this approach, we fitted different analytic models to simulated observations obtained from a suite of direct N-body simulations of star clusters in different stages of their evolution and under different levels of tidal stress to derive mass, mass function and degree of anisotropy. We find that masses can be under/over-estimated up to 50% depending on the degree of relaxation reached by the cluster, the available range of observed masses and distances of radial velocity measures from the cluster center and the strength of the tidal field. The mass function slope appears to be better constrainable and less sensitive to model inadequacies unless strongly dynamically evolved clusters and a non-optimal location of the measured luminosity function are considered. The degree and the characteristics of the ...
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
International Nuclear Information System (INIS)
Research highlights: → Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. → Half height widths are used in modeling of Lorentzian doublets. → 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.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Energy Technology Data Exchange (ETDEWEB)
Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy)
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Liu, H.W.; Le, Y.; Nishitani, Ryusuke; Aso, Y; Iwasaki, H.
2007-01-01
We investigated scanning tunneling microscope (STM)-excited luminescence from porphyrin (PhTPP and H2TPP) thin films on metal substrate (Au and Ag) under ambient conditions. Molecular fluorescence similar to the corresponding photoluminescence was observed from PhTPP/Au and H2TPP/Ag at both STM bias polarities. We found that at the same experimental condition and parameters, the STM-induced luminescence intensities of maxima peak are similar for PhTPP and H2TPP but weaker by a factor of about...
Modeling shockwave deformation via molecular dynamics
International Nuclear Information System (INIS)
Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too
Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics
Lin, Lin; Shao, Sihong
2013-01-01
We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition as well as the accuracy of TRBOMD for computing physical properties such as the phonon frequency obtained from the molecular dynamic simulation. We connect and compare TRBOMD with the Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one dimensional model for Kohn-Sham density functional theory.
Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics
Directory of Open Access Journals (Sweden)
Lin Lin
2013-12-01
Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.
International Nuclear Information System (INIS)
This paper presents the design and experimental validation of dc-dynamic biasing for > 50× switching time improvement in severely underdamped fringing-field electrostatic MEMS actuators. The electrostatic fringing-field actuator is used to demonstrate the concept due to its robust device design and inherently low damping conditions. In order to accurately quantify the gap height versus voltage characteristics, a heuristic model is developed. The difference between the heuristic model and numerical simulation is less than 5.6% for typical MEMS geometries. MEMS fixed–fixed beams are fabricated and measured for experimental validation. Good agreement is observed between the calculated and measured results. For a given voltage, the measured and calculated displacements are typically within 10%. Lastly, the derived model is used to design a dc-dynamic bias waveform to improve the switching time of the underdamped MEMS actuators. With dynamic biasing, the measured up-to-down and down-to-up switching time of the actuator is ∼35 μs. On the other hand, coventional step biasing results in a switching time of ∼2 ms for both up-to-down and down-to-up states. (paper)
International Nuclear Information System (INIS)
Graphical abstract: - Highlights: • Self-assembled monolayers (SAMs) of 18-pentatriacontanone (as ketone) and stearyl stearate (as ester) were formed on a graphite surface at the liquid–solid interface. • Orientations of the molecules in SAMs on the substrate were studied by scanning tunneling microscopy. • A perpendicular carbon skeleton-plane orientation with the CO pointing up on the surface is favorable for a substrate with negative charge and vice versa. - Abstract: Molecular orientations of self-assembled 18-pentatriacontanone (as ketone) and stearyl stearate (as ester) monolayers adsorbed on a graphite surface were studied by scanning tunneling microscopy (STM) at the liquid–solid interface. At a positive sample bias, the central areas of the dialkyl ketone and fatty acid alkyl ester molecules in the STM images appeared as two bright regions on both sides of a dim spot and a bright region on one side of a dim spot, whereas at a negative sample bias, the areas appeared dim. This contrast variation indicates that a perpendicular carbon skeleton-plane orientation with the CO pointing down on the surface is favorable for a substrate with positive charge and vice versa because of the greater electronegativity of the oxygen atom. Upon the bias voltage reversal, the delay time for the STM image contrast change in the region was observed on a time scale of minutes. The difference between the delay time lengths for the direction of bias polarity change indicates that the perpendicular configuration with CO pointing up is more stable than that with CO pointing down. These results indicate that the use of an electric field along a direction vertical to the monolayer on the substrate provides control over the orientations of the molecules between two stable states at the liquid–solid interface
Visualization and orchestration of the dynamic molecular society in cells
Institute of Scientific and Technical Information of China (English)
Xuebiao Yao; Guowei Fang
2009-01-01
@@ Visualization of specific molecules and their interactions in real space and time is essential to delineate how cellular plasticity and dynamics are achieved and orchestrated as perturbation of cellular plasticity and dynamics is detrimental to health. Elucidation of cellular dynamics requires molecular imaging at nanometer scale at millisecond resolution. The 1st International Conference on Cellular Dynamics and Chemical Biology held in Hefei, China (from 12 September to 15 September,2008) launched the quest by bringing synergism among photonics, chemistry and biology.
Open-boundary Ehrenfest molecular dynamics: towards a model of current induced heating in nanowires
International Nuclear Information System (INIS)
We present a time-dependent method based on the single-particle electron density matrix that allows the electronic and ionic degrees of freedom to be modelled within the Ehrenfest approximation in the presence of open boundaries. We describe a practical implementation using tight binding, and use it to investigate steady-state conduction through a single-atom device and to perform molecular dynamics. We find that in the Ehrenfest approximation an electric current allows both ionic heating and cooling to take place, depending on the bias. (letter to the editor)
Molecular dynamics simulations of an apoliprotein A I derived peptide in explicit water
Stavrakoudis, Athanassios
2008-08-01
Molecular dynamics simulations have been performed for the 104-117 α-helical fragment of apoliprotein A-I using the CHARMM22 force field and the N AMD simulation engine. Simulation (50 ns in explicit water) resulted in significant appearance of π-helix conformation, which was totally diminished when the CMAP correction of the CHARMM force field was applied. This is consistent with other similar studies which suggest that the observation of π-helix in peptide conformation was force field biased rather actually existed. This study suggests that the 104-117 fragment of apoliprotein A-I has a stable α-helical conformation in water.
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to
Modelling of Spectroscopic and Structural Properties using Molecular Dynamics
Francesco Muniz Miranda
2013-01-01
The following dissertation is about the study that I performed at the Chemistry Department of the University of Florence and at the European Laboratory for Non- Linear Spectroscopy (LENS) to recover and elucidate structural, dynamical, and spectroscopic molecular features adopting computer simulations. In particular, here ab initio molecular dynamics simulations and time-frequency analysis are the most employed “tools”, in order to have a better understanding of the origins ...
Multi CPU clusters and calculations by molecular dynamics method
International Nuclear Information System (INIS)
The technical characteristics of multi CPU (Central Processor Unit) clusters in Institute of Ion-Plasma and Laser Technologies AS RUz and Institute of Mathematics and Information Technologies AS RUz are described. There is detail information about cluster s architecture, installed programs and their productivity for decision of molecular dynamics tasks. Molecular dynamics program packages GROMACS, OPENMX and AutoDock-4.2.3 are described. The results of calculations using these program packages are presented. (author)
Applications of Molecular Dynamics in Atmospheric and Solution Chemistry
Li, Xin
2011-01-01
This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial ch...
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding
Yaman Arkun; Mert Gur
2012-01-01
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding Yaman Arkun1*, Mert Gur2¤ 1 Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey, 2 Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey Abstract A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamic...
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.
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
Rampersad, Sephra N; Hosein, Fazeeda N; Carrington, Christine Vf
2014-01-01
The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than for the ITS and TUB2 markers. A discernible bimodal gap in the genetic distance frequency histograms was produced for the ACT and GAPDH markers which indicated successful separation of intra- and inter-specific sequences in the data set. Overall, analyses indicated clear differences in the ability of these markers to phylogenetically separate individuals to the intra-specific level which coincided with information bias. PMID:25392785
Dynamical analysis of highly excited molecular spectra
Energy Technology Data Exchange (ETDEWEB)
Kellman, M.E. [Univ. of Oregon, Eugene (United States)
1993-12-01
The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.
Current-driven dynamics in molecular-scale devices
International Nuclear Information System (INIS)
We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)
A fermionic molecular dynamics technique to model nuclear matter
International Nuclear Information System (INIS)
Full text: At sub-nuclear densities of about 1014 g/cm3, nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)
Unified rotational dynamics of molecular crystals with orientational phase transition
Michel, K.H.; Raedt, H. De
1976-01-01
A unified theory for the rotational dynamics of molecular crystals with orientational phase transitions is given. As basic secular variables one takes symmetry adapted functions, which describe the molecular orientations, and the angular momenta of the molecules. Using Mori’s projection operator tec
Elucidation of molecular dynamics of invasive species of rice
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...
Shapiro like steps reveals molecular nanomagnets' spin dynamics
Babak Abdollahipour; Jahanfar Abouie; Navid Ebrahimi
2015-01-01
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 junct...
Tunable Interfacial Thermal Conductance by Molecular Dynamics
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
Molecular Dynamics Simulations of Protein Dynamics and their relevance to drug discovery
Salsbury, Freddie R.
2010-01-01
Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery.
Energy conservation in molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren; Heilmann, Ole; Dyre, J. C.
2012-01-01
Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...
The Computer Simulation of Liquids by Molecular Dynamics.
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)
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
Energy Technology Data Exchange (ETDEWEB)
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.
Order parameter prediction from molecular dynamics simulations in proteins
Perilla, Juan R
2011-01-01
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter -- a reduced descriptor for the major subset of degrees of freedom -- that can be used to aid sampling for the large conformational change. We present a novel way to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that ma...
Molecular Dynamics Simulation of Amyloid Beta Dimer Formation
Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V
2004-01-01
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...
Interfacial Molecular Searching Using Forager Dynamics
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.
Molecular dynamics with deterministic and stochastic numerical methods
Leimkuhler, Ben
2015-01-01
This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...
Energy Technology Data Exchange (ETDEWEB)
Cheng, Jue-Fei [College of Physics, Optoelectronics and Energy and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215006 (China); School of Electronics and Information Engineering, Suzhou Vocational University, Suzhou 215104 (China); Zhou, Liping, E-mail: zhoulp@suda.edu.cn, E-mail: leigao@suda.edu.cn; Liu, Man; Yan, Qiang; Han, Qin; Gao, Lei, E-mail: zhoulp@suda.edu.cn, E-mail: leigao@suda.edu.cn [College of Physics, Optoelectronics and Energy and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215006 (China)
2014-11-07
The electronic transport properties of benzene–porphyrin–benzene (BPB) molecules coupled to gold (Au) electrodes were investigated. By successively removing the front-end Au atoms, several BPB junctions with different molecule-electrode contact symmetries were constructed. The calculated current–voltage (I–V) curves depended strongly on the contact configurations between the BPB molecules and the Au electrodes. In particular, a significant low-voltage negative differential resistance effect appeared at −0.3 V in the junctions with pyramidal electrodes on both sides. Along with the breaking of this tip-contact symmetry, the low-bias negative differential resistance effect gradually disappeared. This tip-contact may be ideal for use in the design of future molecular devices because of its similarity with experimental processes.
International Nuclear Information System (INIS)
The electronic transport properties of benzene–porphyrin–benzene (BPB) molecules coupled to gold (Au) electrodes were investigated. By successively removing the front-end Au atoms, several BPB junctions with different molecule-electrode contact symmetries were constructed. The calculated current–voltage (I–V) curves depended strongly on the contact configurations between the BPB molecules and the Au electrodes. In particular, a significant low-voltage negative differential resistance effect appeared at −0.3 V in the junctions with pyramidal electrodes on both sides. Along with the breaking of this tip-contact symmetry, the low-bias negative differential resistance effect gradually disappeared. This tip-contact may be ideal for use in the design of future molecular devices because of its similarity with experimental processes
Dynamics Studies on Molecular Diffusion in Zeolites
Institute of Scientific and Technical Information of China (English)
王秋霞; 樊建芬; 肖鹤鸣
2003-01-01
A review about the applications of molecular dynamics（MD）simulation in zeolites is presented. MD simulation has been proved to be a useful tool due to its applications in this field for the recent two decades. The fundamental theory of MD is introduced and the hydrocarbon diffusion in zeolites is mainly focused on in this paper.
Pleutin, S; Ingold, G L; Nitzan, A; Pleutin, St\\'ephane; Grabert, Hermann; Ingold, Gert-Ludwig; Nitzan, Abraham
2003-01-01
We study the electrostatic potential of a molecular wire bridging two metallic electrodes in the limit of weak contacts. With the use of a tight-binding model including a fully three-dimensional treatment of the electrostatics of the molecular junction, the potential is shown to be poorly screened, dropping mostly along the entire molecule. In addition, we observe pronounced Friedel oscillations that can be related to the breaking of electron-hole symmetry. Our results are in semi-quantitative agreement with recent state-of-the-art ab initio calculations and point to the need of a three-dimensional treatment to properly capture the behavior of the electrostatic potential. Based on these results, current-voltage curves are calculated within the Landauer formalism. It is shown that Coulomb interaction partially compensates the localization of the charges induced by the electric field and consequently tends to suppress zones of negative differential resistance.
Directory of Open Access Journals (Sweden)
G. Mao
2015-04-01
Full Text Available Dynamically downscaled precipitation fields from regional climate models (RCMs often cannot be used directly for regional climate studies. Due to their inherent biases, i.e., systematic over- or underestimations compared to observations, several correction approaches have been developed. Most of the bias correction procedures such as the quantile mapping approach employ a transfer function that is based on the statistical differences between RCM output and observations. Apart from such transfer function-based statistical correction algorithms, a stochastic bias correction technique, based on the concept of Copula theory, is developed here and applied to correct precipitation fields from the Weather Research and Forecasting (WRF model. For dynamically downscaled precipitation fields we used high-resolution (7 km, daily WRF simulations for Germany driven by ERA40 reanalysis data for 1971–2000. The REGNIE (REGionalisierung der NIEderschlagshöhen data set from the German Weather Service (DWD is used as gridded observation data (1 km, daily and aggregated to 7 km for this application. The 30-year time series are split into a calibration (1971–1985 and validation (1986–2000 period of equal length. Based on the estimated dependence structure (described by the Copula function between WRF and REGNIE data and the identified respective marginal distributions in the calibration period, separately analyzed for the different seasons, conditional distribution functions are derived for each time step in the validation period. This finally allows to get additional information about the range of the statistically possible bias-corrected values. The results show that the Copula-based approach efficiently corrects most of the errors in WRF derived precipitation for all seasons. It is also found that the Copula-based correction performs better for wet bias correction than for dry bias correction. In autumn and winter, the correction introduced a small dry
Dynamic strength of molecular adhesion bonds.
