Nonadiabatic Molecular Dynamics Based on Trajectories
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.
Towards the molecular bases of polymerase dynamics
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
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.
Accelerating convergence of molecular dynamics-based structural relaxation
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...
Classical molecular dynamics investigations of biphenyl-based carbon nanomembranes
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.
Molecular dynamics study of surfactant-like peptide based nanostructures.
Colherinhas, Guilherme; Fileti, Eudes
2014-10-23
Surfactant-like peptide (SLP) based nanostructures are investigated using all-atomistic molecular dynamics (MD) simulations. We report structure properties of nanostructures belonging to the ANK peptide group. In particular, the mathematical models for the two A3K membranes, A6K nanotube, and A9K nanorod were developed. Our MD simulation results are consistent with the experimental data, indicating that A3K membranes are stable in two different configurations: (1) SLPs are tilted relative to the normal membrane plane; (2) SLPs are interdigitated. The former configuration is energetically more stable. The cylindrical nanostructures feature a certain order of the A6K peptides. In turn, the A9K nanorod does not exhibit any long-range ordering. Both nanotube and nanorod structure contain large amounts of water inside. Consequently, these nanostructures behave similar to hydrogels. This property may be important in the context of biotechnology. Binding energy analysis-in terms of Coulomb and van der Waals contributions-unveils an increase as the peptide size increases. The electrostatic interaction constitutes 70-75% of the noncovalent attraction energy between SLPs. The nanotubular structures are notably stable, confirming that A6K peptides preferentially form nanotubes and A9K peptides preferentially form nanorods. PMID:25264942
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.
Molecular dynamics computer simulations based on NMR data
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
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.
Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture
Wei Feng
2014-07-01
Full Text Available Mixed-quantum-classical molecular dynamics simulation implies an effective quantum measurement on the electronic states by the classical motion of atoms. Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.
Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios
2015-12-01
We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.
We investigated the characteristics of a capacitive nano-accelerometer based on a telescoping carbon nanotube by means of classical molecular dynamics simulations. The position of the telescoping nanotube was controlled by an externally applied force, and feedback sensing was based on the capacitance change. The capacitance variations, which were almost linearly proportional to the applied acceleration, were monitored within an error tolerance
Molecular diagnostics based on clustering dynamics of magnetic nanobeads
Donolato, Marco; Bejhed, Rebecca S.; de la Torre, Teresa Zardán Gómez;
2014-01-01
polymerase chain reaction (PCR) [1]. In this work we demonstrate detection of DNA coils formed from a Vibrio Cholerae DNA target at pM concentrations using a novel opto-magnetic approach exploiting the dynamic collective behavior of magnetic nanobeads. The technique relies on measurements of the light...... isothermal rolling circle amplification from Vibrio cholerae DNA. The detection method is shown in Figure 1. MNBs which specifically bind to the micrometric sized DNA coil cannot rotate under the field action as free beads and form chains; this results in a strongly modified opto-magnetic signal. As a core...
Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions
Fattebert, J.-L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Richards, D.F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Glosli, J.N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2012-12-01
We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·10^{6} particles on 65,536 MPI tasks.
Molecular group dynamics study on slip flow of thin fluid film based on the Hamaker hypotheses
无
2010-01-01
The thin fluid film was assumed to consist of a number of spherical fluid molecular groups and the attractive forces of molecular group pairs were calculated by the derived equation according to the three Hamaker homogeneous material hypotheses. Regarding each molecular group as a dynamics individual, the simulation method for the shearing motion of multilayer fluid molecular groups, which was initiated by two moving walls, was proposed based on the Verlet velocity iterative algorithm. The simulations reveal that the velocities of fluid molecular groups change about their respective mean velocities within a narrow range in steady state. It is also found that the velocity slips occur at the wall boundary and in a certain number of fluid film layers close to the wall. Because the dimension of molecular group and the number of group layers are not restricted, the hypothetical thickness of fluid film model can be enlarged from nanometer to micron by using the proposed simulation method.
Ab initio based force field and molecular dynamics simulations of crystalline TATB.
Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E
2004-04-15
An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608
Curchod, Basile F E; Tavernelli, Ivano; Rothlisberger, Ursula
2011-02-28
The non-relativistic quantum dynamics of nuclei and electrons is solved within the framework of quantum hydrodynamics using the adiabatic representation of the electronic states. An on-the-fly trajectory-based nonadiabatic molecular dynamics algorithm is derived, which is also able to capture nuclear quantum effects that are missing in the traditional trajectory surface hopping approach based on the independent trajectory approximation. The use of correlated trajectories produces quantum dynamics, which is in principle exact and computationally very efficient. The method is first tested on a series of model potentials and then applied to study the molecular collision of H with H(2) using on-the-fly TDDFT potential energy surfaces and nonadiabatic coupling vectors. PMID:21264437
Orbital free molecular dynamics
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)
Modeling of Car-Following Required Safe Distance Based on Molecular Dynamics
Dayi Qu; Xiufeng Chen; Wansan Yang; Xiaohua Bian
2014-01-01
In car-following procedure, some distances are reserved between the vehicles, through which drivers can avoid collisions with vehicles before and after them in the same lane and keep a reasonable clearance with lateral vehicles. This paper investigates characters of vehicle operating safety in car following state based on required safe distance. To tackle this problem, we probe into required safe distance and car-following model using molecular dynamics, covering longitudinal and lateral safe...
Kinetic Energy-Based Temperature Computation in Non-Equilibrium Molecular Dynamics Simulation
Liu, Bin; Xu, Ran; He, Xiaoqiao
2009-01-01
The average kinetic energy is widely used to characterize temperature in molecular dynamics (MD) simulation. In this letter, the applicability of three types of average kinetic energy as measures of temperature is investigated, i.e., the total kinetic energy, kinetic energy without the centroid translation part, and thermal disturbance kinetic energy. Our MD simulations indicate that definitions of temperature based on the kinetic energy including rigid translational or rotational motion may ...
Hydration of methanol in water. A DFT-based molecular dynamics study
Van Erp, T S; Erp, Titus S. van; Meijer, Evert Jan
2000-01-01
We studied the hydration of a single methanol molecule in aqueous solution by first-principle DFT-based molecular dynamics simulation. The calculations show that the local structural and short-time dynamical properties of the water molecules remain almost unchanged by the presence of the methanol, confirming the observation from recent experimental structural data for dilute solutions. We also see, in accordance with this experimental work, a distinct shell of water molecules that consists of about 15 molecules. We found no evidence for a strong tangential ordering of the water molecules in the first hydration shell.
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.
Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
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
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 ...
Polymer friction Molecular Dynamics
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....
Zhang, Peng; Gao, Chao; Zhang, Na; Slepian, Marvin J.; Deng, Yuefan; Bluestein, Danny
2014-01-01
We developed a multiscale particle-based model of platelets, to study the transport dynamics of shear stresses between the surrounding fluid and the platelet membrane. This model facilitates a more accurate prediction of the activation potential of platelets by viscous shear stresses - one of the major mechanisms leading to thrombus formation in cardiovascular diseases and in prosthetic cardiovascular devices. The interface of the model couples coarse-grained molecular dynamics (CGMD) with dissipative particle dynamics (DPD). The CGMD handles individual platelets while the DPD models the macroscopic transport of blood plasma in vessels. A hybrid force field is formulated for establishing a functional interface between the platelet membrane and the surrounding fluid, in which the microstructural changes of platelets may respond to the extracellular viscous shear stresses transferred to them. The interaction between the two systems preserves dynamic properties of the flowing platelets, such as the flipping motion. Using this multiscale particle-based approach, we have further studied the effects of the platelet elastic modulus by comparing the action of the flow-induced shear stresses on rigid and deformable platelet models. The results indicate that neglecting the platelet deformability may overestimate the stress on the platelet membrane, which in turn may lead to erroneous predictions of the platelet activation under viscous shear flow conditions. This particle-based fluid-structure interaction multiscale model offers for the first time a computationally feasible approach for simulating deformable platelets interacting with viscous blood flow, aimed at predicting flow induced platelet activation by using a highly resolved mapping of the stress distribution on the platelet membrane under dynamic flow conditions. PMID:25530818
Yoshida, Hiroaki
2016-01-01
In this paper we investigate the hydrodynamic permeance of water through graphene-based membranes, inspired by recent experimental findings on graphene-oxide membranes. We consider the flow across multiple graphene layers having nanoslits in a staggered alignment, with an inter-layer distance ranging from sub- nanometer to a few nanometers. We compare results for the permeability obtained by means of molecular dynamics simulations to continuum predictions obtained by using the lattice Boltzmann calculations and hydrodynamic modelization. This highlights that, in spite of extreme confinement, the permeability across the graphene-based membrane is quantitatively predicted on the basis of a continuum expression, taking properly into account entrance and slippage effects of the confined water flow. Our predictions refute the breakdown of hydrodynamics at small scales in these membrane systems. They constitute a benchmark to which we compare published experimental data.
Molecular dynamics method is used for the properties prediction of new lanthanum-strontium cuprates La2-xSrxCuO4-δ based functional materials. The most interesting phases have been synthesized, and electrophysical and thermomechanical properties have been investigated for the verification of acquired calculated data. High values of oxygen diffusion constants is demonstrated to be occurred in solid solutions La2-xSrxCuO4-δ with fine degree of substitution Sr→La (to x=1). Values of lattice parameters, thermal expansion coefficients and oxygen diffusion constants are agree with experimental data. Observed anisotropy of anion transport for all studied compositions is responsible for peculiarities of crystal structure of complex oxides. Applied molecular dynamics method permits to reveal the contribution of separate kinds of oxygen ions (equatorial and apical) in ionic transport at microscopic level, as well as really prove that the oxygen diffusion happens in the ordinary jump mechanism, mainly in (CuO2)-layers
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.
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
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.)
Detection of molecular charge dynamics through current noise in a GaAs-based nanowire FET
Inoue, Shinya; Kuroda, Ryota; Yin, Xiang; Sato, Masaki; Kasai, Seiya
2015-04-01
The detection of static and dynamic molecular charge states using a GaAs-based nanowire field-effect transistor (FET) was investigated. Tetraphenylporphyrin (TPP) was put on the device as target molecules. After coating TPP on the FET, the drain current clearly decreased. On the other hand, the current largely increased by 405-nm light irradiation, indicating that TPP worked as a photo-excited donor. The light irradiation on the FET also induced a Lorentzian noise component, which was superimposed onto conventional 1/f noise. These behaviors were not seen in the gateless nanowire even with TPP. The obtained results indicated that electrical interaction between TPP and the nanowire was enhanced when a metal gate existed, although the channel was protected from TPP by the gate metal. We discuss the observed behaviors on the basis of a model where only TPP in the gate periphery modulated the channel potential and the drain current.
