one-microsecond molecular dynamics: Topics by WorldWideScience.org

Sample records for one-microsecond molecular dynamics

Microsecond atomic-scale molecular dynamics simulations of polyimides

NARCIS (Netherlands)

Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

2013-01-01

We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long
Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel

DEFF Research Database (Denmark)

Bjelkmar, Pär; Niemelä, Perttu S; Vattulainen, Ilpo

2009-01-01

transitions occur in membrane proteins-not to mention numerous applications in drug design. Here, we present a full 1 micros atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements......Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how...... and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations....
Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response.

Directory of Open Access Journals (Sweden)

Elio A Cino

Full Text Available Intrinsically disordered proteins (IDPs are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTα and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2, with a common binding partner, Kelch-like ECH-associated protein 1(Keap1, are essential for regulating cellular response to oxidative stress. Misregulation of this pathway can lead to neurodegenerative diseases, premature aging and cancer. In order to understand the mechanisms these two disordered proteins employ to bind to Keap1, we performed extensive 0.5-1.0 microsecond atomistic molecular dynamics (MD simulations and isothermal titration calorimetry experiments to investigate the structure/dynamics of free-state ProTα and Neh2 and their thermodynamics of bindings. The results show that in their free states, both ProTα and Neh2 have propensities to form bound-state-like β-turn structures but to different extents. We also found that, for both proteins, residues outside the Keap1-binding motifs may play important roles in stabilizing the bound-state-like structures. Based on our findings, we propose that the binding of disordered ProTα and Neh2 to Keap1 occurs synergistically via preformed structural elements (PSEs and coupled folding and binding, with a heavy bias towards PSEs, particularly for Neh2. Our results provide insights into the molecular mechanisms Neh2 and ProTα bind to Keap1, information that is useful for developing therapeutics to enhance the oxidative stress response.
Increasing the power of accelerated molecular dynamics methods and plans to exploit the coming exascale

Science.gov (United States)

Voter, Arthur

Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

DEFF Research Database (Denmark)

Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

2008-01-01

. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...
Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

Directory of Open Access Journals (Sweden)

Kai Wang

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

Science.gov (United States)

Shinoda, Wataru; Hatanaka, Yuta; Hirakawa, Masashi; Okazaki, Susumu; Tsuzuki, Seiji; Ueno, Kazuhide; Watanabe, Masayoshi

2018-05-01

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions.
Challenges in analysing and visualizing large-scale molecular dynamics simulations: domain and defect formation in lung surfactant monolayers

International Nuclear Information System (INIS)

Mendez-Villuendas, E; Baoukina, S; Tieleman, D P

2012-01-01

Molecular dynamics simulations have rapidly grown in size and complexity, as computers have become more powerful and molecular dynamics software more efficient. Using coarse-grained models like MARTINI system sizes of the order of 50 nm × 50 nm × 50 nm can be simulated on commodity clusters on microsecond time scales. For simulations of biological membranes and monolayers mimicking lung surfactant this enables large-scale transformation and complex mixtures of lipids and proteins. Here we use a simulation of a monolayer with three phospholipid components, cholesterol, lung surfactant proteins, water, and ions on a ten microsecond time scale to illustrate some current challenges in analysis. In the simulation, phase separation occurs followed by formation of a bilayer fold in which lipids and lung surfactant protein form a highly curved structure in the aqueous phase. We use Voronoi analysis to obtain detailed physical properties of the different components and phases, and calculate local mean and Gaussian curvatures of the bilayer fold.
Molecular dynamics studies of crystalline nucleation in one-component Yukawa plasmas

International Nuclear Information System (INIS)

Ravelo, R.; Hammerberg, J.E.; Holian, B.L.

1992-01-01

We report on molecular dynamics studies of one-component Yukawa plasmas undergoing rapid quenches from a fluid state with a Coulomb parameter Γ = 40 to solid states in the range 350 < Γ < 800. The detailed dynamical structure of ordering appears more complicated than results from classical theories of nucleation, with planar formation being observed before fully 3-dimensional ordering appears
Computational exploration of single-protein mechanics by steered molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Sotomayor, Marcos [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio (United States)

2015-12-31

Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.
Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

Science.gov (United States)

Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

2014-09-01

Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.
Design and testing of a surface switch for the dynamic load current multiplier on the SPHINX microsecond LTD

International Nuclear Information System (INIS)

Maysonnave, T.; Bayol, F.; Demol, G.; Almeida, T. d'; Morell, A.; Lassalle, F.; Grunenwald, J.; Chuvatin, A.S.; Pecastaing, L.; De Ferron, A.S.