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 k...
Hong, Inki; Cho, Sanghee; Michel, Christian J.; Casey, Michael E.; Schaefferkoetter, Joshua D.
2014-09-01
A new data handling method is presented for improving the image noise distribution and reducing bias when reconstructing very short frames from low count dynamic PET acquisition. The new method termed ‘Complementary Frame Reconstruction’ (CFR) involves the indirect formation of a count-limited emission image in a short frame through subtraction of two frames with longer acquisition time, where the short time frame data is excluded from the second long frame data before the reconstruction. This approach can be regarded as an alternative to the AML algorithm recently proposed by Nuyts et al, as a method to reduce the bias for the maximum likelihood expectation maximization (MLEM) reconstruction of count limited data. CFR uses long scan emission data to stabilize the reconstruction and avoids modification of algorithms such as MLEM. The subtraction between two long frame images, naturally allows negative voxel values and significantly reduces bias introduced in the final image. Simulations based on phantom and clinical data were used to evaluate the accuracy of the reconstructed images to represent the true activity distribution. Applicability to determine the arterial input function in human and small animal studies is also explored. In situations with limited count rate, e.g. pediatric applications, gated abdominal, cardiac studies, etc., or when using limited doses of short-lived isotopes such as 15O-water, the proposed method will likely be preferred over independent frame reconstruction to address bias and noise issues.
International Nuclear Information System (INIS)
A new data handling method is presented for improving the image noise distribution and reducing bias when reconstructing very short frames from low count dynamic PET acquisition. The new method termed ‘Complementary Frame Reconstruction’ (CFR) involves the indirect formation of a count-limited emission image in a short frame through subtraction of two frames with longer acquisition time, where the short time frame data is excluded from the second long frame data before the reconstruction. This approach can be regarded as an alternative to the AML algorithm recently proposed by Nuyts et al, as a method to reduce the bias for the maximum likelihood expectation maximization (MLEM) reconstruction of count limited data. CFR uses long scan emission data to stabilize the reconstruction and avoids modification of algorithms such as MLEM. The subtraction between two long frame images, naturally allows negative voxel values and significantly reduces bias introduced in the final image. Simulations based on phantom and clinical data were used to evaluate the accuracy of the reconstructed images to represent the true activity distribution. Applicability to determine the arterial input function in human and small animal studies is also explored. In situations with limited count rate, e.g. pediatric applications, gated abdominal, cardiac studies, etc., or when using limited doses of short-lived isotopes such as 15O-water, the proposed method will likely be preferred over independent frame reconstruction to address bias and noise issues. (paper)
Tunneling Dynamics Between Atomic and Molecular Bose-Einstein Condensates
Institute of Scientific and Technical Information of China (English)
CHEN Chang-Yong
2004-01-01
Tunneling dynamics of multi-atomic molecules between atomic and multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated.It is indicated that the tunneling in the two Bose-Einstein condensates depends on not only the inter-atomic-molecular nonlinear interactions and the initial number of atoms in these condensates,but also the tunneling coupling between the atomic condensate and the multi-atomic molecular condensate.It is discovered that besides oscillating tunneling current between the atomic condensate and the multi-atomic molecular condensate,the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance:a macroscopic quantum self-trapping effect.The influence of de-coherence caused by non-condensate atoms on the tunneling dynamics is studied.It is shown that de-coherence suppresses the multi-atomic molecular tunneling.Moreover,the conception of the molecular Bose-Einstein condensate,which is different from the conventional single-atomic Bose-Einstein condensate,is specially emphasized in this paper.
Passage from quantum to classical molecular dynamics in the presence of Coulomb interactions
Ambrosio, Luigi; Friesecke, Gero; Giannoulis, Jannis
2009-01-01
We present a rigorous derivation of classical molecular dynamics (MD) from quantum molecular dynamics (QMD) that applies to the standard Hamiltonians of molecular physics with Coulomb interactions. The derivation is valid away from possible electronic eigenvalue crossings.
Desjardins, T. R.; Gilmore, M.
2016-05-01
Grid biasing is utilized in a large-scale helicon plasma to modify an existing instability. It is shown both experimentally and with a linear stability analysis to be a hybrid drift-Kelvin-Helmholtz mode. At low magnetic field strengths, coherent fluctuations are present, while at high magnetic field strengths, the plasma is broad-band turbulent. Grid biasing is used to drive the once-coherent fluctuations to a broad-band turbulent state, as well as to suppress them. There is a corresponding change in the flow shear. When a high positive bias (10Te) is applied to the grid electrode, a large-scale ( n ˜/n ≈50 % ) is excited. This mode has been identified as the potential relaxation instability.
Xu, Zhongfeng
2012-09-01
An improved dynamical downscaling method (IDD) with general circulation model (GCM) bias corrections is developed and assessed over North America. A set of regional climate simulations is performed with the Weather Research and Forecasting Model (WRF) version 3.3 embedded in the National Center for Atmospheric Research\\'s (NCAR\\'s) Community Atmosphere Model (CAM). The GCM climatological means and the amplitudes of interannual variations are adjusted based on the National Centers for Environmental Prediction (NCEP)-NCAR global reanalysis products (NNRP) before using them to drive WRF. In this study, the WRF downscaling experiments are identical except the initial and lateral boundary conditions derived from the NNRP, original GCM output, and bias-corrected GCM output, respectively. The analysis finds that the IDD greatly improves the downscaled climate in both climatological means and extreme events relative to the traditional dynamical downscaling approach (TDD). The errors of downscaled climatological mean air temperature, geopotential height, wind vector, moisture, and precipitation are greatly reduced when the GCM bias corrections are applied. In the meantime, IDD also improves the downscaled extreme events characterized by the reduced errors in 2-yr return levels of surface air temperature and precipitation. In comparison with TDD, IDD is also able to produce a more realistic probability distribution in summer daily maximum temperature over the central U.S.-Canada region as well as in summer and winter daily precipitation over the middle and eastern United States. © 2012 American Meteorological Society.
Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics
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.
Jang, Seogjoo
2013-01-01
An exact real time quantum dynamics preaveraged over imaginary time path integral is formulated for general condensed phase equilibrium ensemble. This formulation results in the well-known centroid dynamics approach upon filtering of centroid constraint, and provides a rigorous framework to understand and analyze a related quantum dynamics approximation method called ring polymer molecular dynamics. The formulation also serves as the basis for developing new kinds of quantum dynamics that uti...
Nonlocalized cluster dynamics and nuclear molecular structure
Zhou, Bo; Funaki, Yasuro; Horiuchi, Hisashi; Ren, Zhongzhou; Röpke, Gerd; Schuck, Peter; Tohsaki, Akihiro; Xu, Chang; Yamada, Taiichi
2013-01-01
A container picture is proposed for understanding cluster dynamics where the clusters make nonlocalized motion occupying the lowest orbit of the cluster mean-field potential characterized by the size parameter $``B"$ in the THSR (Tohsaki-Horiuchi-Schuck-R\\"{o}pke) wave function. The nonlocalized cluster aspects of the inversion-doublet bands in $^{20}$Ne which have been considered as a typical manifestation of localized clustering are discussed. So far unexplained puzzling features of the THS...
EXCITON DYNAMICS IN ORGANIC MOLECULAR CRYSTALS
A. Matsui; Mizuno, K.; Kobayashi, M.
1985-01-01
Dynamical behavior of Frenkel excitons in aromatic hydrocarbon crystals, pyrene, α-perylene, β-perylene, and tetracene are overviewed based on the published references and in terms of the self-trap depth. Then pressure-induced instability in exciton states (the change in the self-trap depth) in α-perylene and anthracene is demonstrated and discussed. Finally a quasi-free exciton state is suggested to be the origin of the luminescence in anthracene at room temperature.
On the stochastic dynamics of molecular conformation
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.
Theoretical analysis of dynamic processes for interacting molecular motors
International Nuclear Information System (INIS)
Biological transport is supported by the 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 carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the 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 motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. (paper)
Molecular dynamics insights into human aquaporin 2 water channel.
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
Molecular phenomena in dynamic wetting: superspreading and precursors
Isele-Holder, Rolf Erwin
2015-01-01
Wetting is a multiscale process that can be controlled simultaneously by complex flow patterns on the macroscale and contact line phenomena at the Ångstrom scale. While resolving the latter scale is often circumvented by usage of boundary conditions, there are molecular wetting phenomena in which this approach is infeasible. The focus of this study is to use molecular dynamics simulations to examine two of these phenomena: superspreading, the ultra-rapid wetting of aqueous solutions facilitat...
Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Lipparini, Filippo; Lagardère, Louis; Raynaud, Christophe; Stamm, Benjamin; Cancès, Eric; Mennucci, Benedetta; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip
2015-01-01
We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a rob...
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
Paolo Ruggerone; Vargiu, Attilio V.; Francesca Collu; Nadine Fischer; Christian Kandt
2013-01-01
Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformation...
Sesana, A; Bernardi, M; Sheth, R K
2016-01-01
Supermassive black hole -- host galaxy relations are key to the computation of the expected gravitational wave background (GWB) in the pulsar timing array (PTA) frequency band. It has been recently pointed out that standard relations adopted in GWB computations are in fact biased-high. We show that when this selection bias is taken into account, the expected GWB in the PTA band is a factor of about three smaller than previously estimated. Compared to other scaling relations recently published in the literature, the median amplitude of the signal at $f=1$yr$^{-1}$ drops from $1.3\\times10^{-15}$ to $4\\times10^{-16}$. Although this solves any potential tension between theoretical predictions and recent PTA limits without invoking other dynamical effects (such as stalling, eccentricity or strong coupling with the galactic environment), it also makes the GWB detection more challenging.
International Nuclear Information System (INIS)
The effect of the static negative bias temperature (NBT) stress on a p-channel power metal—oxide—semiconductor field-effect transistor (MOSFET) is investigated by experiment and simulation. The time evolution of the negative bias temperature instability (NBTI) degradation has the trend predicted by the reaction—diffusion (R—D) model but with an exaggerated time scale. The phenomena of the flat-roof section are observed under various stress conditions, which can be considered as the dynamic equilibrium phase in the R—D process. Based on the simulated results, the variation of the flat-roof section with the stress condition can be explained. (condensed matter: electronic structure, electrical, magnetic, and optical properties)
Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations.
Semrouni, David; Sharma, Ashwani; Dognon, Jean-Pierre; Ohanessian, Gilles; Clavaguéra, Carine
2014-08-12
Infrared spectra of biomolecules are obtained from molecular dynamics simulations at finite temperature using the AMOEBA force field. Diverse examples are presented such as N-methylacetamide and its derivatives and a helical peptide. The computed spectra from polarizable molecular dynamics are compared in each case to experimental ones at various temperatures. The role of high-level electrostatic treatment and explicit polarization, including parameters improvements, is highlighted for obtaining spectral sensitivity to the environment including hydrogen bonds and water molecules and a better understanding of the observed experimental bands. PMID:26588289
The application of molecular dynamics in the uracil
International Nuclear Information System (INIS)
Under the (N, V, T) system, the position, speed, strength and direction of under stress and the changes of bond distance and bond angle of the evolution of each atom in uracil molecule are calculated by using the semiempirical molecular dynamics. The calculations come to the conclusions which are difficult or failed to be obtained on the microcosmic information of particles during the experiment be- cause of the limit of today's technology. It is to provide the theoretical basis that will go a step further to know molecular inner dynamics. (authors)
State-to-state dynamics of molecular energy transfer
Energy Technology Data Exchange (ETDEWEB)
Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)
1993-12-01
The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.
Femtochemistry and femtobiology ultrafast dynamics in molecular science
Douhal, Abderrazzak
2002-01-01
This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol
Electron-phonon interaction within classical molecular dynamics
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.
Nebel, Silke; Cloutier, Alison; Thompson, Graham J.
2004-01-01
Population sex ratios in monogamous birds are often male biased. One factor that can affect population sex ratios is sex-biased predation. However, most estimates of sex-biased predation in birds have focused on species with obvious sexual colour dimorphism or body size dimorphism. Data on sexually monomorphic birds are generally lacking. In the present study, we adopt a PCR-based sexing procedure to help test for sex-biased predation in a wintering population of western sandpipers (Calidris ...
Shapiro like steps reveals molecular nanomagnets' spin dynamics
Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid
2015-09-01
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.
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp
2012-06-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.
Imaging the molecular dynamics of dissociative electron attachment to water
Energy Technology Data Exchange (ETDEWEB)
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.
Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties
Czech Academy of Sciences Publication Activity Database
Fojtíková, J.; Kalvoda, L.; Sedlák, Petr
2015-01-01
Roč. 128, č. 4 (2015), s. 637-639. ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.530, year: 2014 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
Pabis, Anna; Geronimo, Inacrist; York, Darrin M.; Paneth, Piotr
2014-01-01
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specif...
Molecular Dynamics Study of Iron-Nickel Alloys
Meyer, R.; Entel, P.
1995-01-01
We present results of molecular dynamics simulations of disordered iron-nickel alloys. In particular we discuss the α-γ transition and associated anharmonic properties by making use of semiempirical potentials. Our results show that the structural transformation in these alloys is driven by local disorder. From data of specific heat and thermal expansion we conclude that the lattice dynamics at elevated temperatures (above the Curie temperature) can be described correctly without considering ...
ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics
Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
2013-01-01
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 simula...
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Allen, Joshua W.; Green, William H; Suleimanov, Yu. V.
2013-01-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett–Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any ...
Micellar Crystals in Solution from Molecular Dynamics Simulations
Anderson, J A; Lorenz, C. D.; Travesset, A.
2008-01-01
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our result...
Dynamics of excess electrons in atomic and molecular clusters
Young, Ryan Michael
2011-01-01
Femtosecond time-resolved photoelectron imaging (TRPEI) is applied to the study of excess electrons in clusters as well as to microsolvated anion species. This technique can be used to perform explicit time-resolved as well as one-color (single- or multiphoton) studies on gas phase species. The first part of this dissertation details time-resolved studies done on atomic clusters with an excess electron, the excited-state dynamics of solvated molecular anions, and charge-transfer dynamics to...
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation
International Nuclear Information System (INIS)
We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus
Deposition of Small Clusters on Surface: a Molecular Dynamics Simulation
Institute of Scientific and Technical Information of China (English)
DUAN Xiang-Mei; GONG Xin-Gao
2000-01-01
By using the molecular dynamics simulation, we have studied the dynamic behaviors of small energetic clusters deposited on the surface. We find that, at incident energy as low as 1.0eV/atom, the structure of the cluster is destroyed and cluster atoms form an epitaxial layer above the surface. At high energy incidence, the site exchange between cluster atom and surface atom is observed. The effects of the cluster size and orientation are discussed.