Molecular dynamics simulations are performed to verify the deformation characteristics of grain boundaries on the AFM-based nanolithography. The model used has about 750,000 (Cu) atoms and is composed of two different crystal orientations. The grain boundaries are located in the center of model and have 45, 90, 135, and -135 degree angles in the xz-plane. The tool is made of rigid diamond-like carbon and is in the shape of the Berkovich indenter. The simulation has four different stages: relaxation, indentation, re-relaxation, and lithography. The simulation results reveal that the lithography deforms the grain boundary shape by the tool. The deformation of grain boundary's angle proceeds to minimize the total potential energy of whole system. Consequently, the grain boundary angle is changed about 90 degrees
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
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.
Srivastava, Deepak; Saini, Subhash (Technical Monitor)
1998-01-01
The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.
Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li
2015-03-01
It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-Methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al. We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C =C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.
Molecular Dynamics Study of Stability and Diffusion of Graphene-Based Drug Delivery Systems
Xiunan Wang
2015-01-01
Full Text Available Graphene, a two-dimensional nanomaterial with unique biomedical properties, has attracted great attention due to its potential applications in graphene-based drug delivery systems (DDS. In this work graphene sheets with various sizes and graphene oxide functionalized with polyethylene glycol (GO-PEG are utilized as nanocarriers to load anticancer drug molecules including CE6, DOX, MTX, and SN38. We carried out molecular dynamics calculations to explore the energetic stabilities and diffusion behaviors of the complex systems with focuses on the effects of the sizes and functionalization of graphene sheets as well as the number and types of drug molecules. Our study shows that the binding of graphene-drug complex is favorable when the drug molecules and finite graphene sheets become comparable in sizes. The boundaries of finite sized graphene sheets restrict the movement of drug molecules. The double-side loading often slows down the diffusion of drug molecules compared with the single-side loading. The drug molecules bind more strongly with GO-PEG than with pristine graphene sheets, demonstrating the advantages of functionalization in improving the stability and biocompatibility of graphene-based DDS.
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
Graphical abstract: Molecular dynamics method based on multi-component molecular orbital method was applied to basic hydrogen bonding systems, H5O2+, and its isotopomers (D5O2+andT5O2+). Highlights: ► Molecular dynamics method with nuclear quantum effect was developed. ► Multi-component molecular orbital method was used as ab initio MO calculation. ► Developed method applied to basic hydrogen bonding system, H5O2+, and isotopomers. ► O⋯O vibrational stretching reflected to the distribution of protonic wavefunctions. ► H/D/T isotope effect was also analyzed. - Abstract: We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MCMO) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MCMO based MD (MCMO-MD) method is applied to the basic structures, H5O2+ (called “Zundel ion”), and its isotopomers (D5O2+andT5O2+). We clearly demonstrate the geometrical difference of hydrogen bonded O⋯O distance induced by H/D/T isotope effect because the O⋯O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O⋯O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O⋯O distance becomes short during the dynamics. Our proposed MCMO-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.
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.
We have studied the correlation between chemical composition, structure, chemical bonding and elastic properties of amorphous B6O based solids using ab initio molecular dynamics. These solids are of different chemical compositions, but the elasticity data appear to be a function of density. This is in agreement with previous experimental observations. As the density increases from 1.64 to 2.38 g cm-3, the elastic modulus increases from 74 to 253 GPa. This may be understood by analyzing the cohesive energy and the chemical bonding of these compounds. The cohesive energy decreases from -7.051 to -7.584 eV/atom in the elastic modulus range studied. On the basis of the electron density distributions, Mulliken analysis and radial distribution functions, icosahedral bonding is the dominating bonding type. C and N promote cross-linking of icosahedra and thus increase the density, while H hinders the cross-linking by forming OH groups. The presence of icosahedral bonding is independent of the density
Study of AFM-based nanometric cutting process using molecular dynamics
Three-dimensional molecular dynamics (MD) simulations are conducted to investigate the atomic force microscope (AFM)-based nanometric cutting process of copper using diamond tool. The effects of tool geometry, cutting depth, cutting velocity and bulk temperature are studied. It is found that the tool geometry has a significant effect on the cutting resistance. The friction coefficient (cutting resistance) on the nanoscale decreases with the increase of tool angle as predicted by the macroscale theory. However, the friction coefficients on the nanoscale are bigger than those on the macroscale. The simulation results show that a bigger cutting depth results in more material deformation and larger chip volume, thus leading to bigger cutting force and bigger normal force. It is also observed that a higher cutting velocity results in a larger chip volume in front of the tool and bigger cutting force and normal force. The chip volume in front of the tool increases while the cutting force and normal force decrease with the increase of bulk temperature.
The results of molecular dynamics (MD) displacement cascade simulations in bcc iron have been used to obtain effective cross sections for two measures of primary damage production: (1) the number of surviving point defects expressed as a fraction of the displacements calculated using the standard secondary displacement model of Norgett, Robinson, and Torrens (NRT), and (2) the fraction of the surviving interstitials contained in clusters that formed during the cascade event. Primary knockon atom spectra for iron obtained from the SPECTER code have been used to weight these MD-based damage production cross sections in order to obtain spectrally-averaged values for several locations in commercial fission reactors and materials test reactors. An evaluation of these results indicates that neutron energy spectrum differences between the various enviromnents do not lead to significant differences between the average primary damage formation parameters. In particular, the defect production cross sections obtained for PWR and BWR neutron spectra were not significantly different. The variation of the defect production cross sections as a function of depth into the reactor pressure vessel wall is used as a sample application of the cross sections. A slight difference between the attenuation behavior of the PWR and BWR was noted; this difference could be explained by a subtle difference in the energy dependence of the neutron spectra. Overall, the simulations support the continued use of dpa as a damage correlation parameter
Yashiro, Kisaragi; Naito, Masato; Tomita, Yoshihiro [Kobe Univ., Dept. of Mechanical Engineering, Kobe, Hyogo (Japan)
2003-01-01
In order to clarify the fundamental mechanism of dislocations in the {gamma}/{gamma}' microstructure of Ni-based superalloy, three molecular dynamics simulations are conducted on the behavior of edge dislocations nucleated from a free surface and proceeding in the pure Ni matrix ({gamma}) toward cuboidal Ni{sub 3}Al precipitates ({gamma}') under shear force. One involves dislocations near the apices of two precipitates adjoining each other with the distance of 0.04 {mu}m, as large as the width of the {gamma} channel in real superalloys. Others simulate dislocations piled at the precipitates as well, however, the scale of the microstructure is smaller than that in real superalloys by one order of magnitude, and one of them have precipitates with atomistically sharp edge. Dislocations are pinned at precipitates and bowed-out in the {gamma} channel, then they begin to penetrate into the precipitate at the edge in both the real-scale and smaller microstructures when the precipitates have blunt edges. On the other hand, an edge dislocation splits into a superpartial in the {gamma}' precipitate and a misfit screw dislocation bridging between two adjacent precipitates at the atomistically sharp edge of {gamma}' precipitates. It is also observed that two superpartials glide in the precipitate as a superdislocation with anti-phase boundary (APB), of which the width is evaluated to be about 4 nm. (author)
In order to clarify the fundamental mechanism of dislocations in the γ/γ' microstructure of Ni-based superalloy, three molecular dynamics simulations are conducted on the behavior of edge dislocations nucleated from a free surface and proceeding in the pure Ni matrix (γ) toward cuboidal Ni3Al precipitates (γ') under shear force. One involves dislocations near the apices of two precipitates adjoining each other with the distance of 0.04 μm, as large as the width of the γ channel in real superalloys. Others simulate dislocations piled at the precipitates as well, however, the scale of the microstructure is smaller than that in real superalloys by one order of magnitude, and one of them have precipitates with atomistically sharp edge. Dislocations are pinned at precipitates and bowed-out in the γ channel, then they begin to penetrate into the precipitate at the edge in both the real-scale and smaller microstructures when the precipitates have blunt edges. On the other hand, an edge dislocation splits into a superpartial in the γ' precipitate and a misfit screw dislocation bridging between two adjacent precipitates at the atomistically sharp edge of γ' precipitates. It is also observed that two superpartials glide in the precipitate as a superdislocation with anti-phase boundary (APB), of which the width is evaluated to be about 4 nm. (author)
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.
Efficient molecular quantum dynamics in coordinate and phase space using pruned bases
Larsson, Henrik R; Tannor, David J
2016-01-01
We present an efficient implementation of dynamically pruned quantum dynamics, both in coordinate space and in phase space. We combine the ideas behind the biorthogonal von Neumann basis (PvB) with the orthogonalized momentum-symmetrized Gaussians (Weylets) to create a new basis, projected Weylets, that takes the best from both methods. We benchmark pruned dynamics using phase-space-localized PvB, projected Weylets, and coordinate-space-localized DVR bases, with real-world examples in up to six dimensions. We show that coordinate-space localization is most important for efficient pruning and that pruned dynamics is much faster compared to unpruned, exact dynamics. Phase-space localization is useful for more demanding dynamics where many basis functions are required. There, projected Weylets offer a more compact representation than pruned DVR bases.
The nonequilibrium molecular dynamics
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
Drug design based on x-ray diffraction and steered molecular dynamics
Hašek, Jindřich; Skálová, Tereza; Dohnálek, Jan; Dušková, Jarmila; Petroková, Hana; Vondráčková, Eva; Zimmermann, K.
2005-01-01
Roč. 12, č. 3 (2005), s. 208-210. ISSN 1211-5894. [VUFB Conference on Modern Methods in Synthesis and Analysis of Active Pharmaceutical Substances /5./. Praha, 23.11.2005-24.11.2005] R&D Projects: GA AV ČR KJB4050312 Institutional research plan: CEZ:AV0Z40500505 Keywords : drug design * X-ray diffraction * steered molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry
Quasi-classical description of molecular dynamics based on Egorov's theorem
Egorov's theorem on the classical propagation of quantum observables is related to prominent quasi-classical descriptions of quantum molecular dynamics as the linearized semiclassical initial value representation, the Wigner phase space method, or the statistical quasiclassical method. The error estimates show that different accuracies are achievable for the computation of expectation values and position densities. Numerical experiments for a Morse model of diatomic iodine and confined Henon–Heiles systems in various dimensions illustrate the theoretical results
Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.