2013-01-01

SPHINX is a microsecond linear transformer driver located at Atomic Energy Commission (CEA) Gramat (France), which can deliver a current pulse of 6 MA within 800 ns in a Z-pinch load. Using the concept of the dynamic load current multiplier (DLCM), which was proposed by Chuvatin, we expect to increase the load current above 6 MA, while decreasing its rise time to ∼300 ns. The DLCM developed by the CEA Gramat and International Technologies for High Pulsed Power (ITHPP) is a compact system made up of concentric electrodes (auto-transformer), a dynamic flux extruder (cylindrical wire array), a vacuum convolute (eight post-hole rods), and a closing switch (compact vacuum surface switch). The latter is a key component of the system, which is used to prevent the current from flowing into the load until the inductance builds up due to the implosion of the wire array. This paper presents the design and testing of the DLCM surface switch, resulting from both electrostatic simulations and experiments on the SPHINX generator. These studies, carried out either with or without load (open circuit), were valuable for a first experimental evaluation of the DLCM scheme in a microsecond regime and provided detailed information on the surface switch behavior. (authors)
Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

Science.gov (United States)

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

2013-11-07

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

DEFF Research Database (Denmark)

Wei, Michael Yung Chung; Bjørling, Matias; Bonnet, Philippe

2014-01-01

are suboptimal for microsecond devices - they either block the processor for tens of microseconds or yield the processor only to be ready again microseconds later. Speculation is an alternative technique that resolves the issues of yielding and blocking by enabling an application to continue running until...... the application produces an externally visible side effect. State-of-the-art techniques for speculating on I/O requests involve checkpointing, which can take up to a millisecond, squandering any of the performance bene-fits microsecond scale devices have t o offer. In this paper, we survey how speculation can...... address the challenges that microsecond scale devices will bring. We measure applications for the potential benefit to be gained from speculation and examine several classes of speculation techniques. In addition, we propose two new techniques, hardware checkpoint and checkpoint-free speculation. Our...
Spin-diffusions and diffusive molecular dynamics

Science.gov (United States)

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

2017-12-01

Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.
A 2-gigawatt, 1-microsecond, microwave source

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Caryotakis, G; Jongewaard, E; Phillips, R; Scheitrum, G; Tantawi, S [Stanford Univ., CA (United States). Stanford Linear Accelerator Center; Luhmann, Jr, N C [Univ. of California, Davis, CA (United States)

1997-12-31

For the last decade or more, researchers in a number of US government laboratories have been attempting to develop L-band microwave sources capable of generating one or more gigawatts, with one-microsecond pulses. In order to produce the required high beam currents, the common approach has been to employ field emission cathodes. For this and other reasons the devices which have been built (MILOs, RKAs, relativistic magnetrons) have operated with a poor vacuum, a condition not consistent with the necessity to hold off the very high rf and dc gradients encountered at these power levels. As a result, the microsecond goal has never been attained. Although in some cases several gigawatts have been generated, pulse duration is limited to about 100 ns. This condition is referred to as ``pulse shortening``. The proposed source is based on periodic magnetic (PPM) focusing and is an outgrowth of work performed at SLAC on very high peak power X-band klystrons for a future electron-positron linear collider. These tubes must be focused with permanent magnets, for economic reasons. The new device (GMBK, for Gigawatt Multiple Beam Klystron) is entirely within the state-of-the-art and need only depend on good vacuum tube practice to perform to its specification. It employs thermionic cathodes, loaded to about 40 A/cm{sup 2}, a current density which is within the state-of-the-art for microsecond pulses. (author). 8 figs.
Simulations of the structure and dynamics of nanoparticle-based ionic liquids

KAUST Repository

Hong, Bingbing; Chremos, Alexandros; Panagiotopoulos, Athanassios Z.