International Nuclear Information System (INIS)
The target of the present paper is the study of chirality effects in molecular dynamics from both a theoretical and an experimental point of view under the hypothesis of a molecular dynamics mechanism as the origin of chiral discrimination. This is a fundamental problem per se, and of possible relevance for the problem of the intriguing homochirality in Nature, so far lacking satisfactory explanations. We outline the steps that have been taken so far toward this direction, motivated by various experimental studies of supersonic molecular beams carried out in this laboratory, such as the detection of aligned oxygen in gaseous streams and further evidence on nitrogen, benzene and various hydrocarbons, showing the insurgence of molecular orientation in the dynamics of molecules in flows and in molecular collisions. Chiral effects are theoretically demonstrated to show up in the differential scattering of oriented molecules, also when impinging on surfaces. Focus on possible mechanisms for chiral bio-stereochemistry of oriented reactants may be of pre-biotical interest, for example when flowing in atmospheres of rotating bodies, specifically the planet Earth, as well as in vortex motions of celestial objects. Molecular dynamics simulations and experimental verifications of the hypothesis are reviewed and objectives of future research activity proposed.
Energy Technology Data Exchange (ETDEWEB)
Aquilanti, Vincenzo; Grossi, Gaia; Lombardi, Andrea; Maciel, Glauciete S; Palazzetti, Federico [Dipartimento di Chimica, Universita di Perugia, Via Elce di Sotto 8, 06123 Perugia (Italy)], E-mail: abulafia@dyn.unipg.it
2008-10-15
The target of the present paper is the study of chirality effects in molecular dynamics from both a theoretical and an experimental point of view under the hypothesis of a molecular dynamics mechanism as the origin of chiral discrimination. This is a fundamental problem per se, and of possible relevance for the problem of the intriguing homochirality in Nature, so far lacking satisfactory explanations. We outline the steps that have been taken so far toward this direction, motivated by various experimental studies of supersonic molecular beams carried out in this laboratory, such as the detection of aligned oxygen in gaseous streams and further evidence on nitrogen, benzene and various hydrocarbons, showing the insurgence of molecular orientation in the dynamics of molecules in flows and in molecular collisions. Chiral effects are theoretically demonstrated to show up in the differential scattering of oriented molecules, also when impinging on surfaces. Focus on possible mechanisms for chiral bio-stereochemistry of oriented reactants may be of pre-biotical interest, for example when flowing in atmospheres of rotating bodies, specifically the planet Earth, as well as in vortex motions of celestial objects. Molecular dynamics simulations and experimental verifications of the hypothesis are reviewed and objectives of future research activity proposed.
Simplistic Coulomb Forces in Molecular Dynamics
DEFF Research Database (Denmark)
Hansen, Jesper Schmidt; Schrøder, Thomas; Dyre, J. C.
2012-01-01
salt model the SF approximation overall reproduces the structural and dynamical properties as accurately as does the Wolf method. It is shown that the optimal Wolf damping parameter depends on the property in focus and that neither the potential energy nor the radial distribution function are useful...... measures for the convergence of the Wolf method to the Ewald summation method. The SF approximation is also tested for the SPC/Fw model of liquid water at room temperature, showing good agreement with both the Wolf and the particle mesh Ewald methods; this confirms previous findings [Fennell, C. J......In this paper we compare the Wolf method to the shifted forces (SF) method for efficient computer simulation of bulk systems with Coulomb forces, taking results from the Ewald summation and particle mesh Ewald methods as representing the true behavior. We find that for the Hansen–McDonald molten...
Superspreading: molecular dynamics simulations and experimental results
Theodorakis, Panagiotis; Kovalchuk, Nina; Starov, Victor; Muller, Erich; Craster, Richard; Matar, Omar
2015-11-01
The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Recently, we have observed that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. Here, we present the structural characteristics and kinetics of the droplet spreading during the different stages of this process, and we compare our results with experimental data for trisiloxane and poly oxy ethylene surfactants. In this way, we highlight and explore the differences between surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting. EPSRC Platform Grant MACIPh (EP/L020564/).
New ways to boost molecular dynamics simulations.
Krieger, Elmar; Vriend, Gert
2015-05-15
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. PMID:25824339
Molecular circuits for dynamic noise filtering.
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
Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics
International Nuclear Information System (INIS)
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
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives...
Probing Molecular Dynamics by Laser-Induced Backscattering Holography
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.
C60 molecular dynamics studied by muon spin relaxation
International Nuclear Information System (INIS)
In muonium-substituted organic radicals, the muon spin can serve as a probe of molecular dynamics. The motional perturbation induces transitions between the coupled spin states of muon and unpaired electron. Studies of the resultant muon spin relaxation in C60Mu, the species formed by muon implantation in solid C60, yield the correlation time characteristic of the reorientational motion
THE REFINEMENT OF NMR STRUCTURES BY MOLECULAR-DYNAMICS SIMULATION
TORDA, AE; VANGUNSTEREN, WF
1991-01-01
We discuss the use of molecular dynamics simulations as a tool for the refinement of structures based on NMR data. The procedure always involves the construction of a pseudo-energy term to model the experimental data and we consider the various approaches to this problem. We detail recent work where
Active site modeling in copper azurin molecular dynamics simulations
Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R
2004-01-01
Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po
Reasoning with Atomic-Scale Molecular Dynamic Models
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…
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
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.
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
Directory of Open Access Journals (Sweden)
Renata De Paris
2015-01-01
Full Text Available 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.
Molecular Dynamics ofa Coulomb System with Deformable Periodic Boundary Conditions
Totsuji, Hiroo; Shirokoshi, Hideki; Nara, Shigetoshi
1991-01-01
Variable shape molecular dynamics is formulated for the one-component plasma and the structural transition from the fcc lattice to the bcc lattice has been observed. It is emphasized that the condition of constant volume should be imposed when deformations of periodic boundary conditions are taken into account.
Molecular Dynamics Simulations Study on Chiral Room -Temperature Ionic Liquids
Czech Academy of Sciences Publication Activity Database
Lísal, Martin; Chvál, Z.; Storch, Jan; Izák, Pavel; Aim, Karel
Frankfurt : DECHEMA, 2012, P2-35. ISBN N. [European Symposium on Applied Thermodynamics - ESAT 2012 /26./. Potsdam (DE), 07.10.2012-10.10.2012] Institutional support: RVO:67985858 Keywords : ionic liquids * molecular dynamics simulations * thermodynamics properties Subject RIV: CF - Physical ; Theoretical Chemistry http://events.dechema.de/events/en/esat2012.html
Open boundary molecular dynamics of sheared star-polymer melts.
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
Molecular dynamics simulations on PGLa using NMR orientational constraints
International Nuclear Information System (INIS)
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide
Molecular dynamics simulations on PGLa using NMR orientational constraints
Energy Technology Data Exchange (ETDEWEB)
Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)
2015-11-15
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
Molecular dynamics of flows in the Knudsen regime
Cieplak, Marek; Koplik, Joel; Banavar, Jayanth R.
2000-01-01
Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations to study the transition between the dilute gas and the dense fluid regimes as the fluid density is increased.
Optimizing legacy molecular dynamics software with directive-based offload
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.
Molecular dynamics simulation of the Ni(001) surface
Energy Technology Data Exchange (ETDEWEB)
Chirita, V.; Pailthorpe, B.A. (School of Physics, Univ. of Sydney, New South Wales (Australia))
1992-02-10
A Lennard-Jones two-body interatomic potential is used in a molecular dynamics simulation of bulk nickel and of the Ni(001) surface stabilized using a Dion-Barker-Merrill substrate interaction. It is found that the bulk and surface Debye temperatures and surface atomic displacements compare well with previous theoretical and experimental studies. (orig.).
Enhanced molecular dynamics performance with a programmable graphics processor
Rapaport, D C
2009-01-01
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of multistream processor hardware necessitates a reformulation of the underlying algorithm. Performance measurements demonstrate the considerable benefit and cost-effectiveness of such an approach.
A Molecular Dynamics Approach to Grain Boundary Structure and Migration
DEFF Research Database (Denmark)
Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans
1974-01-01
It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...
Molecular dynamics simulation of a charged biological membrane
López Cascales, J.J.; García de la Torre, J.; Marrink, S.J.; Berendsen, H.J.C.
1996-01-01
A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as counterions and water molecules. The behavior of this membrane differs from that was shown by other me
Skill biased technical change: panel evidence of task orientation, wage effects, and labor dynamics
Ross, Matthew
2014-01-01
Existing empirical analyses of Skill Biased Technical Change focus on examining repeated cross-sections of individuals holding occupational task measures fixed. That approach cannot explore how wages respond to temporal variation in task orientation. This analysis examines wage effects using a synthetic panel of occupational task measures constructed from 17 releases of the O*NET database. This synthetic panel is combined with a panel of individual workers. Cross-occupational estimates that c...
Dynamics of prosocial behaviour: subtle bias toward racial and gender groups
Abad Merino, Silvia
2014-01-01
Subtle forms of bias pose significant challenges to achieving equitable intergroup relations and thus have recently received considerable attention in the field of social psychology. Although explicit hostility toward minority groups seems to have faded in modern societies, cross-cultural data show that the status, resources, and the power of women and ethnic/racial minorities, compared to those of male racial/ethnic majority group members remain unequal. The present dissertati...
Harada, Ryuhei; Kitao, Akio
2013-07-01
Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.
Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description
Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco
2015-01-01
A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...
Collisional dynamics in a gas of molecular super-rotors
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh.
2015-07-01
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.
Influence of conformational molecular dynamics on matter wave interferometry
Gring, Michael; Eibenberger, Sandra; Nimmrichter, Stefan; Berrada, Tarik; Arndt, Markus; Ulbricht, Hendrik; Hornberger, Klaus; Müri, Marcel; Mayor, Marcel; Böckmann, Marcus; Doltsinis, Nikos
2014-01-01
We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum object, our experiment demonstrates that the translational quantum phase is sensitive to dynamic conformational state changes inside the diffracted molecules. The structural flexibility of tailor-made hot organic particles is sufficient to admit a mixture of strongly fluctuating dipole moments. These modify the electric susceptibility and through this the quantum interference pattern in the presence of an external electric field. Detailed molecular dynamics simulations combined with density functional theory allow us to quantify the time-dependent structural reconfigurations and to predict the ensemble-averaged square of the dipole moment which is found to be in good agreement with the interferometric result. The experiment thus opens a new perspective on matter wave interfe...
Molecular dynamics computer simulation of permeation in solids
Energy Technology Data Exchange (ETDEWEB)
Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States)
1997-12-31
In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.
Laser-enhanced dynamics in molecular rate processes
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.
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Chiappori, Federica; Merelli, Ivan; Colombo, Giorgio; Milanesi, Luciano; Morra, Giulia
2012-01-01
Author Summary Allostery, or the capability of proteins to respond to ligand binding events with a variation in structure or dynamics at a distant site, is a common feature for biomolecular function and regulation in a large number of proteins. Intra-protein connections and inter-residue coordinations underlie allosteric mechanisms and react to binding primarily through a finely tuned modulation of motions and structures at the microscopic scale. Hence, all-atom molecular dynamics simulations...
Scherer, Christoph
2015-01-01
Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industri...
Directory of Open Access Journals (Sweden)
Marina Voinson
Full Text Available Theoretical studies predict that it is not possible to eradicate a disease under voluntary vaccination because of the emergence of non-vaccinating "free-riders" when vaccination coverage increases. A central tenet of this approach is that human behaviour follows an economic model of rational choice. Yet, empirical studies reveal that vaccination decisions do not necessarily maximize individual self-interest. Here we investigate the dynamics of vaccination coverage using an approach that dispenses with payoff maximization and assumes that risk perception results from the interaction between epidemiology and cognitive biases.We consider a behaviour-incidence model in which individuals perceive actual epidemiological risks as a function of their opinion of vaccination. As a result of confirmation bias, sceptical individuals (negative opinion overestimate infection cost while pro-vaccines individuals (positive opinion overestimate vaccination cost. We considered a feedback between individuals and their environment as individuals could change their opinion, and thus the way they perceive risks, as a function of both the epidemiology and the most common opinion in the population.For all parameter values investigated, the infection is never eradicated under voluntary vaccination. For moderately contagious diseases, oscillations in vaccination coverage emerge because individuals process epidemiological information differently depending on their opinion. Conformism does not generate oscillations but slows down the cultural response to epidemiological change.Failure to eradicate vaccine preventable disease emerges from the model because of cognitive biases that maintain heterogeneity in how people perceive risks. Thus, assumptions of economic rationality and payoff maximization are not mandatory for predicting commonly observed dynamics of vaccination coverage. This model shows that alternative notions of rationality, such as that of ecological
Voinson, Marina; Billiard, Sylvain; Alvergne, Alexandra
2015-01-01
Background Theoretical studies predict that it is not possible to eradicate a disease under voluntary vaccination because of the emergence of non-vaccinating “free-riders” when vaccination coverage increases. A central tenet of this approach is that human behaviour follows an economic model of rational choice. Yet, empirical studies reveal that vaccination decisions do not necessarily maximize individual self-interest. Here we investigate the dynamics of vaccination coverage using an approach that dispenses with payoff maximization and assumes that risk perception results from the interaction between epidemiology and cognitive biases. Methods We consider a behaviour-incidence model in which individuals perceive actual epidemiological risks as a function of their opinion of vaccination. As a result of confirmation bias, sceptical individuals (negative opinion) overestimate infection cost while pro-vaccines individuals (positive opinion) overestimate vaccination cost. We considered a feedback between individuals and their environment as individuals could change their opinion, and thus the way they perceive risks, as a function of both the epidemiology and the most common opinion in the population. Results For all parameter values investigated, the infection is never eradicated under voluntary vaccination. For moderately contagious diseases, oscillations in vaccination coverage emerge because individuals process epidemiological information differently depending on their opinion. Conformism does not generate oscillations but slows down the cultural response to epidemiological change. Conclusion Failure to eradicate vaccine preventable disease emerges from the model because of cognitive biases that maintain heterogeneity in how people perceive risks. Thus, assumptions of economic rationality and payoff maximization are not mandatory for predicting commonly observed dynamics of vaccination coverage. This model shows that alternative notions of rationality, such as
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik
2010-03-17
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
Molecular dynamics analysis on impact behavior of carbon nanotubes
International Nuclear Information System (INIS)
Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: 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
Molecular dynamics analysis on impact behavior of carbon nanotubes
Energy Technology Data Exchange (ETDEWEB)
Seifoori, Sajjad, E-mail: sajjad.seifoori@vru.ac.ir
2015-01-30
Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: 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.