2006-01-01
A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation
Molecular Dynamics Simulation of a Multi-Walled Carbon Nanotube Based Gear
Han, Jie; Globus, Al; Srivastava, Deepak; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
We used molecular dynamics to investigate the properties of a multi-walled carbon nanotube based gear. Previous work computationally suggested that molecular gears fashioned from (14,0) single-walled carbon nanotubes operate well at 50-100 gigahertz. The gears were formed from 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. The gear in this study was based on the smallest multi-walled nanotube supported by some experimental evidence. Each gear was a (52,0) nanotube surrounding a (37,10) nanotube with approximate 20.4 and 16,8 A radii respectively. These sizes were chosen to be consistent with inter-tube spacing observed by and were slightly larger than graphite inter-layer spacings. The benzyne teeth were attached via 2+4 cycloaddition to exterior of the (52,0) tube. 2+4 bonds were used rather than the 2+2 bonds observed by Hoke since 2+4 bonds are preferred by naphthalene and quantum calculations by Jaffe suggest that 2+4 bonds are preferred on carbon nanotubes of sufficient diameter. One gear was 'powered' by forcing the atoms near the end of the outside buckytube to rotate to simulate a motor. A second gear was allowed to rotate by keeping the atoms near the end of its outside buckytube on a cylinder. The ends of both gears were constrained to stay in an approximately constant position relative to each other, simulating a casing, to insure that the gear teeth meshed. The stiff meshing aromatic gear teeth transferred angular momentum from the powered gear to the driven gear. The simulation was performed in a vacuum and with a software thermostat. Preliminary results suggest that the powered gear had trouble turning the driven gear without slip. The larger radius and greater mass of these gears relative to the (14,0) gears previously studied requires a
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.
Introduction to Accelerated Molecular Dynamics
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
Indentation Behavior of Zr-Based Metallic-Glass Films via Molecular-Dynamics Simulations
Wang, Yun-Che; Wu, Chun-Yi; Chu, Jinn P.; Liaw, Peter K.
2010-11-01
Molecular dynamics (MD) models of the Zr-based metallic-glass film (Zr47Cu31Al13Ni9, in atomic percent) were constructed by simulating sputter depositions on the titanium substrate. The as-deposited films were used as initial structures for subsequent nanoindentation simulations. For the deposition simulations, a many-body, tight-binding (TB) potential was adopted for interatomic interactions among the multiple species of atoms. The interactions between the metallic atoms and working gas (Ar+) were modeled with the pairwise Moliere potential. The TB potential parameters for unlike atoms were chosen to be the algebraic average of those for like ones, and hence, the MD simulations provide qualitative information. The deposition simulations revealed an amorphous morphology in the as-deposited films. Indentation simulations with a right-angle conical indenter tip showed a homogeneous flow to form pileups on the surface of the metallic glass around the indent. The pileup index calculated from MD is consistent with that obtained from the experiment. Moreover, our MD results show that the pileup index exhibits anomalies, which are defined as unusual changes in the values of the pileup index, around the experimentally found glass-transformation temperature through in situ indentation simulations at elevated temperatures. From indentation load-displacement curves at various temperatures, indentation modulus and hardness obtained from MD simulations were in qualitative agreement with experimental findings in terms of their decreasing rates with respect to the temperature. Three-dimensional atomic-strain calculations revealed strain localization and propagation of shear bands under the indenter tip at their initial evolution stages after the formation of shear transformation zones. In addition, higher loading rates decrease hardness, cause larger disturbed regions under the indent, and enlarge shear-banding patterns.
Molecular dynamics simulations
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
Rode, Michał F.; Jankowska, Joanna; Sobolewski, Andrzej L.
2016-04-01
In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.
The electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitution
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.
Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A
2016-05-18
Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation. PMID:27121070
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
In this paper, a stochastic model is presented to simulate the flow of gases, which are not in thermodynamic equilibrium, like in rarefied or micro situations. For the interaction of a particle with others, statistical moments of the local ensemble have to be evaluated, but unlike in molecular dynamics simulations or DSMC, no collisions between computational particles are considered. In addition, a novel integration technique allows for time steps independent of the stochastic time scale. The stochastic model represents a Fokker-Planck equation in the kinetic description, which can be viewed as an approximation to the Boltzmann equation. This allows for a rigorous investigation of the relation between the new model and classical fluid and kinetic equations. The fluid dynamic equations of Navier-Stokes and Fourier are fully recovered for small relaxation times, while for larger values the new model extents into the kinetic regime. Numerical studies demonstrate that the stochastic model is consistent with Navier-Stokes in that limit, but also that the results become significantly different, if the conditions for equilibrium are invalid. The application to the Knudsen paradox demonstrates the correctness and relevance of this development, and comparisons with existing kinetic equations and standard solution algorithms reveal its advantages. Moreover, results of a test case with geometrically complex boundaries are presented.
Meduru, Harika; Wang, Yeng-Tseng; Tsai, Jeffrey J P; Chen, Yu-Ching
2016-01-01
Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme that is responsible for inactivating intestinal peptides glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decline in blood glucose levels. The aim of this study was to explore the inhibition activity of small molecule inhibitors to DPP-4 following a computational strategy based on docking studies and molecular dynamics simulations. The thorough docking protocol we applied allowed us to derive good correlation parameters between the predicted binding affinities (pKi) of the DPP-4 inhibitors and the experimental activity values (pIC50). Based on molecular docking receptor-ligand interactions, pharmacophore generation was carried out in order to identify the binding modes of structurally diverse compounds in the receptor active site. Consideration of the permanence and flexibility of DPP-4 inhibitor complexes by means of molecular dynamics (MD) simulation specified that the inhibitors maintained the binding mode observed in the docking study. The present study helps generate new information for further structural optimization and can influence the development of new DPP-4 inhibitors discoveries in the treatment of type-2 diabetes. PMID:27304951
A fast-moving copper-based molecular shuttle: synthesis and dynamic properties.
Durola, Fabien; Lux, Jacques; Sauvage, Jean-Pierre
2009-01-01
Fast-track changes: The synthesis of a new copper-based molecular shuttle is described, with a coordinating macrocycle based on a nonhindering but endocyclic ligand (see scheme), which makes the ligand exchange easier, and thus the motions of the ring along the thread faster.The present report deals with the synthesis of a two-station [2]rotaxane consisting of a dpbiiq-incorporating macrocycle (dpbiiq: 8,8'-diphenyl-3,3'-biisoquinoline) threaded by a coordinating fragment whose complexing units are a dpp and a terpy ligand (dpp: 2,9-diphenyl-1,10-phenanthroline; terpy: 2,2',6',2"-terpyridine). The [2]rotaxane was prepared in 11 steps from commercially available or easy-to-make molecules, without taking into account the preparation of the dpbiiq-containing 39-membered ring, which was available in our group. The ring-incorporated bidentate chelate is at the same time endocyclic and sterically nonhindering, which is a specific property of the dpbiiq-coordinating unit. This unique feature has a profound influence on the rate of the ring-and-copper translation motion between the two stations of the axle. Based on an analogous multistep strategy, a related molecular shuttle has also been prepared that contains exactly the same axle and stoppers as the first compound but whose threaded ring incorporates the sterically hindering dpp chelate. The translation motions of this other system are several orders of magnitude slower than the corresponding movements of the dpbiiq-based compound. The motion corresponding to the rearrangement of the unstable five-coordinate copper(I) form of the compounds is relatively fast for both shuttles; the half lifetime of the five-coordinate Cu(I) species being below 20 ms for the dpbiiq-containing system and below 1 s for the dpp-based molecule. The reverse motion corresponding to the rearrangement of the four-coordinate copper(II) complexes is much slower, especially for the dpp-based system. It is of the order of several hours for the dpp-based
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.
Surjit B Dixit; Mihaly Mezei; David L Beveridge
2012-07-01
Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general
Physical adsorption and molecular dynamics
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 study of internal energy relaxation in shocks using molecular dynamics based models
Recent potential energy surfaces (PESs) for the N2 + N and N2 + N2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N2 + N2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available
A study of internal energy relaxation in shocks using molecular dynamics based models
Li, Zheng, E-mail: zul107@psu.edu; Parsons, Neal, E-mail: neal.parsons@cd-adapco.com [Department of Aerospace Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Levin, Deborah A., E-mail: deblevin@illinois.edu [Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801-2935 (United States)
2015-10-14
Recent potential energy surfaces (PESs) for the N{sub 2} + N and N{sub 2} + N{sub 2} systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N{sub 2} + N{sub 2} system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N{sub 2} dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available.
A nonequilibrium molecular dynamics method for thermal conductivities based on thermal noise.
Terao, Takamichi; Müller-Plathe, Florian
2005-02-22
We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81 W m(-1) K(-1). It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system. PMID:15836013
Xu, Meng; Yi, Junyan; Feng, Decheng; Huang, Yudong; Wang, Dongsheng
2016-05-18
Asphalt binder is a very important building material in infrastructure construction; it is commonly mixed with mineral aggregate and used to produce asphalt concrete. Owing to the large differences in physical and chemical properties between asphalt and aggregate, adhesive bonds play an important role in determining the performance of asphalt concrete. Although many types of adhesive bonding mechanisms have been proposed to explain the interaction forces between asphalt binder and mineral aggregate, few have been confirmed and characterized. In comparison with chemical interactions, physical adsorption has been considered to play a more important role in adhesive bonding between asphalt and mineral aggregate. In this study, the silicon tip of an atomic force microscope was used to represent silicate minerals in aggregate, and a nanoscale analysis of the characteristics of adhesive bonding between asphalt binder and the silicon tip was conducted via an atomic force microscopy (AFM) test and molecular dynamics (MD) simulations. The results of the measurements and simulations could help in better understanding of the bonding and debonding procedures in asphalt-aggregate mixtures during hot mixing and under traffic loading. MD simulations on a single molecule of a component of asphalt and monocrystalline silicon demonstrate that molecules with a higher atomic density and planar structure, such as three types of asphaltene molecules, can provide greater adhesive strength. However, regarding the real components of asphalt binder, both the MD simulations and AFM test indicate that the colloidal structural behavior of asphalt also has a large influence on the adhesion behavior between asphalt and silicon. A schematic model of the interaction between asphalt and silicon is presented, which can explain the effect of aging on the adhesion behavior of asphalt. PMID:27115043
Ren, Jiaqi; Zhao, Jinsheng; Dong, Zeguang; Liu, Pinkuan
2015-08-01
The atomic force microscopy (AFM) based direct nanoscratching has been thoroughly studied but the mechanism of nanoscratching with water-layer lubrication is yet to be well understood. In current study, three-dimensional molecular dynamics (MD) simulations are conducted to evaluate the effects of the water-layer lubrication on the AFM-based nanoscratching process on monocrystalline copper. Comparisons of workpiece deformation, scratching forces, and friction coefficients are made between the water-lubricated and dry scratching under various thickness of water layer, scratching depth and scratching velocity. Simulation results reveal that the water layer has positive impact on the surface quality and significant influence on the scratching forces (normal forces and tangential forces). The friction coefficients of the tip in water-lubricated nanoscratching are significantly bigger than those in the dry process. Our simulation results shed lights on a promising AFM-based nanofabrication method, which can assist to get nanoscale surface morphologies with higher quality than traditional approaches.