2012-01-01

We use molecular dynamics simulations over microsecond time scales to study the structure and dynamics of coarse-grained models for nanoparticle-based ionic liquids. The systems of interest consist of particles with charged surface groups and linear
Modelling Protein Dynamics on the Microsecond Time Scale

DEFF Research Database (Denmark)

Siuda, Iwona Anna

Recent years have shown an increase in coarse-grained (CG) molecular dynamics simulations, providing structural and dynamic details of large proteins and enabling studies of self-assembly of biological materials. It is not easy to acquire such data experimentally, and access is also still limited...... in atomistic simulations. During her PhD studies, Iwona Siuda used MARTINI CG models to study the dynamics of different globular and membrane proteins. In several cases, the MARTINI model was sufficient to study conformational changes of small, purely alpha-helical proteins. However, in studies of larger......ELNEDIN was therefore proposed as part of the work. Iwona Siuda’s results from the CG simulations had biological implications that provide insights into possible mechanisms of the periplasmic leucine-binding protein, the sarco(endo)plasmic reticulum calcium pump, and several proteins from the saposin-like proteins...
Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

Science.gov (United States)

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.
Microsecond MD Simulations of Nano-patterned Polymer Brushes on Self-Assembled Monolayers

Science.gov (United States)

Buie, Creighton; Qiu, Liming; Cheng, Kwan; Park, Soyeun

2010-03-01

Nano-patterned polymer brushes end-grafted onto self-assembled monolayers have gained increasing research interests due to their unique thermodynamic properties and their chemical and biomedical applications in colloids, biosensing and tissue engineering. So far, the interactions between the polymer brushes with the surrounding environments such as the floor and solvent at the nanometer length scale and microsecond time scale are still difficult to obtained experimentally and computationally. Using a Coarse-Grained MD approach, polymer brushes of different monomeric lengths, grafting density and hydrophobicity of the monomers grafted on self-assembled monolayers and in explicit solvent were studied. Molecular level information, such as lateral diffusion, transverse height and volume contour of the brushes, were calculated from our microsecond-MD simulations. Our results demonstrated the significance of the hydration of the polymer in controlling the conformational arrangement of the polymer brushes.

Investigation of switch designs for the dynamic load current multiplier scheme on the SPHYNX microsecond linear transformer driver

International Nuclear Information System (INIS)

Maysonnave, T.; Bayol, F.; Demol, G.; Almeida, T. d'; Lassalle, F.; Morell, A.; Grunenwald, J.; Chuvatin, A.S.; Pecastaing, L.; De Ferron, A.S.

2014-01-01

SPHINX is a microsecond linear transformer driver LTD, used essentially for implosion of Z-pinch loads in direct drive mode. It can deliver a 6-MA current pulse within 800 ns into a Z-pinch load. The dynamic load current multiplier concept enables the current pulse to be modified by increasing its amplitude while reducing its rise time before being delivered to the load. This compact system is made up of concentric electrodes (auto transformer), a dynamic flux extruder (cylindrical wire array), a vacuum convolute (eight post-holes), and a vacuum closing switch, which is the key component of the system. Several different schemes are investigated for designing a vacuum switch suitable for operating the dynamic load current multiplier on the SPHINX generator for various applications, including isentropic compression experiments and Z-pinch radiation effects studies. In particular, the design of a compact vacuum surface switch and a multichannel vacuum switch, located upstream of the load are studied. Electrostatic simulations supporting the switch designs are presented along with test bed experiments. Initial results from shots on the SPHINX driver are also presented. (authors)
Color molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Hatsuda, Tetsuo

2000-01-01

We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)
Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

Science.gov (United States)

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Microsecond time-scale kinetics of transient biochemical reactions

NARCIS (Netherlands)

Mitic, S.; Strampraad, M.J.F.; Hagen, W.R.; de Vries, S.

2017-01-01

To afford mechanistic studies in enzyme kinetics and protein folding in the microsecond time domain we have developed a continuous-flow microsecond time-scale mixing instrument with an unprecedented dead-time of 3.8 ± 0.3 μs. The instrument employs a micro-mixer with a mixing time of 2.7 μs
Dynamical properties and transport coefficients of one-dimensional Lennard-Jones fluids: A molecular dynamics study

Science.gov (United States)

Bazhenov, Alexiev M.; Heyes, David M.