Biased and g protein-independent signaling of chemokine receptors
DEFF Research Database (Denmark)
Steen, Anne; Larsen, Olav; Thiele, Stefanie;
2014-01-01
-switches based on recently published 7TM crystals and molecular dynamics studies. All three forms of biased signaling are abundant in the chemokine system. This challenges our understanding of "classic" redundancy inevitably ascribed to this system, where multiple chemokines bind to the same receptor and where a......Biased signaling or functional selectivity occurs when a 7TM-receptor preferentially activates one of several available pathways. It can be divided into three distinct forms: ligand bias, receptor bias, and tissue or cell bias, where it is mediated by different ligands (on the same receptor...... absolute, i.e., full versus no activation. Here we discuss biased signaling in the chemokine system, including the structural basis for biased signaling in chemokine receptors, as well as in class A 7TM receptors in general. This includes overall helical movements and the contributions of micro...
Orbital free molecular dynamics; Approche sans orbitale des plasmas denses
Energy Technology Data Exchange (ETDEWEB)
Lambert, F
2007-08-15
The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)
Imaging molecular structure and dynamics using laser driven recollisions
International Nuclear Information System (INIS)
Complete test of publication follows. Laser driven electron recollision provides a unique tool for measuring the structure and dynamics of matter. We illustrate this with experiments that use HHG to measure molecular structure with sub-Angstrom spatial and sub-femtosecond temporal resolution. Our recent work has looked in particular at the signal from high order harmonic generation which contains rich information about the structure and intra-molecular dynamics of small molecules. This we will illustrate by two types of experiment; (a) measurements of HHG from aligned molecular samples to observe two-centre recombination interference and electronic structure dependence of the angle dependent yield, (b) reconstruction of intra-molecular proton dynamics from the spectral dependence of the HHG using the intrinsic chirp of recolliding electrons. We experimentally investigate the process of intramolecular quantum interference in high-order harmonic generation in impulsively aligned CO2 molecules. The recombination interference effect is clearly seen through the order dependence of the harmonic yield in an aligned sample. This confirms that the effective de Broglie wavelength of the returning electron wave is not significantly altered by acceleration in the Coulomb field of the molecular ion. For the first time, to our knowledge, we demonstrate that such interference effects can be effectively controlled by changing the ellipticity of the driving laser field. Here we also report the results of angular dependence measurements of high order harmonics (17tth - 27th) from impulsively aligned organic molecules: Acetylene, Ethylene, and Allene. Since these molecules have a relatively low Ip an appropriately short pulse is required to produce as many harmonic orders as possible. This was provided by the ∼ 10 fs beam line of the ASTRA laser at Rutherford Appleton Laboratory whilst a somewhat longer pulse, properly forwarded with respect to the driving pulse, induced the
Rarefied Gas Flow in Rough Microchannels by Molecular Dynamics Simulation
Institute of Scientific and Technical Information of China (English)
曹炳阳; 陈民; 过增元
2004-01-01
The molecular dynamics simulation method is applied to investigate the rarefied gas flow in a submicron channel with surface roughness which is modelled by an array of triangle modules. The boundary conditions are found to be determined not only by the Knudsen number but also the roughness, which implies that the breakdown of the Maxwell slip model under the conditions that the surface roughness is comparable to the molecular mean free path. The effects of the rarefaction and the surface roughness on the boundary conditions and the flow characteristics are strongly coupled. The flow friction increases with increasing roughness and with decreasing Knudsen number.
Spectra modelling combining molecular dynamics and quantum mechanics
Czech Academy of Sciences Publication Activity Database
Novák, Vít; Bouř, Petr
2015-01-01
Roč. 22, č. 1 (2015), s. 48. ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] R&D Projects: GA ČR GAP208/11/0105; GA ČR GA15-09072S Grant ostatní: GA MŠk(CZ) LM2010005; GA MŠk(CZ) ED3.2.00/08.0144 Institutional support: RVO:61388963 Keywords : Raman scattering * molecular dynamics * autocorrelation function Subject RIV: CF - Physical ; Theoretical Chemistry
Accelerating convergence of molecular dynamics-based structural relaxation
DEFF Research Database (Denmark)
Christensen, Asbjørn
2005-01-01
We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to...
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
Energy Technology Data Exchange (ETDEWEB)
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-03-14
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Molecular-Level Organization of the Tear Film Lipid Layer: A Molecular Dynamics Simulation Study
Czech Academy of Sciences Publication Activity Database
Wizert, A.; Iskander, D. R.; Jungwirth, Pavel; Cwiklik, Lukasz
Elsevier. Roč. 106, č. 2 (2014), 710A. ISSN 0006-3495. [Annual Meeting of the Biophysical Society /58./. 15.02.2014-19.02.2014, San Francisco] Institutional support: RVO:61388963 ; RVO:61388955 Keywords : tear film * lipid layer * molecular dynamics simulations Subject RIV: BO - Biophysics
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,…
Czech Academy of Sciences Publication Activity Database
Chocholoušová, Jana; Feig, M.
2006-01-01
Roč. 27, č. 6 (2006), s. 719-729. ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006
Microscopic study of nuclear 'pasta' by quantum molecular dynamics
International Nuclear Information System (INIS)
Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. and be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple 'pasta' phases in neutron star crusts. (author)
Ab initio molecular dynamics study of liquid methanol
Handgraaf, J W; Meijer, E J; Handgraaf, Jan-Willem; Erp, Titus S. van; Meijer, Evert Jan
2003-01-01
We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
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.
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
Energy Technology Data Exchange (ETDEWEB)
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.
Coalescence of silver unidimensional structures by molecular dynamics simulation
International Nuclear Information System (INIS)
The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Molecular dynamical simulations of melting behaviors of metal clusters
International Nuclear Information System (INIS)
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
The chaos and order in nuclear molecular dynamics
International Nuclear Information System (INIS)
The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12C, 16O and 20Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs
Excitation Dynamics and Relaxation in a Molecular Heterodimer
Balevicius, V; Abramavicius, D; Mancal, T; Valkunas, L
2011-01-01
The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the energy gap of the molecular excitation, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
Coherent Amplification of Ultrafast Molecular Dynamics in an Optical Oscillator
Aharonovich, Igal; Pe'er, Avi
2016-02-01
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.
Fermionic molecular dynamics for ground states and collisions of nuclei
International Nuclear Information System (INIS)
The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)
Kinetic distance and kinetic maps from molecular dynamics simulation
Noe, Frank
2015-01-01
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...
Serine Proteases an Ab Initio Molecular Dynamics Study
De Santis, L
1999-01-01
In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.
Tensor-optimized antisymmetrized molecular dynamics in nuclear physics
Myo, Takayuki; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro
2015-01-01
We develop a new formalism to treat nuclear many-body systems using bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays important role in nuclear many-body systems due to the role of the pion in strongly interacting system. We take the antisymmetrized molecular dynamics (AMD) as a basic framework and add a tensor correlation operator acting on the AMD wave function using the concept of the tensor-optimized shell model (TOSM). We demonstrate a systematical and straightforward formulation utilizing the Gaussian integration and differentiation method and the antisymmetrization technique to calculate all the matrix elements of the many-body Hamiltonian. We can include the three-body interaction naturally and calculate the matrix elements systematically in the progressive order of the tensor correlation operator. We call the new formalism "tensor-optimized antisymmetrized molecular dynamics".
Optical spectra and lattice dynamics of molecular crystals
Zhizhin, GN
1995-01-01
The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.
Surface hopping methodology in laser-driven molecular dynamics
Fiedlschuster, T; Gross, E K U; Schmidt, R
2016-01-01
A theoretical justification of the empirical surface hopping method for the laser-driven molecular dynamics is given utilizing the formalism of the exact factorization of the molecular wavefunction [Abedi et al., PRL $\\textbf{105}$, 123002 (2010)] in its quantum-classical limit. Employing an exactly solvable $\\textrm H_2^{\\;+}$-like model system, it is shown that the deterministic classical nuclear motion on a single time-dependent surface in this approach describes the same physics as stochastic (hopping-induced) motion on several surfaces, provided Floquet surfaces are applied. Both quantum-classical methods do describe reasonably well the exact nuclear wavepacket dynamics for extremely different dissociation scenarios. Hopping schemes using Born-Oppenheimer surfaces or instantaneous Born-Oppenheimer surfaces fail completely.
Reaction dynamics of molecular hydrogen on silicon surfaces
DEFF Research Database (Denmark)
Bratu, P.; Brenig, W.; Gross, A.; Hartmann, M.; Höfer, U.; Kratzer, Peter; Russ, R.
1996-01-01
Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective...... five-dimensional model is presented taking lattice distortion, corrugation, and molecular vibrations into account within the framework of coupled-channel calculations. While the temperature dependence of the sticking is dominated by lattice distortion, the main effect of corrugation is a reduction of...
An implicit divalent counterion force field for RNA molecular dynamics
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.
Shock induced phase transition of water: Molecular dynamics investigation
Energy Technology Data Exchange (ETDEWEB)
Neogi, Anupam, E-mail: anupamneogi@atdc.iitkgp.ernet.in [Advanced Technology Development Center, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India); Mitra, Nilanjan, E-mail: nilanjan@civil.iitkgp.ernet.in [Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India)
2016-02-15
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.
Shock induced phase transition of water: Molecular dynamics investigation
International Nuclear Information System (INIS)
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
Tensor-optimized antisymmetrized molecular dynamics in nuclear physics
Myo, Takayuki; Toki, Hiroshi; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro
2015-07-01
We develop a new formalism to treat nuclear many-body systems using the bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays an important role in nuclear many-body systems due to the role of the pion in strongly interacting systems. We take the antisymmetrized molecular dynamics (AMD) as a basic framework and add a tensor correlation operator acting on the AMD wave function using the concept of the tensor-optimized shell model. We demonstrate a systematical and straightforward formulation utilizing the Gaussian integration and differentiation method and the antisymmetrization technique to calculate all the matrix elements of the many-body Hamiltonian. We can include the three-body interaction naturally and calculate the matrix elements systematically in the progressive order of the tensor correlation operator. We call the new formalism "tensor-optimized antisymmetrized molecular dynamics".
Ab initio molecular dynamics on the electronic Boltzmann equilibrium distribution
Energy Technology Data Exchange (ETDEWEB)
Alonso, J L; Echenique, P [Departamento de Fisica Teorica, Universidad de Zaragoza, Pedro Cerbuna 12, E-50009 Zaragoza (Spain); Castro, A; Polo, V [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, E-50018 Zaragoza (Spain); Rubio, A [Nano-Bio Spectroscopy group and ETSF Scientific Development Centre, Departamento de Fisica de Materiales, Universidad del PaIs Vasco, Centro de Fisica de Materiales, CSIC-UPV/EHU-MPC and DIPC, E-20018 San Sebastian (Spain); Zueco, D, E-mail: dzueco@unizar.e [Instituto de Ciencia de Materiales de Aragon and Departamento de Fisica de la Materia Condensada, CSIC-Universidad de Zaragoza, E-50009 Zaragoza (Spain)
2010-08-15
We prove that for a combined system of classical and quantum particles, it is possible to describe a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In addition, these molecular dynamics (MD) do not need to assume that the electrons immediately follow the nuclear motion (in contrast to any adiabatic approach) and do not present problems in the presence of crossing points between different potential energy surfaces (conical intersections or spin-crossings). A practical application of this MD to the study of the effect of temperature on molecular systems presenting (nearly) degenerate states-such as the avoided crossing in the ring-closure process of ozone-is presented.
Nonequilibrium Molecular Dynamics Simulation of the Thermocapillary Effect
Maier, Holger Andreas
2011-01-01
A natural convection occurs at lateral spatially variable solid-fluid or liquid-fluid interfaces [probstein1994]. It can play an important role in the transport of heat or mass across such interfaces, e.g. in evaporation or solvent extraction as they are often employed in chemical engineering [sherwood1975]. Model systems of such interfacial systems have been studied by different methods [colinet2001]. A very fundamental method is the usage of so-called molecular dynamics (MD) simulation...
Molecular Dynamics Study of the Primary Ferrofluid Aggregate Formation
Tanygin, B. M.; Kovalenko, V. F.; Petrychuk, M.V.; Dzyan, S. A.
2011-01-01
Investigations of the phase transitions and self-organization in the magnetic aggregates are of the fundamental and applied interest. The long-range ordering structures described in the Tom\\'anek's systematization (M. Yoon, and D. Tom\\'anek, 2010 [1]) are not yet obtained in the direct molecular dynamics simulations. The resulted structures usually are the linear chains or circles, or, else, amorphous (liquid) formations. In the present work, it was shown, that the thermodynamically equilibri...
Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane.
Bernèche, S; Nina, M; Roux, B
1998-01-01
Molecular dynamics trajectories of melittin in an explicit dimyristoyl phosphatidylcholine (DMPC) bilayer are generated to study the details of lipid-protein interactions at the microscopic level. Melittin, a small amphipathic peptide found in bee venom, is known to have a pronounced effect on the lysis of membranes. The peptide is initially set parallel to the membrane-solution interfacial region in an alpha-helical conformation with unprotonated N-terminus. Solid-state nuclear magnetic reso...
Nonlinear dynamics of zigzag molecular chains (in Russian)
DEFF Research Database (Denmark)
Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth;
1999-01-01
Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...... types (such as extension and compression varieties) develop simultaneously in the chain. Accordingly, the inclusion of chain geometry is necessary if physical phenomena are to be described in terms of solitary waves...
Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A; Parrinello, M.; Frenkel, D
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting transition to a metallic state. In contrast to ordinary liquid silicon, the new liquid is characterized by a high coordination number and a strong reduction of covalent bonding effects.
Understanding disordered and membrane protein recognition by molecular dynamics
Stanley, Nathaniel H., 1983-
2015-01-01
This thesis has been about the use of a simulation technique, known as molecular dynamics simulations, to study biophysics in proteins that have historically been difficult to study with other methods. We have studied numerous systems, namely binding to the membrane proteins Fatty acid amide hydrolase (FAAH) and the sphingosine-1-phosphate receptor 1 (S1P1R), and folding in the disordered protein kinase inducible domain (KID). In each case we have been able to analyze processes and uncover be...
Automated processing of data generated by molecular dynamics
International Nuclear Information System (INIS)
A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)
Efficient stochastic thermostatting of path integral molecular dynamics
Ceriotti, Michele; Parrinello, Michele; Markland, Thomas E.; Manolopoulos, David E.
2010-01-01
The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high-frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat...
Quantum tunneling splittings from path-integral molecular dynamics.