Molecular dynamics studies of palladium
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)
Zhou, Yanguang; Zhang, Xiaoliang; Hu, Ming
2015-11-01
Probing detailed spectral dependence of phonon transport properties in bulk materials is critical to improve the function and performance of structures and devices in a diverse spectrum of technologies. Currently, such information can only be provided by the phonon spectral energy density (SED) or equivalently, time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics simulations (EMD), but has not been realized in nonequilibrium molecular dynamics simulations (NEMD) so far. In this paper we generate a scheme directly based on NEMD and lattice dynamics theory, called the time domain direct decomposition method (TDDDM), to predict the phonon mode specific thermal conductivity. Two benchmark cases of Lennard-Jones (LJ) argon and Stillinger-Weber (SW) Si are studied by TDDDM to characterize contributions of individual phonon modes to overall thermal conductivity and the results are compared with that predicted using SED and TDNMA. Similar trends are found for both cases, which indicate that our TDDDM approach captures the major phonon properties in NEMD run. The biggest advantage of TDDDM is that it can be used to investigate the size effect of individual phonon modes in NEMD simulations, which cannot be tackled by SED and TDNMA in EMD simulations currently. We found that the phonon modes with mean free path larger than the system size are truncated in NEMD and contribute little to the overall thermal conductivity. The TDDDM provides direct physical origin for the well-known strong size effects in thermal conductivity prediction by NEMD. Moreover, the well-known common sense of the zero thermal conductivity contribution from the Γ point is rigorously proved by TDDDM. Since TDDDM inherently possesses the nature of both NEMD simulations and lattice dynamics, we anticipate that TDDDM is particularly useful for offering a deep understanding of phonon behaviors in nanostructures or under strong confinement, especially when the
Galilei invariant molecular dynamics
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.)
The effect of H impurity on the misfit dislocation in Ni-based single-crystal superalloy is investigated using the molecular dynamic simulation. It includes the site preferences of H impurity in single crystals Ni and Ni3Al, the interaction between H impurity and the misfit dislocation and the effect of H impurity on the moving misfit dislocation. The calculated energies and simulation results show that the misfit dislocation attracts H impurity which is located at the γ/γ' interface and Ni3Al and H impurity on the glide plane can obstruct the glide of misfit dislocation, which is beneficial to improving the mechanical properties of Ni based superalloys. (condensed matter: structural, mechanical, and thermal properties)
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
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.
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.
Vicent-Luna, Jose Manuel; Ortiz-Roldan, Jose Manuel; Hamad, Said; Tena-Zaera, Ramon; Calero, Sofia; Anta, Juan Antonio
2016-08-18
Compositional effects on the charge-transport properties of electrolytes for batteries based on room-temperature ionic liquids (RTILs) are well-known. However, further understanding is required about the molecular origins of these effects, in particular regarding the replacement of Li by Na. In this work, we investigate the use of RTILs in batteries, by means of both classical molecular dynamics (MD), which provides information about structure and molecular transport, and ab initio molecular dynamics (AIMD), which provides information about structure. The focus has been placed on the effect of adding either Na(+) or Li(+) to 1-methyl-1-butyl-pyrrolidinium [C4 PYR](+) bis(trifluoromethanesulfonyl)imide [Tf2 N](-) . Radial distribution functions show excellent agreement between MD and AIMD, which ensures the validity of the force fields used in the MD. This is corroborated by the MD results for the density, the diffusion coefficients, and the total conductivity of the electrolytes, which reproduce remarkably well the experimental observations for all studied Na/Li concentrations. By extracting partial conductivities, it is demonstrated that the main contribution to the conductivity is that of [C4 PYR](+) and [Tf2 N](-) . However, addition of Na(+) /Li(+) , although not significant on its own, produces a dramatic decrease in the partial conductivities of the RTIL ions. The origin of this indirect effect can be traced to the modification of the microscopic structure of the liquid as observed from the radial distribution functions, owing to the formation of [Na(Tf2 N)n ]((n-1)-) and [Li(Tf2 N)n ]((n-1)-) clusters at high concentrations. This formation hinders the motion of the large ions, hence reducing the total conductivity. We demonstrate that this clustering effect is common to both Li and Na, showing that both ions behave in a similar manner at a microscopic level in spite of their distinct ionic radii. This is an interesting finding for extending Li-ion and Li
Scalable Molecular Dynamics for Large Biomolecular Systems
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.
Zheleznyakova, A. L.
2015-05-01
A new computational approach for automated triangulation of Computer-Aided Design (CAD) surface models, applicable to various CFD (Computational Fluid Dynamics) problems of practical interest is proposed. The complex shaped product configurations are represented by a set of Non-Uniform Rational B-Splines (NURBS) surface patches. The suggested technique is based on the molecular dynamics method. The main idea of the approach is that the mesh nodes are considered as similarly charged interacting particles which move within the region to be meshed under the influence of internal (such as particle-particle interaction forces) and external forces as well as optional additional forces. Moreover, the particles experience a medium resistance due to which the system comes to equilibrium within a relatively short period of time. The proposed 3D surface mesh generation algorithm uses a parametric NURBS representation as initial definition of the domain boundary. This method first distributes the interacting nodes into optimal locations in the parametric domain of the NURBS surface patch using molecular dynamics simulation. Then, the well-shaped triangles can be created after connecting the nodes by Delaunay triangulation. Finally, the mapping from parametric space to 3D physical space is performed. Since the presented interactive algorithm allows to control the distance between a pair of nodes depending on the curvature of the NURBS surface, the method generates high quality triangular mesh. The algorithm enables to produce uniform mesh, as well as anisotropic adaptive mesh with refinement in the large gradient regions. The mesh generation approach has the abilities to preserve the representation accuracy of the input geometry model, create a close relationship between geometry modeling and grid generation process, be automated to a large degree. Some examples are considered in order to illustrate the method's ability to generate a surface mesh for a complicated CAD model.
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...
YANG Ping; LIAO Linbo; DING Jianning; YANG Jichang; LI Changsheng; FAN Zen; LIN Zhiyong
2006-01-01
The aim of this article was to provide a systematic method to perform molecular dynamics simulation or evaluation for nano-scale interfacial friction behavior between two kinds of materials in MEMS design. Friction is an important factor affecting the performance and reliability of MEMS. The model of the nano-scale interfacial friction behavior between two kinds of materials was presented based on the Newton's equations of motion. The Morse potential function was selected for the model. The improved Verlet algorithm was employed to resolve the model, the atom trajectories and the law of the interfacial friction behavior. Comparisons with experimental data in other paper confirm the validity of the model. Using the model it is possible to simulate or evaluate the importance of different factors for designing of the nano-scale interfacial friction behavior between two kinds of materials in MEMS.
Mahdi Bagherpoor Helabad
2014-07-01
Full Text Available Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.
Molecular dynamics simulation of diffusivity
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
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.)
Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei
2016-01-21
The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman-Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation. PMID:26688211
Donolato, Marco; Antunes, Paula Soares Martins; Bejhed, Rebecca S.;
2015-01-01
behavior. We prove that the optical transmission spectra are highly sensitive to the formation of permanent MNB clusters and, thereby to the target analyte concentration. As a specific clinically relevant diagnostic case, we detect DNA coils formed via padlock probe recognition and isothermal rolling......We demonstrate detection of DNA coils formed from a Vibrio cholerae DNA target at picomolar concentrations using a novel optomagnetic approach exploiting the dynamic behavior and optical anisotropy of magnetic nanobead (MNB) assemblies. We establish that the complex second harmonic optical...... transmission spectra of MNB suspensions measured upon application of a weak uniaxial AC magnetic field correlate well with the rotation dynamics of the individual MNBs. Adding a target analyte to the solution leads to the formation of permanent MNB clusters, namely, to the suppression of the dynamic MNB...
The Application of Molecular Dynamics in Fullerene-Based Journal Bearing Simulation
Alexey Kornaev
2014-02-01
Full Text Available The article is devoted to modeling of the molecular microscopic journal bearing. The walls and the lubricant of the bearing are fullerene-like molecules. On the basis of similarity theory and analysis of the dimensions, the similarity criterion is proposed. This criterion characterizes the convergence of a numerical solution. The test calculation is also made to evaluate the quality of the proposed criterion.
Villa, Alessandra; Wöhnert, Jens; Stock, Gerhard
2009-01-01
Riboswitches are a novel class of genetic control elements that function through the direct interaction of small metabolite molecules with structured RNA elements. The ligand is bound with high specificity and affinity to its RNA target and induces conformational changes of the RNA's secondary and tertiary structure upon binding. To elucidate the molecular basis of the remarkable ligand selectivity and affinity of one of these riboswitches, extensive all-atom molecular dynamics simulations in...
Zhou, Yanguang; Hu, Ming
2015-11-01
From a nanoscale heat transfer point of view, currently one of the most interesting and challenging tasks is to quantitatively analyze phonon mode specific transport properties in solid materials, which plays a vital role in many emerging and diverse technological applications. It has not been long that such information can be provided by the phonon spectral energy density (SED) or equivalently time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics (EMD) simulations. However, few methods have been developed for nonequilibrium molecular dynamics (NEMD) simulations [Phys. Rev. B 91, 115426 (2015), 10.1103/PhysRevB.91.115426], the other widely used computational method for calculating thermal transport of materials in addition to EMD. In this work, a computational scheme based on time Fourier transform of atomistic heat current, called the frequency domain direct decomposed method (FDDDM), is proposed to analyze the contributions of frequency dependent thermal conductivity in NEMD simulations. The FDDDM results of Lennard-Jones argon and Stillinger-Weber Si are compared with the TDNMA method from EMD simulation. Similar trends are found for both cases, which confirm the validity of our FDDDM approach. Benefiting from the inherent nature of NEMD and the theoretical formula that does not require any temperature assumption, the FDDDM can be directly used to investigate the size and temperature effect. Moreover, the unique advantage of FDDDM prior to previous methods (such as SED and TDNMA) is that it can be straightforwardly used to characterize the phonon frequency dependent thermal conductivity of disordered systems, such as amorphous materials. The FDDDM approach can also be a good candidate to be used to understand the phonon behaviors and thus provides useful guidance for designing efficient structures for advanced thermal management.