1990-01-01

The thermodynamics, structure, and transport coefficients, as defined by the Green-Kubo integrals, of the one-dimensional Lennard-Jones fluid are evaluated for a wide range of state points by molecular dynamics computer simulation. These calculations are performed for the first time for thermal conductivity and the viscosity. We observe a transition from hard-rod behavior at low number density to harmonic-spring fluid behavior in the close-packed limit. The self-diffusion coefficient decays with increasing density to a finite limiting value. The thermal conductivity increases with density, tending to ∞ in the close-packed limit. The viscosity in contrast maximizes at intermediate density, tending to zero in the zero density and close-packed limits.
Probing the energy landscape of alanine dipeptide and decalanine using temperature as a tunable parameter in molecular dynamics

International Nuclear Information System (INIS)

Chatterjee, A; Bhattacharya, S

2016-01-01

We perform several molecular dynamics (MD) calculations of solvated alanine dipeptide and decalanine in vacuum with temperature as a tunable parameter and in the process, generate Markov state models (MSMs) at each temperature. An interesting observation that the kinetic rates appear to obey the Arrhenius rate law allows us to predict the dynamics of alanine dipeptide at 300 K at the microsecond timescales using the nanoseconds long high temperature calculations without actually performing MD simulations at 300 K. We conclude that the energy landscape of alanine dipeptide contains superbasins deeper than k B T and determine the energy barriers associated with the moves from the Arrhenius rate expression. Similar insights regarding the energy landscape associated with folding/unfolding pathways of a deca-alanine molecule are obtained using kinetic rates calculated at different temperatures. (paper)
Structural and functional analysis of glycoprotein butyrylcholinesterase using atomistic molecular dynamics

Science.gov (United States)

Bernardi, Austen; Faller, Roland

Atomistic molecular dynamics (MD) has proven to be a powerful tool for studying the structure and dynamics of biological systems on nanosecond to microsecond time scales and nanometer length scales. In this work we study the effects of modifying the glycan distribution on the structure and function of full length monomeric butyrylcholinesterase (BChE). BChE exists as a monomer, dimer, or tetramer, and is a therapeutic glycoprotein with nine asparagine glycosylation sites per monomer. Each monomer acts as a stoichiometric scavenger for organophosphorus (OP) nerve agents (e.g. sarin, soman). Glycan distributions are highly heterogeneous and have been shown experimentally to affect certain glycoproteins' stability and reactivity. We performed structural analysis of various biologically relevant glycoforms of BChE using classical atomistic MD. Functional analysis was performed through binding energy simulations using umbrella sampling with BChE and OP cofactors. Additionally, we assess the quality of the glycans' conformational sampling. We found that the glycan distribution has a significant effect on the structure and function of BChE on timescales available to atomistic MD. This project is funded by the DTRA Grant HDTRA1-15-1-0054.
Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

Directory of Open Access Journals (Sweden)

Lin Lin

2013-12-01

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

Czech Academy of Sciences Publication Activity Database

Dans, P. D.; Danilane, L.; Ivani, I.; Dršata, Tomáš; Lankaš, Filip; Hospital, A.; Walther, J.; Pujagut, R. I.; Battistini, F.; Gelpí, J. L.; Lavery, R.; Orozco, M.

2016-01-01

Roč. 44, č. 9 (2016), s. 4052-4066 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GA14-21893S Institutional support: RVO:61388963 Keywords : microsecond molecular dynamics * B-DNA dodecamer * analyzing ion distributions Subject RIV: CE - Biochemistry Impact factor: 10.162, year: 2016 http://nar.oxfordjournals.org/content/44/9/4052.full
A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

Science.gov (United States)

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

2017-06-20

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

Energy Technology Data Exchange (ETDEWEB)

Ginger, David; Giridharagopal, Rajiv; Moore, David; Rayermann, Glennis; Reid, Obadiah

2014-04-01

Methods and apparatus are provided herein for time-resolved analysis of the effect of a perturbation (e.g., a light or voltage pulse) on a sample. By operating in the time domain, the provided method enables sub-microsecond time-resolved measurement of transient, or time-varying, forces acting on a cantilever.
Molecular dynamics of shock waves in one-dimensional chains. II. Thermalization

International Nuclear Information System (INIS)

Straub, G.K.; Holian, B.L.; Petschek, R.G.