Mátyus, Edit; Wales, David J; Althorpe, Stuart C
2016-03-21
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. PMID:27004863
Viscosity in molecular dynamics with periodic boundary conditions
Viscardy, S.; Gaspard, P.
2003-01-01
We report a study of viscosity by the method of Helfand moment in systems with periodic boundary conditions. We propose a new definition of Helfand moment which takes into account the minimum image convention used in molecular dynamics with periodic boundary conditions. Our Helfand-moment method is equivalent to the method based on the Green-Kubo formula and is not affected by ambiguities due to the periodic boundary conditions. Moreover, in hard-ball systems, our method is equivalent to the ...
Coupling Lattice Boltzmann and Molecular Dynamics models for dense fluids
Dupuis, A.; Kotsalis, E. M.; Koumoutsakos, P.
2006-01-01
We propose a hybrid model, coupling Lattice Boltzmann and Molecular Dynamics models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with r...
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
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
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
Rapaport, D C
2009-01-01
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.
Molecular dynamics simulations of HIV-1 protease complexed with saquinavir
Watson, S. J.
2009-01-01
Inhibition of the Human Immunode�ficiency virus type-1 (HIV-1) protease enzyme blocks HIV-1 replication. Protease inhibitor drugs have successfully been used as a therapy for HIV-infected individuals to reduce their viral loads and slow the progression to Acquired Immune Defi�ciency Syndrome (AIDS). However, mutations readily and rapidly accrue in the protease gene resulting in a reduced sensitivity of the protein to the inhibitor. In this thesis, molecular dynamics simulations (MDS)...
Molecular dynamics simulation of nanoindentation on nanocomposite pearlite
Ghaffarian, Hadi; Taheri, Ali Karimi; Ryu, Seunghwa; Kang, Keonwook
2016-01-01
We carry out molecular dynamics simulations of nanoindentation to investigate the effect of cementite size and temperature on the deformation behavior of nanocomposite pearlite composed of alternating ferrite and cementite layers. We find that, instead of the coherent transmission, dislocation propagates by forming a widespread plastic deformation in cementite layer. We also show that increasing temperature enhances the distribution of plastic strain in the ferrite layer, which reduces the st...
Molecular Dynamics for Low Temperature Plasma-Surface Interaction Studies
Graves, David B.; Brault, Pascal
2009-01-01
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms through integration of atomic equations of motion, using inter-atomic potentials that can account for bond breaking and formation that result when energetic species from the plasma impact surfaces. This article summarizes the current status of the technique for ...
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
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.
DNA basepair step deformability inferred from molecular dynamics simulations
Czech Academy of Sciences Publication Activity Database
Lankaš, Filip; Šponer, Jiří; Langowski, J.; Cheatham III, T. E.
2003-01-01
Roč. 85, č. 5 (2003), s. 2872-2883. ISSN 0006-3495 R&D Projects: GA MŠk LN00A032 Grant ostatní: National Science Foundation(US) CHE-0218739; Wellcome Trust(GB) GR067507MF Institutional research plan: CEZ:AV0Z5004920; CEZ:AV0Z4040901 Keywords : molecular dynamics simulations * DNA basepair step deformability Subject RIV: BO - Biophysics Impact factor: 4.463, year: 2003
Spin dynamics of an ultra-small nanoscale molecular magnet
Directory of Open Access Journals (Sweden)
Ciftja Orion
2007-01-01
Full Text Available AbstractWe present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high Heisenberg spins. We derive exact analytic expressions (in integral form for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail.
Molecular Dynamics Simulation of Myoglobin Collision with Low Energy Ions
Institute of Scientific and Technical Information of China (English)
CHENG Wei; ZHANG Feng-Shou; ZHOU Hong-Yu
2007-01-01
Collisions of a low energy heavy ion with a myoglobin in water are simulated by molecular dynamics model. The increase of total energy is very small. The mean squared fluctuation decreases at 300 K and increases at 250K.This is an important novel cooling effect that protects the protein from ion damage. The possible collision side effect is the change of tertiary structure that blocks the normal functions of the myogiobin.
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
Energy Technology Data Exchange (ETDEWEB)
Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche
1997-09-01
Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.
Thermal conductivity of ZnTe investigated by molecular dynamics
International Nuclear Information System (INIS)
The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
Leone, Stephen R.
2010-01-01
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction me...
Molecular dynamics in electrospun amorphous plasticized polylactide fibers
MONNIER, X; DELPOUVE, N; BASSON, N; GUINAULT, A; DOMENEK, S; Saiter, A; MALLON, P.E; Dargent, E
2015-01-01
The molecular dynamics in the amorphous phase of electrospun fibers of polylactide (PLA) has been investigated using the cooperative rearranging region concept. An unusual and significant increase of the cooperativity length at the glass transition induced by the electrospinning has been observed. This behavior is attributed to the singularity of the amorphous phase organization. Electrospun PLA fibers rearrange in a pre-ordered metastable state which is characterized by highly oriented but n...
Accelerating Molecular Dynamic Simulation on Graphics Processing Units
Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.
2009-01-01
We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.
Enhanced molecular dynamics performance with a programmable graphics processor
Rapaport, D. C.
2009-01-01
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware necessitates a reformulation of the underlying algorithm. Performance measurements demonstrate the considerable benefit and cost-effectiveness of such an approach, which produces a factor of 2.5 speed improvement over previous work for the case of the soft-sp...
Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit
Xu, Ji; Ren, Ying; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai
2010-01-01
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU ar...
Molecular dynamics simulations of complex shaped particles using Minkowski operators
Galindo-Torres, Sergio-Andres; Alonso-Marroquin, Fernando
2008-01-01
The Minkowski operators (addition and substraction of sets in vectorial spaces) has been extensively used for Computer Graphics and Image Processing to represent complex shapes. Here we propose to apply those mathematical concepts to extend the Molecular Dynamics (MD) Methods for simulations with complex-shaped particles. A new concept of Voronoi-Minkowski diagrams is introduced to generate random packings of complex-shaped particles with tunable particle roundness. By extending the classical...
Molecular Dynamics study of Pb overlayer on Cu(100)
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.
Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins
Fogolari, Federico; Brigo, Alessandro; Molinari, Henriette
2003-01-01
Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poi...
Molecular dynamics investigation of radiation damage in semiconductors
Good, Brian S.
1991-01-01
Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.
Molecular dynamics simulation study of polyelectrolyte adsorption on cellulose surfaces
Biermann, Oliver
2002-01-01
The adsorption of two polyelectrolyte ((carboxy methyl) cellulose and poly(acrylate) in water on crystalline cellulose is studied in this work. The multi-component problem has been splitted up into simulations of solutions of the polyelectrolyte (polyanions including sodium counterions) in water, into simulations of the interface of crystalline cellulose towards water. Finally polyelectrolyte-cellulose systems were studied. Molecular dynamics simulations of diluted (_ 2:5 weight percent) aque...
Hydration of polyelectrolytes studied by molecular dynamics simulation
Biermann, Oliver; Haedicke, Erich; Koltzenburg, Sebastian; Seufert, Michael; Mueller-Plathe, Florian
2001-01-01
Molecular dynamics simulations of diluted (~2.5 weight percent) aqueous solutions of two polyelectrolytes, namely sodium carboxy methyl cellulose (CMC) and sodium poly(acrylate) (PAA) have been performed. Water and counterions were taken into account explicitly. For CMC the substitution pattern and starting conformation is all-important. Two simulations of CMC oligomers resulted in different structures: One molecule takes a stretched conformation, while the second one keeps a globule-like, to...
Incorporation of quantum statistical features in molecular dynamics
International Nuclear Information System (INIS)
We formulate a method for incorporating quantum fluctuations into molecular-dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum-statistical equilibrium. (author)
Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation
DEFF Research Database (Denmark)
Pedersen, U.R.; Peters, Günther H.j.; Westh, P.
2007-01-01
on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results......The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C...
International Nuclear Information System (INIS)
Dielectric TiO2 thin films were fabricated on p-(100) Si substrates by arc ion plating. A pulsed substrate bias ranging from 0 V to − 900 V was applied to investigate the effect of pulsed bias on phase structure and growth of the films. Phase, microstructure, and growth morphology of TiO2 films prepared at different bias voltages were evaluated with grazing incident x-ray diffraction and atomic force microscopy (AFM). The results show that pulsed bias exerts an evident influence on phase structure and growth morphology. High substrate bias facilitates the formation of rutile phase, a (220) preferred orientation is observed in TiO2 films obtained at − 900 V. AFM images show that pulsed substrate bias exerts a strong influence on the growth of TiO2 films. With increasing bias voltage, the film is initially composed of tiny surface islands separated by shallow boundaries, then of large and spiky surface islands isolated by deep boundaries. Correspondingly, surface roughness increases from 1.1 nm at 0 V to 3.8 nm at − 900 V. To explain the phenomena observed in this study, pulsed plasma sheath model was used to simulate the ion sheath dynamics. By analyzing experimental and simulated results, it can be concluded that film growth and property relate close to ion density and energy in the sheath, which is dominantly governed by negative substrate bias.
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
International Nuclear Information System (INIS)
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
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
Energy Technology Data Exchange (ETDEWEB)
Abdollahipour, Babak, E-mail: b-abdollahi@tabrizu.ac.ir [Faculty of Physics, University of Tabriz, Tabriz 51666-16471 (Iran, Islamic Republic of); Abouie, Jahanfar, E-mail: jahan@iasbs.ac.ir; Ebrahimi, Navid [Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731 (Iran, Islamic Republic of)
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.
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
Directory of Open Access Journals (Sweden)
Babak Abdollahipour
2015-09-01
Full Text Available 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.
Molecular dynamics of a water jet from a carbon nanotube.
Hanasaki, Itsuo; Yonebayashi, Toru; Kawano, Satoyuki
2009-04-01
A carbon nanotube (CNT) can be viewed as a molecular nozzle. It has a cylindrical shape of atomistic regularity, and the diameter can be even less than 1 nm. We have conducted molecular-dynamics simulations of water jet from a (6,6) CNT that confines water in a form of single-file molecular chain. The results show that the water forms nanoscale clusters at the outlet and they are released intermittently. The jet breakup is dominated by the thermal fluctuations, which leads to the strong dependence on the temperature. The cluster size n decreases and the release frequency f increases at higher temperatures. The f roughly follows the reaction kinetics by the transition state theory. The speed of a cluster is proportional to the 1/sqrt[n] because of the central limit theorem. These properties make great contrast with the macroscopic liquid jets. PMID:19518333
Molecular Dynamics Studies on the Buffalo Prion Protein
Zhang, Jiapu
2015-01-01
It was reported that buffalo is a low susceptibility species resisting to TSEs (Transmissible Spongiform Encephalopathies) (same as rabbits, horses and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (in humans prion diseases are (v)CJDs, GSS, FFI, and kulu etc). It was reported that buffalo is a low susceptibility species resisting to prion diseases (as rabbits, dogs, horses). In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to find out the reason why buffaloes are resistant to prion diseases. We first did molecular modeling a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonanc...
Applications of the molecular dynamics flexible fitting method.
Trabuco, Leonardo G; Schreiner, Eduard; Gumbart, James; Hsin, Jen; Villa, Elizabeth; Schulten, Klaus
2011-03-01
In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to landmark advances in experimental and computational techniques, resulting in sub-nanometer resolution structures being obtained routinely. The remaining gap between these data and revealing the mechanisms of molecular function can be closed through hybrid modeling tools that incorporate known atomic structures into the cryo-EM data. One such tool, molecular dynamics flexible fitting (MDFF), uses molecular dynamics simulations to combine structures from X-ray crystallography with cryo-EM density maps to derive atomic models of large biomolecular complexes. The structures furnished by MDFF can be used subsequently in computational investigations aimed at revealing the dynamics of the complexes under study. In the present work, recent applications of MDFF are presented, including the interpretation of cryo-EM data of the ribosome at different stages of translation and the structure of a membrane-curvature-inducing photosynthetic complex. PMID:20932910
Exploiting molecular dynamics in Nested Sampling simulations of small peptides
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.
International Nuclear Information System (INIS)
The dynamical correlation between quantum entanglement and intramolecular energy in realistic molecular vibrations is explored using the Lie algebraic approach. The explicit expression of entanglement measurement can be achieved using algebraic operations. The common and different characteristics of dynamical entanglement in different molecular vibrations are also provided. The dynamical study of quantum entanglement and intramolecular energy in small molecular vibrations can be helpful for controlling the entanglement and further understanding the intramolecular dynamics. (atomic and molecular physics)
Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A
2013-03-21
The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio
A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations
van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.
2012-01-01
Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However, perf
A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations
van Dijk, Marc; Wassenaar, Tsjerk A.; Bonvin, Alexandre M. J. J.
2012-01-01
Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However, perf
Energy Technology Data Exchange (ETDEWEB)
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.
Energy Technology Data Exchange (ETDEWEB)
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.
Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer
Casuyac Miqueas; Bantaculo Rolando
2016-01-01
This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNR)using the classical molecular dynamic (MD) simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H...
Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations.
Oakes, V; Furini, S; Domene, C
2016-01-01
The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs. PMID:27586285
The classical and quantum dynamics of molecular spins on graphene.
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
Molecular dynamics investigation of tracer diffusion in a simple liquid
International Nuclear Information System (INIS)
Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs
Wave packet dynamics in molecular excited electronic states
International Nuclear Information System (INIS)
We theoretically explore the use of UV pump – UV probe schemes to resolve in time the dynamics of nuclear wave packets in excited electronic states of the hydrogen molecule. The pump pulse ignites the dynamics in singly excited states, that will be probed after a given time delay by a second identical pulse that will ionize the molecule. The field-free molecular dynamics is first explored by analyizing the autocorrelation function for the pumped wave packet and the excitation probabilities. We investigate both energy and angle differential ionization probabilities and demonstrate that the asymmetry induced in the electron angular distributions gives a direct map of the time evolution of the pumped wave packet
Molecular dynamics of coalescence and collisions of silver nanoparticles
International Nuclear Information System (INIS)
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy
Steered molecular dynamics simulations of protein-ligand interactions
Institute of Scientific and Technical Information of China (English)
XU Yechun; SHEN Jianhua; LUO Xiaomin; SHEN Xu; CHEN Kaixian; JIANG Hualiang
2004-01-01
Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APA from HIV-1 reverse transcriptase.
Molecular dynamics of coalescence and collisions of silver nanoparticles
Energy Technology Data Exchange (ETDEWEB)
Guevara-Chapa, Enrique, E-mail: enrique_guevara@hotmail.com [Universidad Autónoma de Nuevo León, Facultad de Ciencias Físico Matemáticas (Mexico); Mejía-Rosales, Sergio [Universidad Autónoma de Nuevo León, Center for Innovation, Research and Development in Engineering and Technology (CIIDIT), and CICFIM-Facultad de Ciencias Físico Matemáticas (Mexico)
2014-12-15
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy.