Kah, Cherno Baba; Yu, M.; Jayanthi, C. S.; Wu, S. Y.
2014-03-01
Our previous study on one-dimensional icosahedral B12 cluster (α-B12) based chain [Bulletin of APS Annual Meeting, p265 (2013)] and ring structures has prompted us to study the two-dimensional (2D) α-B12 based structures. Recently, we have carried out a systematic molecular dynamics study on the structural stabilities and electronic properties of the 2D α-B12 based structures using the SCED-LCAO method [PRB 74, 15540 (2006)]. We have considered several types of symmetry for these 2D structures such as δ3, δ4, δ6 (flat triangular), and α' types. We have found that the optimized structures are energetically in the order of δ6 < α' < δ3 < δ4 which is different from the energy order of α'< δ6 < δ4 < δ3 found in the 2D boron monolayer sheets [ACS Nano 6, 7443 (2012)]. A detailed discussion of this study will be presented. The first author acknowledges the McSweeny Fellowship for supporting his research in this work.
Musyoka, Thommas M; Kanzi, Aquillah M; Lobb, Kevin A; Tastan Bishop, Özlem
2016-01-01
Identification of potential drug targets as well as development of novel antimalarial chemotherapies with unique mode of actions due to drug resistance by Plasmodium parasites are inevitable. Falcipains (falcipain-2 and falcipain-3) of Plasmodium falciparum, which catalyse the haemoglobin degradation process, are validated drug targets. Previous attempts to develop peptide based drugs against these enzymes have been futile due to the poor pharmacological profiles and susceptibility to degradation by host enzymes. This study aimed to identify potential non-peptide inhibitors against falcipains and their homologs from other Plasmodium species. Structure based virtual docking approach was used to screen a small non-peptidic library of natural compounds from South Africa against 11 proteins. A potential hit, 5α-Pregna-1,20-dien-3-one (5PGA), with inhibitory activity against plasmodial proteases and selectivity on human cathepsins was identified. A 3D similarity search on the ZINC database using 5PGA identified five potential hits based on their docking energies. The key interacting residues of proteins with compounds were identified via molecular dynamics and free binding energy calculations. Overall, this study provides a basis for further chemical design for more effective derivatives of these compounds. Interestingly, as these compounds have cholesterol-like nuclei, they and their derivatives might be well tolerated in humans. PMID:27030511
Zhang, Congyan; Xin, Zihua; Yu, Ming; Jayanthi, C. S.; Wu, S. Y.; Shanghai University Collaboration
2014-03-01
A molecular dynamics study to investigate a plausible way of fabricating SiC based cage structures has been performed. In this work, the existence of the stable SiC based cage nanostructures SimCn with the size up to about 2.05nm in diameter and the compositions n/(n +m) from 0.4 to 0.6 has been demonstrated using an efficient semi-empirical Hamiltonian method (SCED-LCAO) [PRB 74, 15540 (2006)]. The structural properties are analyzed in terms of the composition, the bonding nature, the surface environment, the local strain, and types of ring structures. It is found that the sp2 bonding nature between Si and C atoms and the environmental mediation are two key factors for the self-assembly of the stable SiC based cage structures. In particular, the transition from one stable cage structure to another of similar composition might occur due to the mending process in the self-assembly. The first and second authors acknowledge the support from the NSFC (grant No.: 61176118) and 085 project of Shanghai University (China) for this work.
Highlights: • MD simulations are conducted to study the water-lubricated nanoscratching process. • The water layer has positive impact on the surface quality. • Comparisons are made in aspects of deformation, forces, and fricion coefficients. • Effects of water thickness, scratching depth and velocity are thoroughly studied. - Abstract: The atomic force microscopy (AFM) based direct nanoscratching has been thoroughly studied but the mechanism of nanoscratching with water-layer lubrication is yet to be well understood. In current study, three-dimensional molecular dynamics (MD) simulations are conducted to evaluate the effects of the water-layer lubrication on the AFM-based nanoscratching process on monocrystalline copper. Comparisons of workpiece deformation, scratching forces, and friction coefficients are made between the water-lubricated and dry scratching under various thickness of water layer, scratching depth and scratching velocity. Simulation results reveal that the water layer has positive impact on the surface quality and significant influence on the scratching forces (normal forces and tangential forces). The friction coefficients of the tip in water-lubricated nanoscratching are significantly bigger than those in the dry process. Our simulation results shed lights on a promising AFM-based nanofabrication method, which can assist to get nanoscale surface morphologies with higher quality than traditional approaches
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.
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...
A. Mobeen
2013-07-01
Full Text Available Background: Alzheimer's disease (AD is a neurodegenerative disorder in elderly persons aged above 65 years. The cleavage of amyloid precursor protein (APP by -secretase generates peptide fragment A42, the main cause of memory and cognitive defects in AD. Therefore, elevated level of -secretase results in accumulation of insoluble form of A peptides (senile plaques representing the protein as an attractive drug target of AD. Methods: Five recently reported -secretase antagonist (thiazolidinediones, rosiglitazone, pioglitazone, SC7 and tartaric acid structural analogs were searched from ligand info database and prepared using LigPrep. The crystal structure of -secretase was optimized using Maestro v9.2 protein preparation wizard applying optimized potential for liquid simulations (OPLS-2005 force field. Structure based virtual screening was performed for -secretase from prepared ligands using virtual screening workflow of Maestro v9.2 and was ranked based on XP Gscore. Results: Eight lead molecules were identified to have better binding affinity (lower XP Gscore compared to five existing -secretase antagonists and appear to have good pharmacological properties. Binding orientations of the lead molecules were in well agreement with existing inhibitors. Lead1 showed lowest XP Gscore (-10.72 Kcal/mol. Molecular dynamics (MD simulations of -secretase-lead1 complex was stable in all trajectories. Conclusion: Lead1 is proposed as potent inhibitor of -secretase and thus could be considered for rational drug design against AD.
Wang, Shijian; Fan, Ming; Zhang, Juan; Zheng, Bin; Wang, Xiaojia; Li, Lihua
2016-03-01
Breast cancer is one of the most common malignant tumor with upgrading incidence in females. The key to decrease the mortality is early diagnosis and reasonable treatment. Molecular classification could provide better insights into patient-directed therapy and prognosis prediction of breast cancer. It is known that different molecular subtypes have different characteristics in magnetic resonance imaging (MRI) examination. Therefore, we assumed that imaging features can reflect molecular information in breast cancer. In this study, we investigated associations between dynamic contrasts enhanced MRI (DCE-MRI) features and molecular subtypes in breast cancer. Sixty patients with breast cancer were enrolled and the MR images were pre-processed for noise reduction, registration and segmentation. Sixty-five dimensional imaging features including statistical characteristics, morphology, texture and dynamic enhancement in breast lesion and background regions were semiautomatically extracted. The associations between imaging features and molecular subtypes were assessed by using statistical analyses, including univariate logistic regression and multivariate logistic regression. The results of multivariate regression showed that imaging features are significantly associated with molecular subtypes of Luminal A (p=0.00473), HER2-enriched (p=0.00277) and Basal like (p=0.0117), respectively. The results indicated that three molecular subtypes are correlated with DCE-MRI features in breast cancer. Specifically, patients with a higher level of compactness or lower level of skewness in breast lesion are more likely to be Luminal A subtype. Besides, the higher value of the dynamic enhancement at T1 time in normal side reflect higher possibility of HER2-enriched subtype in breast cancer.
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...
Olasagasti, Felix; Deamer, David W.
Nucleic acids are linear polynucleotides in which each base is covalently linked to a pentose sugar and a phosphate group carrying a negative charge. If a pore having roughly the crosssectional diameter of a single-stranded nucleic acid is embedded in a thin membrane and a voltage of 100 mV or more is applied, individual nucleic acids in solution can be captured by the electrical field in the pore and translocated through by single-molecule electrophoresis. The dimensions of the pore cannot accommodate anything larger than a single strand, so each base in the molecule passes through the pore in strict linear sequence. The nucleic acid strand occupies a large fraction of the pore's volume during translocation and therefore produces a transient blockade of the ionic current created by the applied voltage. If it could be demonstrated that each nucleotide in the polymer produced a characteristic modulation of the ionic current during its passage through the nanopore, the sequence of current modulations would reflect the sequence of bases in the polymer. According to this basic concept, nanopores are analogous to a Coulter counter that detects nanoscopic molecules rather than microscopic [1,2]. However, the advantage of nanopores is that individual macromolecules can be characterized because different chemical and physical properties affect their passage through the pore. Because macromolecules can be captured in the pore as well as translocated, the nanopore can be used to detect individual functional complexes that form between a nucleic acid and an enzyme. No other technique has this capability.
Minoshima, Yusuke; Seki, Yusuke; Takayanagi, Toshiyuki; Shiga, Motoyuki
2016-06-01
The dynamical process of electron attachment to a guanine-cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.
Vasenkov, Alex; Newsome, David; Verners, Osvalds; Russo, Michael F.; Zaharieva, Roussislava; van Duin, Adri C. T.
2012-07-01
Structural metal alloys are of vital importance for a clean energy economy, but the current trial-and-error alloy development methodology is expensive and time consuming. In this study, we demonstrate the capability of the ReaxFF force field model to predict mechanical properties and provide a fully dynamic description of oxidation and sulfidation of Mo-based alloys under high-pressure, high-temperature conditions using molecular dynamics (MD) method. The advantage of the ReaxFF approach is in its ability to model the formation and breaking of chemical bonds within the quantum framework but several orders of magnitude faster than the traditional density functional theory models. ReaxFF-MD predictions were compared to the literature Mo shock compression measurements at 300 K and 1673 K in the pressure range of 0-350 Pa, and densities and Young's modulus in the temperature range of 300-1500 K. Analysis of oxidation of Mo and Ni clusters and surface slabs showed that Mo oxidation proceeded at a significantly higher rate than the Ni oxidation and involved oxygen transport inside the metal cluster coupled to large heat release that caused extensive surface melting. The oxidation simulations of Mo3Ni clusters showed high production of Mo oxides and a low concentration of Ni-oxides in the gas phase. This was attributed to the higher chemical stability of Mo-oxide gas phase species. Modeling of H2S interactions with Mo slab demonstrated that sulfur atoms increasingly agglomerated in the surfaces layers of the slab as the simulation proceeded, diffusing deeper into the slab in their atomic forms. A combined ReaxFF Mo/Ni/C/O/N/S/H parameter set enabled us to obtain a detailed atomistic analysis of complex physical and chemical events during the combustion of a complex fuel molecule on a reactor surface.