1979-01-01

The thermalization behavior behind a shock front in one-dimensional chains has been studied in a series of molecular-dynamics computer experiments. We have found that a shock wave generated in a chain initially at finite temperature has essentially the same characteristics as in a chain initially at zero temperature. We also find that the final velocity distribution function for particles behind the shock front is not the Maxwell-Boltzmann distribution for an equilibrium system of classical particles. For times long after the shock has passed, we propose a nonequilibrium velocity distribution which is based upon behavior in the harmonic and hard-rod limits and agrees with our numerical results. Temperature profiles for both harmonic and anharmonic chains are found to exhibit a long-time tail that decays inversely with time. Finally, we have run a computer experiment to generate what qualitatively resembles solitons in Toda chains by means of shock waves
Accelerated molecular dynamics methods: introduction and recent developments

Energy Technology Data Exchange (ETDEWEB)

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

2009-01-01

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

International Nuclear Information System (INIS)

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

2009-01-01

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

Science.gov (United States)

Luengo, Elisa; Martínez, Juan Manuel; Coustets, Mathilde; Álvarez, Ignacio; Teissié, Justin; Rols, Marie-Pierre; Raso, Javier

2015-10-01

The interdependencies of the two main processing parameters affecting "electroporation" (electric field strength and pulse duration) while using pulse duration in the range of milliseconds and microseconds on the permeabilization, inactivation, and extraction of pigments from Chlorella vulgaris was compared. While irreversible "electroporation" was observed above 4 kV/cm in the millisecond range, electric field strengths of ≥10 kV/cm were required in the microseconds range. However, to cause the electroporation of most of the 90 % of the population of C. vulgaris in the millisecond (5 kV/cm, 20 pulses) or microsecond (15 kV/cm, 25 pulses) range, the specific energy that was delivered was lower for microsecond treatments (16.87 kJ/L) than in millisecond treatments (150 kJ/L). In terms of the specific energy required to cause microalgae inactivation, treatments in the microsecond range also resulted in greater energy efficiency. The comparison of extraction yields in the range of milliseconds (5 kV, 20 ms) and microseconds (20, 25 pulses) under the conditions in which the maximum extraction was observed revealed that the improvement in the carotenoid extraction was similar and chlorophyll a and b extraction was slightly higher for treatments in the microsecond range. The specific energy that was required for the treatment in the millisecond range (150 kJ/L) was much higher than those required in the microsecond range (30 kJ/L). The comparison of the efficacy of both types of pulses on the extraction enhancement just after the treatment and after a post-pulse incubation period seemed to indicate that PEF in the millisecond range created irreversible alterations while, in the microsecond range, the defects were a dynamic structure along the post-pulse time that caused a subsequent increment in the extraction yield.
Microsecond yellow laser for subfoveal leaks in central serous chorioretinopathy

Directory of Open Access Journals (Sweden)

Ambiya V

2016-08-01

Full Text Available Vikas Ambiya, Abhilash Goud, Annie Mathai, Padmaja Kumari Rani, Jay Chhablani Srimati Kanuri Santhamma Retina Vitreous Center, Kallam Anji Reddy Campus, L. V. Prasad Eye Institute, Hyderabad, India Purpose: To evaluate the role of navigated yellow microsecond laser in treating subfoveal leaks in nonresolving central serous chorioretinopathy (CSC. Methods: This prospective study included ten eyes of ten consecutive patients with nonresolving CSC with subfoveal leaks. All eyes were treated with 577 nm navigated yellow microsecond laser (5% duty cycle. Key inclusion criteria include a vision loss for a duration of minimum 3 months duration due to focal subfoveal leak on fluorescein angiography. Key exclusion criteria include prior treatment for CSC and any signs of chronic CSC. Comprehensive examination, in addition to low-contrast visual acuity assessment, microperimetry, autofluorescence, spectral domain optical coherence tomography, and fundus fluorescein angiography, was done at baseline, 1, 3, and 6 months after treatment. Rescue laser was performed as per predefined criteria at 3 months. Results: The average best-corrected visual acuity improved from 73.3±16.1 letters to 75.8±14.0 (P=0.69 at 3 months and 76.9±13.0 (P=0.59 at 6 months, but was not statistically significant. Low-contrast visual acuity assessment (logMAR improved from 0.41±0.32 to 0.35±0.42 (P=0.50 at 3 months and 0.28±0.33 (P=0.18 at 6 months. Average retinal sensitivity significantly improved from baseline 18.93±7.19 dB to 22.49±6.67 dB (P=0.01 at 3 months and 21.46±8.47 dB (P=0.04 at 6 months. Rescue laser was required only in one eye at 3 months; however, laser was required in three eyes at 6 months. Conclusion: Microsecond laser is a safe and effective modality for treating cases of nonresolving CSC with subfoveal leaks. Keywords: CSC, central serous chorioretinopathy, Navilas®, navigated laser, microsecond yellow laser
Molecular dynamics with deterministic and stochastic numerical methods