Two methods for molecular dynamics on curved surfaces
Paquay, Stefan
2014-01-01
Lateral diffusion along membranes is an important transport mechanism in biology. Dynamical simulations of this transport can greatly aid in understanding biological processes where this diffusion plays a role. Brownian dynamics simulations in local coordinates are one possibility, but we show here that it is also possible to combine constraint algorithms with a velocity Verlet scheme to perform molecular dynamics simulations of particles confined on arbitrary time-independent curved surfaces. The main advantage is that this method is based on Cartesian coordinates instead of local coordinates, allowing the reuse of many other standard tools, including parallelisation through domain decomposition, without adapting those to local coordinates. Of the two constraint algorithms we considered, RATTLE is more computationally efficient and easier to implement, while the symmetric projection method has slightly better energy conservation. By applying the schemes to the Langevin equation, Brownian motion on various cu...
The classical and quantum dynamics of molecular spins on graphene
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.
Koniakhin, S V; Terterov, I N; Shvidchenko, A V; Eidelman, E D; Dubina, M V
2016-01-01
The determination of particle size by dynamic light scattering uses the Stokes-Einstein relation, which can break down for nanoscale objects. Here we employ a molecular dynamics simulation of fully solvated 1-5 nm carbon nanoparticles for the refinement of the experimental data obtained for nanodiamonds in water by using dynamic light scattering. We performed molecular dynamics simulations in differently sized boxes and calculated nanoparticles diffusion coefficients using the velocity autocorrelation function and mean-square displacement. We found that the predictions of the Stokes-Einstein relation are accurate for nanoparticles larger than 3 nm while for smaller nanoparticles the diffusion coefficient should be corrected and different boundary conditions should be taken into account.
Molecular imaging with dynamic contrast-enhanced computed tomography
International Nuclear Information System (INIS)
Dynamic contrast-enhanced computed tomography (DCE-CT) is a quantitative technique that employs rapid sequences of CT images after bolus administration of intravenous contrast material to measure a range of physiological processes related to the microvasculature of tissues. By combining knowledge of the molecular processes underlying changes in vascular physiology with an understanding of the relationship between vascular physiology and CT contrast enhancement, DCE-CT can be redefined as a molecular imaging technique. Some DCE-CT derived parameters reflect tissue hypoxia and can, therefore, provide information about the cellular microenvironment. DCE-CT can also depict physiological processes, such as vasodilatation, that represent the physiological consequences of molecular responses to tissue hypoxia. To date the main applications have been in stroke and oncology. Unlike some other molecular imaging approaches, DCE-CT benefits from wide availability and ease of application along with the use of contrast materials and software packages that have achieved full regulatory approval. Hence, DCE-CT represents a molecular imaging technique that is applicable in clinical practice today.
Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite
Van den Berg, A.W.C.; Bromley, S.T.; Flikkema, E.; Wojdel, J.; Maschmeyer, T; Jansen, J C
2004-01-01
In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the temperature range of 700–1200 K, the diffusion coefficient is found to range from 1.6⋅10−10 to 1.8⋅10−9 m2/s. The energy barrier for hydrogen diffusion is determined from the simulations allowing the applica...
Dynamical properties of liquid Al near melting. An orbital-free molecular dynamics study
Gonzalez, David J; Gonzalez, Luis Enrique; Lopez, Jose Manuel; Stott, Malcolm J.
2001-01-01
The static and dynamic structure of liquid Al is studied using the orbital free ab-initio molecular dynamics method. Two thermodynamic states along the coexistence line are considered, namely T = 943 K and 1323 K for which X-ray and neutron scattering data are available. A new kinetic energy functional, which fulfills a number of physically relevant conditions is employed, along with a local first principles pseudopotential. In addition to a comparison with experiment, we also compare our ab-...
Energy Technology Data Exchange (ETDEWEB)
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.
Arrese-Igor, Silvia; Alegría, Ángel; Moreno Segurado, Ángel J.; Colmenero de León, Juan
2011-01-01
We address the general question of how the molecular weight dependence of chain dynamics in unentangled polymers is modified by blending. By dielectric spectroscopy we measure the normal mode relaxation of polyisoprene in blends with a slower component of poly(ter-butylstyrene). Unentangled polyisoprene in the blend exhibits strong deviations from Rouse scaling, approaching 'entangled-like' behavior at low temperatures in concomitance with the increase of the dynamic asymmetry in the blend. T...
Dynamics of the Manakov Solitons in Biased Guest-Host Photorefractive Polymer
International Nuclear Information System (INIS)
In the biased guest-host photorefractive polymer, the Manakov equations can be used to describe the optical soliton propagation and interaction. Hereby for such equations, via the Hirota method and symbolic computation, analytic soliton solutions in the bright-dark and dark-dark forms are obtained. Based on the choice of photorefractive polymer parameter and incident-optical-beam parameter, the bright-dark and dark-dark solitons as well as their interaction can occur in the polymer when the total intensity is much lower than the background illumination, and our analysis indicates that the incident light with different polarization directions influence little on the soliton propagation. γ, representing the soliton intensity far away from the soliton center, determines the appearance of bright or dark soliton under the background illumination. Through the graphic and asymptotic analysis on the two-soliton solutions along with the different γ, we find that there exist the elastic and inelastic interactions between the bright-dark solitons, while the interactions between the dark-dark solitons are always elastic. (general)
Squared visibility estimator. Calibrating biases to reach very high dynamic range
Perrin, G
2005-01-01
In the near infrared where detectors are limited by read-out noise, most interferometers have been operated in wide band in order to benefit from larger photon rates. We analyze in this paper the biases caused by instrumental and turbulent effects to $V^2$ estimators for both narrow and wide band cases. Visibilities are estimated from samples of the interferogram using two different estimators, $V^{2}_1$ which is the classical sum of the squared modulus of Fourier components and a new estimator $V^{2}_2$ for which complex Fourier components are summed prior to taking the square. We present an approach for systematically evaluating the performance and limits of each estimator, and to optimizing observing parameters for each. We include the effects of spectral bandwidth, chromatic dispersion, scan length, and differential piston. We also establish the expression of the Signal-to-Noise Ratio of the two estimators with respect to detector and photon noise. The $V^{2}_1$ estimator is insensitive to dispersion and ...
Accelerated molecular dynamics methods: introduction and recent developments
Energy Technology Data Exchange (ETDEWEB)
Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what
Zero-bias-field microwave dynamic magnetic properties in trapezoidal ferromagnetic stripe
Bi, Mei; Wang, Xin; Lu, Haipeng; Zhang, Li; Deng, Longjiang; Xie, Jianliang
2016-06-01
Dynamic magnetization response of the axially magnetized ferromagnetic stripe with trapezoidal cross section has been studied. The stripe with beveled edges exhibits multiple resonant peaks modes under an in-plane microwave excitation compared with the single resonant of vertical edge surfaces. The complexity of the observed response is attributed to the spatially nonuniform equilibrium spin distribution at the stripe edges. Micromagnetic simulations identify spin waves as spatially localized mode at the modified edges. This one is also described by effective pinning boundary conditions taking into account finite-size effects, which is related to the exchange interaction, surface anisotropy and dipole-dipole interaction. These results provide detailed insights into the nonlinear spin dynamics of microstructures influenced by the edge properties.
Aging and emotional expressions: is there a positivity bias during dynamic emotion recognition?
Directory of Open Access Journals (Sweden)
Alberto eDi Domenico
2015-08-01
Full Text Available In this study, we investigated whether age-related differences in emotion regulation priorities influence online dynamic emotional facial discrimination. A group of 40 younger and a group of 40 older adults were invited to recognize a positive or negative expression as soon as the expression slowly emerged and subsequently rate it in terms of intensity. Our findings show that older adults recognized happy expressions faster than angry ones, while the direction of emotional expression does not seem to affect younger adults’ performance. Furthermore, older adults rated both negative and positive emotional faces as more intense compared to younger controls. This study detects age-related differences with a dynamic online paradigm and suggests that different regulation strategies may shape emotional face recognition.
Computational Studies on the Anharmonic Dynamics of Molecular Clusters
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
The effect of heart motion on parameter bias in dynamic cardiac SPECT
International Nuclear Information System (INIS)
Dynamic cardiac SPECT can be used to estimate kinetic rate parameters which describe the wash-in and wash-out of tracer activity between the blood and the myocardial tissue. These kinetic parameters can in turn be correlated to myocardial perfusion. There are, however, many physical aspects associated with dynamic SPECT which can introduce errors into the estimates. This paper describes a study which investigates the effect of heart motion on kinetic parameter estimates. Dynamic SPECT simulations are performed using a beating version of the MCAT phantom. The results demonstrate that cardiac motion has a significant effect on the blood, tissue, and background content of regions of interest. This in turn affects estimates of wash-in, while it has very little effect on estimates of wash-out. The effect of cardiac motion on parameter estimates appears not to be as great as effects introduced by photon noise and geometric collimator response. It is also shown that cardiac motion results in little extravascular contamination of the left ventricle blood region of interest
Molecular Dynamics Simulation of Carbon Nanotube Based Gears
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.
A molecular understanding of the dynamic mechanism of aquaporin osmosis
Shua, Liangsuo; Qian, Xin; Wanga, Xiyun; Lin, Yixin; Tan, Kai; Shu, Chaohui; Jin, Shiping
2014-01-01
AQPs (aquaporins), the rapid water channels of cells, play a key role in maintaining osmotic equilibrium of cells. In this paper, we reported the dynamic mechanism of AQP osmosis at the molecular level. A theoretical model based on molecular dynamics was carried out and verified by the published experimental data. The reflection coefficients ({\\sigma}) of neutral molecules are mainly decided by their relative size with AQPs, and increase with a third power up to a constant value 1. This model also indicated that the reflection coefficient of a complete impermeable solute can be smaller than 1. The H+ concentration of solution can influence the driving force of the AQPs by changing the equivalent diameters of vestibules surrounded by loops with abundant polar amino acids. In this way, pH of solution can regulate water permeability of AQPs. Therefore, an AQP may not only work as a switch to open or close, but as a rapid response molecular valve to control its water flow. The vestibules can prevent the channel b...
Li, R.; Wang, S.-Y.; Gillies, R. R.
2016-04-01
Large biases associated with climate projections are problematic when it comes to their regional application in the assessment of water resources and ecosystems. Here, we demonstrate a method that can reduce systematic biases in regional climate projections. The global and regional climate models employed to demonstrate the technique are the Community Climate System Model (CCSM) and the Weather Research and Forecasting (WRF) model. The method first utilized a statistical regression technique and a global reanalysis dataset to correct biases in the CCSM-simulated variables (e.g., temperature, geopotential height, specific humidity, and winds) that are subsequently used to drive the WRF model. The WRF simulations were conducted for the western United States and were driven with (a) global reanalysis, (b) original CCSM, and (c) bias-corrected CCSM data. The bias-corrected CCSM data led to a more realistic regional climate simulation of precipitation and associated atmospheric dynamics, as well as snow water equivalent (SWE), in comparison to the original CCSM-driven WRF simulation. Since most climate applications rely on existing global model output as the forcing data (i.e., they cannot re-run or change the global model), which often contain large biases, this method provides an effective and economical tool to reduce biases in regional climate downscaling simulations of water resource variables.
Czech Academy of Sciences Publication Activity Database
Andrushchenko, Valery; Bouř, Petr
Katowice : University of Silesia, 2014. O6. [Chemistry towards Biology. Central Europe Conference /7./. 09.09.2014-12.09.2014, Katowice] R&D Projects: GA ČR(CZ) GA14-03564S Grant ostatní: AV ČR(CZ) M200550902 Institutional support: RVO:61388963 Keywords : molecular dynamics * quantum chemistry * multi-scale spectra Subject RIV: CF - Physical ; Theoretical Chemistry
Structural and Dynamic Properties of Amorphous Silicon:Tight-Binding Molecular Dynamics Simulation
Institute of Scientific and Technical Information of China (English)
HUANG Shi-Ping; WANG Wen-Chuan
2004-01-01
@@ The tight-binding molecular dynamics simulation has been performed to study structural and dynamical properties of amorphous silicon. It is found that the radial distribution function and static structure factor are in good agreement with the experimental measurements. The bond order parameters Ql are sensitive to the structure change at different quenching rates. For the dynamical properties, we have calculated the vibration and electronic density of states. The simulation results show that the transverse acoustic is in good agreement with the experimental data, and the high frequency transverse optical (TO) peak shifts to the right of the experimental TO peak.
Study of critical dynamics in fluids via molecular dynamics in canonical ensemble.
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
Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics
Energy Technology Data Exchange (ETDEWEB)
Yu H. G.; Muckerman, J.T.
2012-05-29
The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.
DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS
JUFFER, AH; BERENDSEN, HJC
1993-01-01
A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the surfa
Molecular dynamics simulations of Pd-Ni transition metal alloys
International Nuclear Information System (INIS)
Molecular Dynamics simulations are performed to study bulk properties of fcc metals and metal alloys by using the quantum Sutton-Chen many-body potentials within the context of the tight-binding approach. The Molecular Dynamics algorithms we used in the simulations of Pd-Ni alloys are based on an extended Hamiltonian formalism arising from the works of Andersen (1980), Parinello and Rahman (1980), Nose (1984), Hoover (1985) and Cagin (1988). In these simulations, the effect of temperature and concentration on the solid and liquid properties are studied. Elastic constants and phonon dispersion relation are the solid properties we simulated in this work. Dynamic and static properties of liquid Pd-Ni are also computed by examining the behavior of density, enthalpy, pair distribution function and structure factor. The melting temperatures of Pd-Ni alloys are investigated. The diffusion coefficients are calculated from the mean square displacement using Einstein relation and from velocity auto-correlation function using Green-Kubo relations. The simulation results are in good agreement with the experiments
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
International Nuclear Information System (INIS)
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
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
International Nuclear Information System (INIS)
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
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
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.
Error and efficiency of replica exchange molecular dynamics simulations.