Rheology via nonequilibrium molecular dynamics
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
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.
Ma, Song; Li, Yajin; Li, Yang; Luo, Yunjun
2016-02-01
To improve the practicality and safety of a novel explosive dihydroxylamm onium 5,5'-bis (tetrazole)-1,1'-diolate (TKX-50), polyvinylidene difluoride (PVDF) and polychlorotrifluoroe-thylene (PCTFE) were respectively added to the TKX-50, forming the polymer-bonded explosives (PBX). Interfacial and mechanical properties of PBX were investigated through molecular dynamics (MD) method, desensitizing mechanisms of fluorine-polymers for TKX-50 were researched by compression and bulk shear simulations. Results show that the binding energies (E bind ) between polymers (PVDF or PCTFE) and TKX-50 surfaces all rank in order of (011) > (100) > (010), shorter interatomic distance and the resulted higher potentials lead to higher E bind on TKX-50/PVDF interfaces than that on PCTFE/TKX-50 interfaces. Compared with TKX-50, the ductility of PBX is improved due to the isotropic mechanical property and flexibility of fluorine-polymers especially the PCTFE. Desensitizing effect of fluorine-polymers for TKX-50 is found under loading condition, which is attributed to the enhanced compressibility and buffer capacity against external pressure in compression, as well as the improved lubricity to reduce the sliding potentials in bulk shear process. Graphical Abstract Comparisons of the internal stress and slide potentials of the novel explosive,TKX-50 and its based PBX. Desensitizing effects can be found by the adding of fluorine-polymers, it owes to their better flexibility and lubricity as well as the amorphous nature. PMID:26809515
Anusuya, Shanmugam; Velmurugan, Devadasan; Gromiha, M Michael
2016-07-01
Dengue is a major public health concern in tropical and subtropical countries of the world. There are no specific drugs available to treat dengue. Even though several candidates targeted both viral and host proteins to overcome dengue infection, they have not yet entered into the later stages of clinical trials. In order to design a drug for dengue fever, newly emerged fragment-based drug designing technique was applied. RNA-dependent RNA polymerase, which is essential for dengue viral replication is chosen as a drug target for dengue drug discovery. A cascade of methods, fragment screening, fragment growing, and fragment linking revealed the compound [2-(4-carbamoylpiperidin-1-yl)-2-oxoethyl]8-(1,3-benzothiazol-2-yl)naphthalene-1-carboxylate as a potent dengue viral polymerase inhibitor. Both strain energy and binding free energy calculations predicted that this could be a better inhibitor than the existing ones. Molecular dynamics simulation studies showed that the dengue polymerase-lead complex is stable and their interactions are consistent throughout the simulation. The hydrogen-bonded interactions formed by the residues Arg792, Thr794, Ser796, and Asn405 are the primary contributors for the stability and the rigidity of the polymerase-lead complex. This might keep the polymerase in closed conformation and thus inhibits viral replication. Hence, this might be a promising lead molecule for dengue drug designing. Further optimization of this lead molecule would result in a potent drug for dengue. PMID:26262439
Ghodsi, Hossein; Darvish, Kurosh
2016-10-01
Collagen fibril is a major component of connective tissues such as bone, tendon, blood vessels, and skin. The mechanical properties of this highly hierarchical structure are greatly influenced by the presence of covalent cross-links between individual collagen molecules. This study investigates the viscoelastic behavior of a collagen lysine-lysine cross-link based on creep simulations with applied forces in the range or 10 to 2000pN using steered molecular dynamics (SMD). The viscoelastic model of the cross-link was combined with a system composed by two segments of adjacent collagen molecules hence representing a reduced viscoelastic model for a simplified micro-fibril. It was found that the collagen micro-fibril assembly had a steady-state Young׳s modulus ranging from 2.24 to 3.27GPa, which is in agreement with reported experimental measurements. The propagation of longitudinal force wave along the molecule was implemented by adding a delay element to the model. The force wave speed was found to be correlated with the speed of one-dimensional elastic waves in rods. The presented reduced model with three degrees of freedom can serve as a building block for developing models of the next level of hierarchy, i.e., a collagen fibril. PMID:27341288
We derive the fundamental equations of an optimal control theory for systems containing both quantum electrons and classical ions. The system is modeled with Ehrenfest dynamics, a non-adiabatic variant of molecular dynamics. The general formulation, that needs the fully correlated many-electron wavefunction, can be simplified by making use of time-dependent density-functional theory. In this case, the optimal control equations require some modifications that we will provide. The abstract general formulation is complemented with the simple example of the H2+ molecule in the presence of a laser field. (paper)
Laser Controlled Molecular Orientation Dynamics
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
Dynamical quenching of tunneling in molecular magnets
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
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.
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.
Molecular dynamics investigation of dynamic crack stability
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
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
Displacement cascade formation in iron has been investigated by the method of molecular dynamics (MD) for cascade energies up to 40 keV. The results of these simulations have been used in the specomp code to obtain effective, energy-dependent cross sections for two measures of primary damage production: (1) the number of surviving point defects expressed as a fraction of the those predicted by the standard secondary displacement model by Norgett et al., 1975 [M.J. Norgett, M.T. Robinson, and I.M. Torrens (1975)] and (2) the fraction of the surviving interstitials contained in clusters that formed during the cascade event. The primary knock-on atom (PKA) spectra for iron obtained from the specter code have been used to weight these MD-based damage production cross sections in order to obtain spectrally-averaged values for several locations in commercial fission reactors and test reactors. An evaluation of these results indicates that neutron energy spectrum differences between the various environments do not lead to significant differences between the average primary damage formation parameters. In particular, spectrum-averaged defect production cross sections obtained for PWR and BWR neutron spectra were not significantly different. A representative application of the new defect production cross sections is provided by examining how they vary as a function of depth into the reactor pressure vessel wall. A slight difference was noted between the damage attenuation in a PWR vessel and a BWR vessel. This observation could be explained by a subtle difference in the energy dependence of the neutron spectra. Overall, the simulations indicate that spectrum-averaged defect production cross sections do not vary much among the various environments in light-water moderated fission reactors
Hansen, Halvor S; Daura, Xavier; Hünenberger, Philippe H
2010-09-14
A new method, fragment-based local elevation umbrella sampling (FB-LEUS), is proposed to enhance the conformational sampling in explicit-solvent molecular dynamics (MD) simulations of solvated polymers. The method is derived from the local elevation umbrella sampling (LEUS) method [ Hansen and Hünenberger , J. Comput. Chem. 2010 , 31 , 1 - 23 ], which combines the local elevation (LE) conformational searching and the umbrella sampling (US) conformational sampling approaches into a single scheme. In LEUS, an initial (relatively short) LE build-up (searching) phase is used to construct an optimized (grid-based) biasing potential within a subspace of conformationally relevant degrees of freedom, which is then frozen and used in a (comparatively longer) US sampling phase. This combination dramatically enhances the sampling power of MD simulations but, due to computational and memory costs, is only applicable to relevant subspaces of low dimensionalities. As an attempt to expand the scope of the LEUS approach to solvated polymers with more than a few relevant degrees of freedom, the FB-LEUS scheme involves an US sampling phase that relies on a superposition of low-dimensionality biasing potentials optimized using LEUS at the fragment level. The feasibility of this approach is tested using polyalanine (poly-Ala) and polyvaline (poly-Val) oligopeptides. Two-dimensional biasing potentials are preoptimized at the monopeptide level, and subsequently applied to all dihedral-angle pairs within oligopeptides of 4, 6, 8, or 10 residues. Two types of fragment-based biasing potentials are distinguished: (i) the basin-filling (BF) potentials act so as to "fill" free-energy basins up to a prescribed free-energy level above the global minimum; (ii) the valley-digging (VD) potentials act so as to "dig" valleys between the (four) free-energy minima of the two-dimensional maps, preserving barriers (relative to linearly interpolated free-energy changes) of a prescribed magnitude
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 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.
Theoretical Concepts in Molecular Photodissociation Dynamics
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
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.
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.
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of 15N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S2) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S2) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S2 values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S2 parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S2 calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S2) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models
Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)
2015-02-13
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
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
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.
Density Functional Theory calculations and Molecular Dynamics with a recently developed potential for W–He were used to evaluate the thermal stability of helium–vacancy clusters (nHe.mv) as well as pure interstitial helium clusters in tungsten. The stability of such objects results from a competitive process between thermal emission of vacancies, self interstitial atoms (SIAs) and helium, depending on the helium-to-vacancy ratio in mixed clusters or helium number in pure interstitial helium clusters. We investigated in particular the thermodynamics and kinetics of self trapping and trap mutation, i.e. the emission of one SIA along with the creation of one vacancy from a vacancy–helium or pure helium object
Pal, Anirban; Raha, Soumyendu; Bhattacharya, Baidurya
2015-01-01
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nanoindentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr Cr interaction and the Morse potential for Cr C interactions. We study the performance of our algorithm for a range of MPIthread combinations and find the performance to depend strongly on the computational task and load sharing in the multicore processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favourably with that achieved by stan...
Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.
Insight into interaction mechanism of the inhibitor pDI5W with MDM2 based on molecular dynamics
The p53-MDM2 interaction has been an important target of drug design curing cancers. In this work, molecular dynamics (MD) simulation coupled with molecular mechanics/Poisson Boltzmann surface area method (MM-PBSA) was performed to calculate the binding free energy of peptide inhibitor pDI6W to MDM2. The results show that van der Waals energy is the dominant factor of the pDI6W— MDM2 interaction. Cross-correlation matrix calculated suggests that the main motion of the residues in MMDM2 induced by the inhibitor binding is anti-correlation motion. The calculations of residue-residue interactions between pDI6W and MDM2 not only prove that five residues Phe19', Trp22', Trp23', Leu26' and Thr27' from pDI6W can produce strong interaction with MDM2, but also show that CH-π, CH-CH and π-π interactions drive the binding of pDI6W in the hydrophobic cleft of MDM2. This study can provide theoretical helps for anti-cancer drug designs. (authors)
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...
Ghatage, Dhairyashil; Tomar, Gaurav, E-mail: gtom@mecheng.iisc.ernet.in; Shukla, Ratnesh K., E-mail: ratnesh@mecheng.iisc.ernet.in [Department of Mechanical Engineering, Indian Institute of Science, Bangalore 560012 (India)
2015-03-28
Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.
Ghatage, Dhairyashil; Tomar, Gaurav; Shukla, Ratnesh K.
2015-03-01
Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.
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...
Thermally driven molecular linear motors - A molecular dynamics study
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...
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.
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.
Li, Jiao Jiao; Tian, Yue Li; Zhai, Hong Lin; Lv, Min; Zhang, Xiao Yun
2016-08-01
DYRK1A is characterized by the early development and regulation of neuronal proliferation, and its over expression gives rise to neurological abnormalities. As the promising DYRK1A inhibitors, the binding mechanism between DYRK1A and pyrido[2,3-d]pyrimidines derivatives at molecular level are still veiled. In this article, it was achieved to get the structural insights into pyrido[2,3-d]pyrimidines derivatives as DYRK1A inhibitors by means of comprehensive computational approaches involving molecular docking, molecular dynamics simulation, free energy calculation, and energy decomposition analysis. The calculated energy values were highly consistent with the experimental activities. Based on the individual energy terms analysis, the van der Waals interaction was the major leading force in the DYRK1A-ligand interaction. Lys188 was the important residue that formed the hydrogen bond, which improved the inhibitory activity. Furthermore, four novel inhibitors with higher predicted activity were designed based on the obtained findings and confirmed by molecular simulations. Our study is expected to provide significant drug design strategy for the development of more promising DYRK1A inhibitors. Proteins 2016; 84:1108-1123. © 2016 Wiley Periodicals, Inc. PMID:27119584
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
A parallel molecular dynamics code based on the liked-cell method and its application to liquids
Full text: Many problems in the Statistical Mechanics of materials may be solved by use of the Molecular Dynamics (MD) technique involving the numerical solution of Newton's equations of motion for a few hundred interacting particles. However, some problems require many thousands to millions of atoms in order to accurately represent the length and/or time scales involved. Examples of such problems are nucleation, phase separation, extended defects and crack propagation. Such large numbers of atoms cannot be treated using existing serial computers and computer codes. Thus, new methods must be sought to tackle such problems. One such method is the use of parallel computers which involves the development of MD codes which will work on computers with parallel architectures. Here we discuss one such implementation of the MD method which uses the linked cells method of Hockney and Eastwood. As an illustration we show how this method performs on a TRANSPUTER array and discuss some applications to problems in liquid state physics
Konieczny, Jan K; Szefczyk, Borys
2015-03-01
Ionic liquid (IL) interfaces with vacuum and water are studied by means of classical molecular dynamics simulations. Five ILs are compared: [C2mim][TfO], [C12mim][TfO], [C2mim][NTf2], [C8mim][NTf2] and [C12mim][NTf2], where [C2mim], [C8mim] and [C12mim] stand for 1-ethyl-, 1-octyl- and 1-dodecyl-3-methylimidazolium cation. Physical properties-density, thermal expansion coefficient, compressibility, surface tension, heat of vaporization, self-diffusion coefficient, electric conductivity and viscosity-are calculated and validated against experimental values. The structure of the interfaces is compared in terms of the orientation of the molecules and segregation into layers. It is observed that ILs with short alkyl chains orient at the surface; however, there is no single preferred orientation. ILs with longer chains, on the other hand, orient with alkyl chains protruding into the vacuum at the IL/vacuum interface and into the bulk IL, at the IL/water interface. Anions and water molecules tend to associate with polar imidazolium groups. PMID:25674908
Kazachenko, Sergey; Giovinazzo, Mark; Hall, Kyle Wm; Cann, Natalie M
2015-09-15
A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n-hexane/2-propanol mixture; and a liquid crystal mesogen, 2-(4-butyloxyphenyl)-5-octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33-119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69-287 fold improvement and three GPUs yield a 101-377 fold speedup. PMID:26174435
Tiwary, C. S., E-mail: cst.iisc@gmail.com; Chattopadhyay, K. [Department of Materials Engineering, Indian Institute of Science, Bangalore 560012 (India); Chakraborty, S.; Mahapatra, D. R. [Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012 (India)
2014-05-28
This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al{sub 2}Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al{sub 2}Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different length scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm.
This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al2Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al2Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different length scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm.
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 ...
Feliks, Mikolaj; Lafaye, Céline; Shu, Xiaokun; Royant, Antoine; Field, Martin
2016-08-01
Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics simulations, we have studied the structure, protonation behavior, and dynamics of the biliverdin chromophore and its molecular environment in a series of genetically engineered infrared fluorescent proteins (IFPs) based on the chromophore-binding domain of the Deinococcus radiodurans bacteriophytochrome. Our study suggests that the experimentally observed enhancement of fluorescent properties results from the improved rigidity and planarity of the biliverdin chromophore, in particular of the first two pyrrole rings neighboring the covalent linkage to the protein. We propose that the increases in the levels of both motion and bending of the chromophore out of planarity favor the decrease in fluorescence. The chromophore-binding pocket in some of the studied proteins, in particular the weakly fluorescent parent protein, is shown to be readily accessible to water molecules from the solvent. These waters entering the chromophore region form hydrogen bond networks that affect the otherwise planar conformation of the first three rings of the chromophore. On the basis of our simulations, the enhancement of fluorescence in IFPs can be achieved either by reducing the mobility of water molecules in the vicinity of the chromophore or by limiting the interactions of the nearby protein residues with the chromophore. Finally, simulations performed at both low and neutral pH values highlight differences in the dynamics of the chromophore and shed light on the mechanism of fluorescence loss at low pH. PMID:27471775
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.
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.
Zhang, Yigang; Yin, Qing-Zhu
2012-11-27
Carbon (C) is one of the candidate light elements proposed to account for the density deficit of the Earth's core. In addition, C significantly affects siderophile and chalcophile element partitioning between metal and silicate and thus the distribution of these elements in the Earth's core and mantle. Derivation of the accretion and core-mantle segregation history of the Earth requires, therefore, an accurate knowledge of the C abundance in the Earth's core. Previous estimates of the C content of the core differ by a factor of ∼20 due to differences in assumptions and methods, and because the metal-silicate partition coefficient of C was previously unknown. Here we use two-phase first-principles molecular dynamics to derive this partition coefficient of C between liquid iron and silicate melt. We calculate a value of 9 ± 3 at 3,200 K and 40 GPa. Using this partition coefficient and the most recent estimates of bulk Earth or mantle C contents, we infer that the Earth's core contains 0.1-0.7 wt% of C. Carbon thus plays a moderate role in the density deficit of the core and in the distribution of siderophile and chalcophile elements during core-mantle segregation processes. The partition coefficients of nitrogen (N), hydrogen, helium, phosphorus, magnesium, oxygen, and silicon are also inferred and found to be in close agreement with experiments and other geochemical constraints. Contents of these elements in the core derived from applying these partition coefficients match those derived by using the cosmochemical volatility curve and geochemical mass balance arguments. N is an exception, indicating its retention in a mantle phase instead of in the core. PMID:23150591
Islam, Md Ataul; Pillay, Tahir S
2016-02-23
Acquired immunodeficiency syndrome (AIDS) is a life-threatening disease which is a collection of symptoms and infections caused by a retrovirus, human immunodeficiency virus (HIV). There is currently no curative treatment and therapy is reliant on the use of existing anti-retroviral drugs. Pharmacoinformatics approaches have already proven their pivotal role in the pharmaceutical industry for lead identification and optimization. In the current study, we analysed the binding preferences and inhibitory activity of HIV-integrase inhibitors using pharmacoinformatics. A set of 30 compounds were selected as the training set of a total 540 molecules for pharmacophore model generation. The final model was validated by statistical parameters and further used for virtual screening. The best mapped model (R = 0.940, RMSD = 2.847, Q(2) = 0.912, se = 0.498, Rpred(2) = 0.847 and rm(test)(2) = 0.636) explained that two hydrogen bond acceptor and one aromatic ring features were crucial for the inhibition of HIV-integrase. From virtual screening, initial hits were sorted using a number of parameters and finally two compounds were proposed as promising HIV-integrase inhibitors. Drug-likeness properties of the final screened compounds were compared to FDA approved HIV-integrase inhibitors. HIV-integrase structure in complex with the most active and final screened compounds were subjected to 50 ns molecular dynamics (MD) simulation studies to check comparative stability of the complexes. The study suggested that the screened compounds might be promising HIV-integrase inhibitors. The new chemical entities obtained from the NCI database will be subjected to experimental studies to confirm potential inhibition of HIV integrase. PMID:26809073
Zhang, Xinzhuang; Gu, Jiangyong; Cao, Liang; Ma, Yimin; Su, Zhenzhen; Luo, Fang; Wang, Zhenzhong; Li, Na; Yuan, Gu; Chen, Lirong; Xu, Xiaojie; Xiao, Wei
2014-12-01
In comparison to the current target-based screening approach, it is increasingly evident that active lead compounds based on disease-related phenotypes are more likely to be translated to clinical trials during drug development. That is, because human diseases are in essence the outcome of the abnormal function of multiple genes, especially in complex diseases. Therefore, as a conventional technology in the early phase of active lead compound discovery, computational methods that can connect molecular interactions and disease-related phenotypes to evaluate the efficacy of compounds are in urgently required. In this work, a computational approach that integrates molecular docking and pathway network analysis (network efficiency and network flux) was developed to evaluate the efficacy of a compound against LPS-induced Prostaglandin E2(PGE2) production. The predicted results were then validated in vitro, and a correlation with the experimental results was analyzed using linear regression. In addition, molecular dynamics (MD) simulations were performed to explore the molecular mechanism of the most potent compounds. There were 12 hits out of 28 predicted ingredients separated from Reduning injection (RDN). The predicted results have a good agreement with the experimental inhibitory potency (IC50) (correlation coefficient = 0.80). The most potent compounds could target several proteins to regulate the pathway network. This might partly interpret the molecular mechanism of RDN on fever. Meanwhile, the good correlation of the computational model with the wet experimental results might bridge the gap between molecule-target interactions and phenotypic response, especially for multi-target compounds. Therefore, it would be helpful for active lead compound discovery, the understanding of the multiple targets and synergic essence of traditional Chinese medicine (TCM). PMID:25228393
We study the effects of small-scale parameter on the buckling loads and strains of nanobeams, based on nonlocal Timoshenko beam model. However, the lack of higher order boundary conditions leads to inconsistencies in critical buckling loads. In this paper, we apply a novel approach based on nonlocal Timoshenko kinematics, strain gradient approach and variational methods for deriving all classical and higher-order boundary conditions as well as governing equations. Therefore, closed-form and exact critical buckling loads of nanobeams with various end conditions are investigated. Moreover, the dependence of buckling loads on the small-scale parameter as well as shear deformation coefficient is studied using these new boundary conditions. Then, numerical results from this new beam model are presented for carbon nanotubes (CNTs). They illustrate a more accurate buckling response as compared to the previous works. Furthermore, the critical strains are compared with results obtained from molecular dynamic simulations as well as Sanders shell theory and are found to be in good agreement. Results show that unlike the other beam theories, this model can capture correctly the small-scale effects on buckling strains of short CNTs for the shell-type buckling. Moreover, the value of nonlocal constant is calculated for CNTs using molecular dynamic simulation results. (author)
A fermionic molecular dynamics technique to model nuclear matter
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)
Molecular Dynamic Simulation of Failure of Ettringite
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.