Rosta, Edina; Hummer, Gerhard
2009-10-28
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Kinetic theory molecular dynamics and hot dense matter: Theoretical foundations
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
Shen, Meng; Lueptow, Richard M
2016-01-01
The Angstrom-scale transport characteristics of water and six different solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polyamide reverse osmosis (RO) membrane, FT-30, using non-equilibrium molecular dynamics (NEMD) simulations. Results indicate that water transport increases with an increasing fraction of connected percolated free volume, or water-accessible open space, in the membrane polymer structure. This free volume is enhanced by the dynamic structure of the membrane at the molecular level as it swells when hydrated and vibrates due to molecular collisions allowing a continuous path connecting the opposite membrane surfaces. The tortuous paths available for transport of solutes result in Brownian motion of solute molecules and hopping from pore to pore as they pass through the polymer network structure of the membrane. The transport of alcohol solutes decreases for solutes with larger Van der Waals volume, which corresponds to less available percolated free volume, or sol...
Nanochannel flow past permeable walls via molecular dynamics
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.
Generalized master equations for exciton dynamics in molecular systems
Schreiber, Michael; May, V.
1995-02-01
The paper demonstrates the applicability of a special type of density matrix theory for the derivation of generalized Master equations. The density matrix theory has been formulated for the description of the dissipative electron transfer dynamics in molecular complexes. The theoretical approach is based on a representation of the density matrix in appropriately taken diabatic electron-vibrational states. Dissipative effects are taken into account by a coupling of these states to further vibrational modes of the molecular complex as well as to environmental degrees of freedom. The approach is applied to a two-center system as well as to a molecular chain. Memory kernels are derived in second order with respect to the inter-center coupling. The kernels are discussed under the assumption of a quick intra-center relaxation for a part of the vibrational modes as well as for all vibrational modes. Standard expressions for the transition rates between different sites are extended to include finite life times of the vibrational levels. Results which have been obtained in the study of the so-called spin boson model can be simply reproduced. The application of the derived generalized Master equations to the investigation of the motion of Frenkel excitons in molecular chains is also presented.
Recovery of saturated video signals from vidicons by dynamic cathode biasing
Yates, G. J.
1991-05-01
Vidicons used for imaging of pulsed or transient light sources must instantaneously record gray scale images on photoconductive targets. Typical targets, which store photocharge proportional to the varying light intensity in the optical image, have larger positive charge storage capacity than the negative charge available from the electron beam used for neutralizing the target during read-out. Therefore, the target has much higher dynamic range, typically 3 to 5 times larger than the beam. The result is that several scans of the target are required to obtain all the charge from a fully charged target. For applications where only one scan of the target is permissible, this can result in reading the target data in saturated form, with the loss of gray scale information. However, with dynamic rebiasing of the vidicon cathode, the data can be recovered unsaturated. This technique is extremely powerful because it allows instantaneous adjustment after the target has been exposed to light pulses but before the target is read out. In effect, a real time gain or sensitivity control function is implemented by the technique. Alternatively, the technique can be viewed as a means to dynamically select strategic portions of the vidicon transfer curve for immediate read-out, which otherwise would either be saturated if read out immediate read-out, which otherwise would either be saturated if read out immediately or would require several read-outs. Although only transient imaging applications (usually with single field read-out) are addressed, the technique should find application in conventional continuous read-write TV cameras. The principle of operation, associated circuitry, and examples of image retrieval are presented.
Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation
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.
Molecular Dynamics Simulations of Solutions at Constant Chemical Potential
Perego, Claudio; Parrinello, Michele
2015-01-01
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, that 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, that 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 C$\\mu$MD 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 C$\\mu$MD method to the paradigmatic case of urea crystall...
Molecular dynamics study of the water/n-alkane interface
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Molecular dynamics simulations on the interface between liquid water and liquid n-alkane (including octane, nonane, decane, undecane and dodecane) have been performed with the purpose to study the interfacial properties: (Ⅰ) density profile; (Ⅱ) molecular orientation; (Ⅲ) interfacial tension and the temperature effect on the interfacial tension. Simulation results show that at the interface the structures of both water and n-alkane are different from those in the bulk. Water has an orientational preference due to the number of hydrogen bonds per molecule maximized. N-alkane has a more lateral orientation with respect to the interface in order to be in close contact with water. The calculated individual phase bulk density and interfacial tension of water/n-alkane systems are in good agreement with the corresponding experimental ones.
Sugar transport across lactose permease probed by steered molecular dynamics
DEFF Research Database (Denmark)
Jensen, Morten Østergaard; Yin, Ying; Tajkhorshid, Emad;
2007-01-01
Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic......, forcing it to interact with channel lining residues. Lactose forms a multitude of direct sugar-channel hydrogen bonds, predominantly with residues of the flexible N-domain, which is known to contribute a major part of LacY's affinity for lactose. In the periplasmic half-channel lactose predominantly......-sugar interaction maximal. Upon unbinding from the binding pocket, lactose undergoes a rotation to permeate either half-channel with its long axis aligned parallel to the channel axis. The results hint at the possibility of a transport mechanism, in which lactose permeates LacY through a narrow periplasmic half...
Molecular Dynamics Simulations of Homogeneous Crystallization in Polymer Melt
Kong, Bin
2015-03-01
Molecular mechanisms of homogeneous nucleation and crystal growth from the melt of polyethylene-like polymer were investigated by molecular dynamics simulations. The crystallinity was determined by using the site order parameter method (SOP), which described local order degree around an atom. Snapshots of the simulations showed evolution of the nucleation and the crystal growth through SOP images clearly. The isothermal crystallization kinetics was determined at different temperatures. The rate of crystallization, Kc, and the Avrami exponents, n, were determined as a function of temperature. The forming of nucleis was traced to reveal that the nucleis were formed with more ordered cores and less ordered shells. A detailed statistical analysis of the MD snapshots and trajectories suggested conformations of the polymer chains changed smoothly from random coil to chain folded lamella in the crystallization processes.
Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar
This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining...... the system size of the simulation box generally used in simulation. Therefore, a method is developed for extending the RDFs to arbitrary distances so that the integrals can be evaluated. The method, which was first used in the classical study of the Lennard-Jones fluid by Verlet (Verlet (1968), Phys. Rev...
Classical molecular dynamics investigations of biphenyl-based carbon nanomembranes
Directory of Open Access Journals (Sweden)
Andreas Mrugalla
2014-06-01
Full Text Available Background: Free-standing carbon nanomembranes (CNM with molecular thickness and macroscopic size are fascinating objects both for fundamental reasons and for applications in nanotechnology. Although being made from simple and identical precursors their internal structure is not fully known and hard to simulate due to the large system size that is necessary to draw definite conclusions.Results: We performed large-scale classical molecular dynamics investigations of biphenyl-based carbon nanomembranes. We show that one-dimensional graphene-like stripes constitute a highly symmetric quasi one-dimensional energetically favorable ground state. This state does not cross-link. Instead cross-linked structures are formed from highly excited precursors with a sufficient amount of broken phenyls.Conclusion: The internal structure of the CNM is very likely described by a disordered metastable state which is formed in the energetic initial process of electron irradiation and depends on the process of relaxation into the sheet phase.
Institute of Scientific and Technical Information of China (English)
张莉莉; 张建华; 周林祥
2002-01-01
We have carried out parallel molecular dynamics simulations of solvated and non-solvated myoglobin and solvated Cu/Zn superoxide dismutase at different temperatures. By analysis of several methods, the simulations reproduce the quasielastic neutron scattering experimental results. Below 200 K these two proteins behave as harmonic solids with essentially only vibrational motion, while above this temperature, there is a striking dynamic transition into anharmonic motion. Moreover, the simulations further show that water molecules play an important role for this dynamical transition. There is no such sharp dynamical transition in non-solvated proteins and the higher the solvate density is, the steeper at transition point the curve of mean square displacement versus temperature will be. The simulations also display that the dynamical transition is a general property for globular protein and this transition temperature is a demarcation of enzyme activity.
Ito, Hiroaki; Shimokawa, Naofumi
2016-01-01
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the p...
Directory of Open Access Journals (Sweden)
Jeffrey A Hussmann
2015-12-01
Full Text Available Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs. These snapshots can be used to make inferences about translation dynamics. Recent ribosome profiling studies in yeast, however, have reached contradictory conclusions regarding the average translation rate of each codon. Some experiments have used cycloheximide (CHX to stabilize ribosomes before measuring their positions, and these studies all counterintuitively report a weak negative correlation between the translation rate of a codon and the abundance of its cognate tRNA. In contrast, some experiments performed without CHX report strong positive correlations. To explain this contradiction, we identify unexpected patterns in ribosome density downstream of each type of codon in experiments that use CHX. These patterns are evidence that elongation continues to occur in the presence of CHX but with dramatically altered codon-specific elongation rates. The measured positions of ribosomes in these experiments therefore do not reflect the amounts of time ribosomes spend at each position in vivo. These results suggest that conclusions from experiments in yeast using CHX may need reexamination. In particular, we show that in all such experiments, codons decoded by less abundant tRNAs were in fact being translated more slowly before the addition of CHX disrupted these dynamics.
Indian Academy of Sciences (India)
Shubin Liu
2005-09-01
Dynamic behaviors of chemical concepts in density functional theory such as frontier orbitals (HOMO/LUMO), chemical potential, hardness, and electrophilicity index have been investigated in this work in the context of Bohn-Oppenheimer quantum molecular dynamics in association with molecular conformation changes. Exemplary molecular systems like CH$^{+}_{5}$ , Cl- (H2O)30 and Ca2+ (H2O)15 are studied at 300 K in the gas phase, demonstrating that HOMO is more dynamic than LUMO, chemical potential and hardness often fluctuate concurrently. It is argued that DFT concepts and indices may serve as a good framework to understand molecular conformation changes as well as other dynamic phenomena.
Molecular dynamics simulation of DPPC bilayer in DMSO.
Smondyrev, A M; Berkowitz, M L
1999-01-01
We performed molecular dynamics simulations on dipalmitoylphosphatidylcholine (DPPC)/dimethylsulfoxide (DMSO) system that has the same lipid:solvent weight ratio as in our previous simulation done on DPPC/water. We did not observe a large change in the size of DPPC membrane when the solvent was changed from water to DMSO. Also, we did not observe that a large number of DMSO molecules is permeating into the membrane, as it was suggested to explain the observed change in the bilayer repeat peri...
Porting of serial molecular dynamics code on MIMD platforms
International Nuclear Information System (INIS)
A molecular Dynamics (MD) code, utilized for the study of atomistic models of metallic systems has been parallelized for MIMD (Multiple Instructions Multiple Data) parallel platforms by means of the Parallel Virtual Machine (PVM) message passing library. Since the parallelization implies modifications of the sequential algorithms, these are described from the point of view of the Statistical Mechanics theory. Furthermore, techniques and parallelization strategies utilized and the MD parallel code are described in detail. Benchmarks on several MIMD platforms (IBM SP1 and SP2, Cray T3D, Cluster of workstations) allow performances evaluation of the code versus the different characteristics of the parallel platforms
Higher-order symplectic Born-Oppenheimer molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Niklasson, Anders [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, Matt [Los Alamos National Laboratory; Odell, Anders [RIT; Delin, Anna [RIT; Johansson, Borje [RIT
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.
Molecular dynamics calculations for sodium using pseudopotential theory
International Nuclear Information System (INIS)
The equation of state of sodium is studied using the molecular dynamics technique whereby the classical motion of a system of ions is solved with the aid of computers. The interaction potential between pairs of sodium ions consists of Coulomb and Born-Mayer repulsion terms and an effective ion-ion interaction derived from pseudopotential theory. This theory includes the effects of electron gas screening, exchange, and correlation. A model pseudopotential with parameters fit to experimental low-temperature data is used. By using this technique, an atomic description of a simple metal proceeds to the calculation of macroscopic thermodynamic properties
A molecular dynamics study of freezing in a confined geometry
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.
Generalized extended Lagrangian Born-Oppenheimer molecular dynamics
International Nuclear Information System (INIS)
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
Molecular dynamics simulations of oscillatory flows in microfluidic channels
DEFF Research Database (Denmark)
Hansen, J.S.; Ottesen, Johnny T.
2006-01-01
In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system with...
Simulation of a flowing snow avalanche using molecular dynamics
Güçer, Denizhan; ÖZGÜÇ, Halil Bülent
2014-01-01
This paper presents an approach for the modeling and simulation of a flowing snow avalanche, which is formed of dry and liquefied snow that slides down a slope, using molecular dynamics and the discrete element method. A particle system is utilized as a base method for the simulation and marching cubes with real-time shaders are employed for rendering. A uniform grid-based neighbor search algorithm is used for collision detection for interparticle and particle-terrain interactions. A mass-spr...
Metal cluster fission: jellium model and Molecular dynamics simulations
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia;
2004-01-01
^2+ --> 2 Na_9^+ are presented. Dependence of the fission barriers on isomer structure of the parent cluster is analyzed. Importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster......Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...
Nonlinear rotor dynamics of 2D molecular array: topology reconstruction
International Nuclear Information System (INIS)
Molecular layers with rotational degrees of freedom and quadrupolar interaction between linear molecules are investigated theoretically. We found earlier that alternative orientation of the molecules along and perpendicular to an axis of the rectangular lattice is preferable. Here we find the integral of motion and give the topology analysis of the possible dynamical phases and special points in the long-wave limit. We find the strong anisotropy in the angle space: directions of easy excitation ('valleys') exist. We show the potential relief reconstruction in dependence on the adsorbed lattice anisotropy.
Large scale molecular dynamics modeling of materials fabrication processes
Energy Technology Data Exchange (ETDEWEB)
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.
Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics
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.
Molecular dynamics computer simulations based on NMR data
International Nuclear Information System (INIS)
In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs
Molecular dynamics of MgSiO3 perovskite melting
Institute of Scientific and Technical Information of China (English)
Liu Zi-Jiang; Cheng Xin-Lu; Yang Xiang-Dong; Zhang Hong; Cai Ling-Cang
2006-01-01
The melting curve of MgSiO3 perovskite is simulated using molecular dynamics simulations method at high pressure. It is shown that the simulated equation of state of MgSiO3 perovskite is very successful in reproducing accurately the experimental data. The pressure dependence of the simulated melting temperature of MgSiO3 perovskite reproduces the stability of the orthorhombic perovskite phase up to high pressure of 13OGPa at ambient temperature, consistent with the theoretical data of the other calculations. It is shown that its transformation to the cubic phase and melting at high pressure and high temperature are in agreement with recent experiments.
Simulations of boundary migration during recrystallization using molecular dynamics
DEFF Research Database (Denmark)
Godiksen, Rasmus Brauner; Trautt, Z.T.; Upmanyu, M.;
2007-01-01
We have applied an atomistic simulation methodology based on molecular dynamics to study grain boundary migration in crystalline materials, driven by the excess energy of dislocation arrangements. This method is used to simulate recrystallization in metals. The simulations reveal that the migration...... process is not uniform as assumed in many recrystallization models, but that the grain boundaries migrate in an irregular fashion and exhibit a strong dependence on the local presence of dislocations, which can distort the local migration process significantly. (c) 2007 Acta Materialia Inc. Published...