The 2011 Dynamics of Molecular Collisions Conference
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
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
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
Dynamics and Thermodynamics of Molecular Machines
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
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
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
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
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
In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfer process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps−1, which is about 2.5 times faster than that in vacuum, 0.27 ps−1. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction
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.
Carbon Nanotube Based Molecular Electronics
Srivastava, Deepak; Saini, Subhash; Menon, Madhu
1998-01-01
Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.
Graphical abstract: Two trajectories for the collision of a proton with the Lithium tetramer. On the left, the proton is scattered away, and a Li2 molecule plus two isolated Lithium atoms result. On the right, the proton is captured and a LiH molecule is created. Highlights: ► Scattering of a proton with Lithium clusters described from first principles. ► Description based on non-adiabatic molecular dynamics. ► The electronic structure is described with time-dependent density-functional theory. ► The method allows to discern reaction channels depending on initial parameters. - Abstract: We have employed non-adiabatic molecular dynamics based on time-dependent density-functional theory to characterize the scattering behavior of a proton with the Li4 cluster. This technique assumes a classical approximation for the nuclei, effectively coupled to the quantum electronic system. This time-dependent theoretical framework accounts, by construction, for possible charge transfer and ionization processes, as well as electronic excitations, which may play a role in the non-adiabatic regime. We have varied the incidence angles in order to analyze the possible reaction patterns. The initial proton kinetic energy of 10 eV is sufficiently high to induce non-adiabatic effects. For all the incidence angles considered the proton is scattered away, except in one interesting case in which one of the Lithium atoms captures it, forming a LiH molecule. This theoretical formalism proves to be a powerful, effective and predictive tool for the analysis of non-adiabatic processes at the nanoscale.
Molecular dynamics simulation of impact test
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
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
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.
Rybakova, K.N.; Tomaszewska, A.; Mourik, S. van; Blom, J.G.; Westerhoff, H.V.; Carlberg, C.; Bruggeman, F.J.
2014-01-01
Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in response to external signals or as a result of a dise
Rybakova, K.N.; Tomaszewska, A.; Mourik, van S.; Blom, Joke; Westerhoff, H.V.; Carlberg, C.; Bruggeman, F.J.
2015-01-01
Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in response to external signals or as a result of a dise
K.N. Rybakova; A. Tomaszewska; S. van Mourik; J. Blom; H.V. Westerhoff; C. Carlberg; F.J. Bruggeman
2015-01-01
Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in response to external signals or as a result of a dise
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
Environmental Phosphorus Recovery Based on Molecular Bioscavengers
Gruber, Mathias Felix
technology based on biological phosphorus scavengers, to examine fundamental molecular system aspects relevant for such a technology, and to motivate the use of computational techniques throughout an iterative design process of such a technology. A wide spectrum of computational methods, from atomic...... characteristic amino acid distributions of the binding sites. Quantum mechanical methods are used to investigate how phosphate moieties are described using electronic structure methods, and molecular dynamics in combination with quantum mechanics are used to show how the dynamical interaction between phosphates......-scale quantum calculations to macro-scale fluid simulations, are employed to hint at the potential of a recovery technology based on molecular bioscavengers. As a first approach, data mining is used to obtain statistical information about how proteins in nature interact with phosphate groups, thereby revealing...
Yuxin Zhang
2012-02-01
Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation
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
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
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
A molecular dynamics simulation code ISIS
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)
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.
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...
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...
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...
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 quantum dynamics. From theory to applications
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
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
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
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
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...
Liu, Y.L. [Institute of Materials Physics and Chemistry, School of Sciences, Northeastern University, Shenyang 110819 (China); Shahzad, M. Babar [Institute of Materials Physics and Chemistry, School of Sciences, Northeastern University, Shenyang 110819 (China); Institute of Metals Research, Chinese Academy of Sciences, Shenyang 110016 (China); Qi, Y., E-mail: qiyang@imp.neu.edu.cn [Institute of Materials Physics and Chemistry, School of Sciences, Northeastern University, Shenyang 110819 (China)
2015-04-15
Highlights: • The O/Zn effect on the non-polar a-axis film growth is studied at the atomic scale. • The optimized film quality is achieved through a series of ReaxFF based MD study. • A film growth mode (singular atom → cluster → chains → continue film) is revealed. • The transformed way of the defective substrate to the perfect stacking is revealed. - Abstract: The understanding of the growth process and formation mechanism of non-polar ZnO films in atomic-scale is crucial in adjusting and controlling the film deposition conditions. Using the advanced reactive force field based molecular dynamics method, we theoretically studied the effect of O/Zn ratios (8/10–10/8) on the quality of ZnO films. The comprehensive investigation of energy and temperature fluctuation profile, radial distribution function, the sputtering and injecting phenomenon, and layer coverage indicated that the film grown under stoichiometric conditions possesses the optimized quality. Furthermore, the auto-transformation ability of the substrate from defective to perfect stacking was presented and discussed by comparing to the perfect structure. The instant film growth configurations, atomic layer snapshots, and the interfacial morphology evolution were provided step-by-step to reveal the defect type and initial film nucleation and growth mechanism.
Oliveira, Edson R A; de Alencastro, Ricardo B; Horta, Bruno A C
2016-09-01
The flavivirus non-structural protein 1 (NS1) is a conserved glycoprotein with as yet undefined biological function. This protein dimerizes when inside infected cells or associated to cell membranes but also forms lipid-associated hexamers when secreted to the extracellular space. A single amino acid substitution (P250L) is capable of preventing the dimerization of NS1 resulting in lower virulence and slower virus replication. In this work, based on molecular dynamics simulations of the dengue-2 virus NS1 [Formula: see text]-ladder monomer as a core model, we found that this mutation can induce several conformational changes that importantly affect critical monomer-monomer interactions. Based on additional simulations, we suggest a mechanism by which a highly orchestrated sequence of events propagate the local perturbations around the mutation site towards the dimer interface. The elucidation of such a mechanism could potentially support new strategies for rational production of live-attenuated vaccines and highlights a step forward in the development of novel anti-flavivirus measures. PMID:27324799
Molecular Dynamics Studies of Nanofluidic Devices
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
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.
Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng
2015-12-01
To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are
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...
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
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.
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
Application of optimal prediction to molecular dynamics
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.
In this work, Pa(V) mono-cations have been studied in liquid water by means of density functional theory (DFT) based molecular dynamic simulations (CPMD) and compared with their U(VI) isoelectronic counterparts to understand the peculiar chemical behavior of Pa(V) in aqueous solution. Four different Pa(V) monocationic isomers appear to be stable in liquid water from our simulations: [PaO2(H2O)5]+(aq), [Pa(OH)4(H2O)2]+(aq), [PaO(OH)2(H2O)4]+(aq), and [Pa(OH)4(H2O)3]+(aq). On the other hand, in the case of U(VI) only the uranyl, [UO2(H2O)5]2+(aq), is stable. The other species containing hydroxyl groups replacing one or two oxo bonds are readily converted to uranyl. The Pa-OH bond is stable, while it is suddenly broken in U-OH. This makes possible the formation of a broad variety of Pa(V) species in water and participates to its unique chemical behavior in aqueous solution. Further, the two actinyl oxo-cations in water are different in the ability of the oxygen atoms to form stable and extended H-bond networks for Pa(V) contrary to U(VI). In particular, prot-actinyl is found to have between 2 and 3 hydrogen bonds per oxygen atom while uranyl has between zero and one. (authors)
Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng
2016-01-14
To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results. PMID:26658834
XUE Xiang-gui; ZHAO Li; L(U) Zhong-yuan; QIAN Hu-iun
2013-01-01
Molecular dynamics simulation was used to study the ionic liquid(IL) crystalline film based on 1-ethyl-3-methylimidazolium bis[trifluoromethylsulfonyl]imide([emim][Tf2N]) and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate([emim][TfO]) on the graphite surface.Our results show that the cations are parallelly dis-tributed to the surface in the l/2 monolayer(ML) crystalline film.The [Tf2N] anions are parallel to the surface with the oxygen atoms at the bottom,whereas the [TfO] anions are perpendicularly distributed to the surface also with the oxygen atoms at the bottom in the 1/2 ML crystalline film.It has been found that the IL-vapor interface strongly influences the arrangement of ions at the interface.The anions in the top layer with the oxygen atoms outmost turn over to make themselves with the F atoms outmost so as to form C-H...O hydrogen bonds with the cations.The calculated orientational ordering shows that in the outmost layer at the IL-vapor interface,the cation rings present either parallel or perpendicular to the surface at 350 K.
Nano-tribology through molecular dynamics simulations
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.
Molecular dynamic results on transport properties
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
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
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
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.
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
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)
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
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.
Stadler, Adrian-Mihail; Ramírez, Juan
2012-01-01
The present chapter is focused on how synthetic molecular machines (e.g. shuttles, switches and molecular motors) and size switches (conversions between polymers and their units, i.e., conversions between relatively large and small molecules) can function through covalent changes. Amongst the interesting examples of devices herein presented are molecular motors and size switches based on dynamic covalent chemistry which is an area of constitutional dynamic chemistry. PMID:22169959
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
Molecular dynamics analysis on impact behavior of carbon nanotubes
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
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.
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.
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 ...
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.
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.
Thermal conductivity of ZnTe investigated by molecular dynamics
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.