Molecular dynamics simulation of Ni3Al melting
Institute of Scientific and Technical Information of China (English)
Rongshan Wang; Huaiyu Hou; Xiaodong Ni; Guoliang Chen
2008-01-01
With the Voter-Chert version of embedded-atom model (EAM) potential and molecular dynamics, the melting of Ni3A1 alloy was simulated by one-phase (conventional) and two-phase approaches. It is shown that the simulated melting point is dependent on the potential and the simulation method. The structures of the melts obtained by different simulation methods were analyzed by the pair correlation function, the coordination number, and the distribution of atom pair type (indexed by the Honeycutt-Andersen pair analysis technique). The results show that the structures are very similar.
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
Wang, Yi; Markwick, Phineus R.L.; de Oliveira, César Augusto F.; McCammon, J. Andrew
2011-01-01
Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC bilayer. Overall, the aMD simulations are found to produce significant speedup in trans–gauche isome...
Molecular nonlinear dynamics and protein thermal uncertainty quantification
Energy Technology Data Exchange (ETDEWEB)
Xia, Kelin [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States)
2014-03-15
This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction.
Testing the method of crystallographic refinement using molecular dynamics
International Nuclear Information System (INIS)
The method of crystallographic refinement using molecular dynamics has been implemented to work with the GROMOS simulation package. It has been tested by applying it to the structure of phospholipase A2. The structure of this molecule had previously been refined at high resolution with conventional methods. The new method successfully refined the initial multi-isomorphous replacement structure, removing most of the errors, without any manual intervention. All the refinement was performed at 300 K. The use of lower-resolution data allows greater conformational transitions to occur whereas the inclusion of high-resolution data results in a more accurate structure. (orig.)
Ti and Zr surfaces studied by molecular dynamics
International Nuclear Information System (INIS)
The interaction between point defects technique and the (0001), (1-210), (10-10) surfaces in Ti and Zr is studied by the molecular dynamics technique. Both of metals are in the hexagonal structure and within a temperature range of 100 to 900 K. The atomic interactions are modeled by EAM-type many-body potentials, that were used previously in static simulations. New migration mechanisms are unraveled and others are verified with respect to those already proposed in the static studies. Also included is an analysis of the vacancy stability in the sub-surface layers of the prismatic surfaces. (author)
Molecular dynamic study of pressure fluctuations spectrum in plasma
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.
A Direct Two-Dimensional Pressure Formulation in Molecular Dynamics
YD, Sumith
2016-01-01
Two-dimensional (2D) pressure field estimation in molecular dynamics (MD) simulations has been done using three-dimensional (3D) pressure field calculations followed by averaging, which is computationally expensive due to 3D convolutions. In this work, we develop a direct 2D pressure field estimation method which is much faster than 3D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor.
Easy creation of polymeric systems for molecular dynamics with Assemble!
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.
The A = 8 isotriplet in Fermionic Molecular Dynamics
Henninger, KR
2016-06-01
Nuclear structure of the A = 8 isotriplet is investigated in the Fermionic Molecular Dynamics (FMD) model. All three nuclei have importance to astrophysics, and exhibit clustering or haloes. FMD uses a wave-packet basis and is well-suited for modelling such structures. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo in 8B, and reasonable reproduction of the T =1 states in 8Be.
Molecular Dynamics Simulations of Field Emission From a Planar Nanodiode
Torfason, Kristinn; Manolescu, Andrei
2014-01-01
High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.
Ratchet dynamics of large polarons in asymmetric diatomic molecular chains.
Brizhik, L.; Eremko, A.; Piette, B.; Zakrzewski, W. J.
2010-01-01
We study the dynamics of large polarons in diatomic molecular chains, at zero temperature, under the influence of an external, periodic in time, electric field of zero mean value. We show that in asymmetric chains, i.e. chains with two different atoms per unit cell, a harmonic unbiased field causes a drift of such polarons. Such a drift current, known as the ratchet phenomenon, depends strongly on the parameters of the chain; in particular, on the extent of the anisotropy of the chain and on ...
Quantum Trajectory Approach to Molecular Dynamics Simulation with Surface Hopping
International Nuclear Information System (INIS)
In this work we propose a quantum trajectory approach to the powerful molecular dynamics simulation with surface hopping, from an insight that an effective ''observation'' is actually implied in the simulation through tracking the forces experienced, just like checking the meter's result in quantum measurement process. This treatment can build the nonadiabatic surface hopping on a physical foundation, instead of the usual fictitious and conceptually inconsistent hopping algorithms. The effects and advantages of the proposed scheme are preliminarily illustrated by a two-surface model system. (general)
Molecular dynamics simulation of hollow thick-walled cylinder collapse
International Nuclear Information System (INIS)
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
Molecular dynamic simulation for laser-cluster interaction
International Nuclear Information System (INIS)
A three dimensional relativistic molecular dynamic model for studying the laser interaction with atomic clusters is presented. The model is used to simulate the interaction dynamics of deuterium, argon, and xenon clusters when irradiated by the short and high intensity laser pulses. The interaction of 82 A argon cluster by 100 fs, 806 nm laser pulse with the peak intensity of 8 x 1015 W/cm2 is studied and compared with the experimental results. The maximum ion energy in this case is found to be about 200 keV. Ion energies along and perpendicular to laser polarization direction is calculated and asymmetry along laser polarization direction is detected which is further explained on the basis of charge flipping model. The effect of cluster density on the energetics of the laser-cluster interaction is also being studied, which provides a qualitative understanding of the presence of optimum cluster size for maximum ion energies.
Molecular dynamics simulations of detonation on the roadrunner supercomputer
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.
Molecular dynamics simulation of radiation damage cascades in diamond
Energy Technology Data Exchange (ETDEWEB)
Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)
2015-06-28
Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.
Molecular dynamics simulation of radiation damage cascades in diamond
International Nuclear Information System (INIS)
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%
Molecular dynamics with coupling to an external bath
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R.
1984-10-01
In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints. The influence of coupling time constants on dynamical variables is evaluated. A leap-frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath.
Molecular dynamics simulations of cluster fission and fusion processes
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia;
2004-01-01
groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual......Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...
Haptization of molecular dynamics simulation with thermal display
International Nuclear Information System (INIS)
Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)
Spontaneous alloying in binary metal microclusters: A molecular dynamics study
International Nuclear Information System (INIS)
Microcanonical molecular-dynamics study of spontaneous alloying (SA), which is a manifestation of fast atomic diffusion in a nanosized metal cluster, is done in terms of a simple two-dimensional binary Morse model. Important features observed by Yasuda and Mori are well reproduced in our simulation. The temperature dependence and size dependence of SA phenomena are extensively explored by examining long-time dynamics. The dominant role of negative heat of solution in completing SA is also discussed. We point out that a presence of melting surface induces the diffusion of core atoms even if they are solidlike. In other words, the surface melting at substantially low temperature plays a key role in attaining SA
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
Energy Technology Data Exchange (ETDEWEB)
Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)
1994-12-31
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
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
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
2013-03-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations
Kastner, Oliver
2012-01-01
Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and covers thermodynamical, micro-mechanical and crystallographical aspects. It addresses scientists in these research fields and thei...
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
International Nuclear Information System (INIS)
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
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
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.
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
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
Tóth, László; Fekete, Attila; Balogh, Gábor; Bereczky, Zsuzsanna; Komáromi, István
2015-09-01
While antithrombin (AT) has small basal inhibitory activity, it reaches its full inhibitory potential against activated blood coagulation factors, FXa, FIXa, and FIIa (thrombin), via an allosteric and/or template (bridging) mechanism by the action of heparin, heparan sulfate, or heparin-mimetic pentasaccharides (PS). From the numerous X-ray structures available for different conformational states of AT, only indirect and incomplete conclusions can be drawn on the inherently dynamic properties of AT. As a typical example, the basal inhibitory activity of AT cannot be interpreted on the basis of "non-activated" free antithrombin X-ray structures since the Arg393 side chain, playing crucial role in antithrombin-proteinase interaction, is not exposed. In order to reveal the intrinsic dynamic properties and the reason of basal inhibitory activity of antithrombin, 2 μs molecular dynamics simulations were carried out on its native free-forms. It was shown from the simulation trajectories that the reactive center loop which is functioning as "bait" for proteases, even without any biasing potential can populate conformational state in which the Arg393 side chain is solvent exposed. It is revealed from the trajectory analysis that the peptide sequences correspond to the helix D extension, and new helix P formation can be featured with especially large root-mean-square fluctuations. Mutual information analyses of the trajectory showed remarkable (generalized) correlation between those regions of antithrombin which changed their conformations as the consequence of AT-PS complex formation. This suggests that allosteric information propagation pathways are present even in the non-activated native form of AT. PMID:25483839
Pulmonary ventilation: dynamic MRI with inhalation of molecular oxygen
International Nuclear Information System (INIS)
We have recently demonstrated a non-invasive technique to visualize pulmonary ventilation in humans with inhalation of molecular oxygen as a paramagnetic contrast agent. In the current study, T1 shortening of lung tissue by inhalation of oxygen was observed (P2) in a pig, resulting in excellent correlation (r2=0.997). Dynamic wash-in and wash-out MR ventilation images as well as dynamic wash-in wash-out signal intensity versus time curves were obtained. The mean wash-in decay constants were 26.8±10.5 s in the right lung, and 26.3±9.5 s in the left lung. The mean wash-out decay constants were 23.3±11.3 s in the right lung, and 20.8±10.5 s in the left lung. Dynamic assessment of pulmonary ventilation is feasible using oxygen-enhanced MR imaging, which could provide dynamic MR ventilation-perfusion imaging in combination with recently developed MR perfusion imaging technique, and thus a robust tool for the study of pulmonary physiology and pathophysiology
Pulmonary ventilation: dynamic MRI with inhalation of molecular oxygen
Energy Technology Data Exchange (ETDEWEB)
Hatabu, Hiroto E-mail: hatabu@oasis.rad.upenn.edu; Tadamura, Eiji; Chen Qun; Stock, Klaus W.; Li, Wei; Prasad, Pottumarthi V.; Edelman, Robert R
2001-03-01
We have recently demonstrated a non-invasive technique to visualize pulmonary ventilation in humans with inhalation of molecular oxygen as a paramagnetic contrast agent. In the current study, T1 shortening of lung tissue by inhalation of oxygen was observed (P<0.001). The T1 values of lung tissue were also correlated with arterial blood oxygen pressure (PaO{sub 2}) in a pig, resulting in excellent correlation (r{sup 2}=0.997). Dynamic wash-in and wash-out MR ventilation images as well as dynamic wash-in wash-out signal intensity versus time curves were obtained. The mean wash-in decay constants were 26.8{+-}10.5 s in the right lung, and 26.3{+-}9.5 s in the left lung. The mean wash-out decay constants were 23.3{+-}11.3 s in the right lung, and 20.8{+-}10.5 s in the left lung. Dynamic assessment of pulmonary ventilation is feasible using oxygen-enhanced MR imaging, which could provide dynamic MR ventilation-perfusion imaging in combination with recently developed MR perfusion imaging technique, and thus a robust tool for the study of pulmonary physiology and pathophysiology.
Biases and improvements in three dynamical downscaling climate simulations over China
Yang, Hao; Jiang, Zhihong; Li, Laurent
2016-02-01
A dynamical downscaling is performed to improve the regional climate simulation in China. It consists of using a variable resolution model LMDZ4 nested into three global climate models (GCMs): BCC-csm1-1-m, FGOALS-g2 and IPSL-CM5A-MR, respectively. The regional climate from different simulations is assessed in terms of surface air temperature and rainfalls through a comparison to observations (both station data and gridded data). The comparison includes climatic trends during the last 40 years, statistical distribution of sub-regional climate, and the seasonal cycle. For surface air temperature, a significant part of the improvement provided by LMDZ4 is related to the effect of surface elevation which is more realistic in high-resolution simulations; the rest is related to changes in regional or local atmospheric general circulation. All GCMs and the downscaling model LMDZ4 are, more or less, able to describe the spatial distribution of surface air temperature and precipitation in China. LMDZ4 does show its superiority, compared to GCMs, in depicting a good regional terrain including the Tibetan Plateau, the Sichuan Basin and the Qilian Mountains.
Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways.
Wang, Lee-Ping; McGibbon, Robert T; Pande, Vijay S; Martinez, Todd J
2016-02-01
We describe a flexible and broadly applicable energy refinement method, "nebterpolation," for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation. The new method is applicable to ab initio simulations with hundreds of atoms containing complex and multimolecular reaction events. A key aspect of nebterpolation is smoothing of the reactive MD trajectory in internal coordinates to initiate the search for the reaction path on the potential energy surface. We apply nebterpolation to analyze the reaction events in an ab initio nanoreactor simulation that discovers new molecules and mechanisms, including a C-C coupling pathway for glycolaldehyde synthesis. We find that the new method, which incorporates information from the MD trajectory that connects reactants with products, produces a dramatically distinct set of minimum energy paths compared to existing approaches that start from information for the reaction end points alone. The energy refinement method described here represents a key component of an emerging simulation paradigm where molecular dynamics simulations are applied to discover the possible reaction mechanisms. PMID:26683346
Huge-scale Molecular Dynamics Simulation of Multibubble Nuclei
Watanabe, Hiroshi; Ito, Nobuyasu
2012-01-01
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can b...
Rigid-body molecular dynamics of DNA inside a nucleosome.
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
Quantum Thermal Bath for Path Integral Molecular Dynamics Simulation.
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. PMID:26799437
Kinetic distance and kinetic maps from molecular dynamics simulation.
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. PMID:26574285
Molecular dynamics simulations through GPU video games technologies
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.
Step by step parallel programming method for molecular dynamics code
International Nuclear Information System (INIS)
Parallel programming for a numerical simulation program of molecular dynamics is carried out with a step-by-step programming technique using the two phase method. As a result, within the range of a certain computing parameters, it is found to obtain parallel performance by using the level of parallel programming which decomposes the calculation according to indices of do-loops into each processor on the vector parallel computer VPP500 and the scalar parallel computer Paragon. It is also found that VPP500 shows parallel performance in wider range computing parameters. The reason is that the time cost of the program parts, which can not be reduced by the do-loop level of the parallel programming, can be reduced to the negligible level by the vectorization. After that, the time consuming parts of the program are concentrated on less parts that can be accelerated by the do-loop level of the parallel programming. This report shows the step-by-step parallel programming method and the parallel performance of the molecular dynamics code on VPP500 and Paragon. (author)
GPU-enabled molecular dynamics simulations of ankyrin kinase complex
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.