CERN Document Server

Leimkuhler, Ben

2015-01-01

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

International Nuclear Information System (INIS)

Li, Shaofan; Tong, Qi

2015-01-01

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

International Nuclear Information System (INIS)

Souvatzis, Petros; Niklasson, Anders M. N.

2014-01-01

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

CERN Document Server

Fisher, David

2013-01-01

The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

Water Dynamics in the Hydration Shells of Biomolecules

Science.gov (United States)

2017-01-01

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water. PMID:28248491
A theory of electron baths: One-electron system dynamics

International Nuclear Information System (INIS)

McDowell, H.K.

1992-01-01

The second-quantized, many-electron, atomic, and molecular Hamiltonian is partitioned both by the identity or labeling of the spin orbitals and by the dynamics of the spin orbitals into a system coupled to a bath. The electron bath is treated by a molecular time scale generalized Langevin equation approach designed to include one-electron dynamics in the system dynamics. The bath is formulated as an equivalent chain of spin orbitals through the introduction of equivalent-chain annihilation and creation operators. Both the dynamics and the quantum grand canonical statistical properties of the electron bath are examined. Two versions for the statistical properties of the bath are pursued. Using a weak bath assumption, a bath statistical average is defined which allows one to achieve a reduced dynamics description of the electron system which is coupled to the electron bath. In a strong bath assumption effective Hamiltonians are obtained which reproduce the dynamics of the bath and which lead to the same results as found in the weak bath assumption. The effective (but exact) Hamiltonian is found to be a one-electron Hamiltonian. A reduced dynamics equation of motion for the system population matrix is derived and found to agree with a previous version. This equation of motion is useful for studying electron transfer in the system when coupled to an electron bath
Study of electron and ion fluxes in a microsecond plasma switch during current switch phase at power level of 0,2TW

International Nuclear Information System (INIS)

Anan'in, P.S.; Bystritskij, V.M.; Karpov, V.B.; Krasik, Ya.E.; Lisitsin, I.V.; Sinebryukhov, A.A.

1991-01-01

Results of experimental study of dynamics of electron and ion losses in a microsecond plasma switch (PS), carring the short-circuited inductance load and operating with open potential electrode, are presented. Investigations were carried out at 'DUBL' microsecond generator with stored energy of 56 kJ and 300 kA current amplitude in inductive storage. The investigations showed that primary channel of energy losses, limiting microsecond plasma switch impedance, are energy losses: they constitute 70% of all losses under inductive load and 30% during operation with an open cathode. It was shown that ion current in PS attains its peak value by the end of conductivity phase and it does not increase in switch phase. With an open cathode, PS impedance is defined by an electron beam, forming during current switch phase and propagating towards external electrode end. In this high-current electron beam H + ions, accelerated up to 3.5-4.2 MeV energy, and outcoming from PS plasma boundary, were detected
An Investigation of the Sub-Microsecond Features of Dynamic Crack Propagation in PMMA and the Rdx-Based Explosive PBX 9205

Science.gov (United States)

Washabaugh, P. D.; Hill, L. G.

2007-12-01

A dynamic crack propagating in a brittle material releases enough thermal energy to produce visible light. The dynamic fracture of even macroscopically amorphous materials becomes unsteady as the crack propagation velocity approaches the material wave-speeds. The heat generated at a crack-tip, especially as it jumps, may be a mechanism to initiate a self-sustaining reaction in an energetic material. Experiments were conducted in specimens to simulate an infinite plate for ˜10 μs. The initial specimens were 152 mm square by 6 mm thick acrylic sheets, and were fabricated to study non-steady near-wave-speed crack propagation. A variant of this specimen embedded a 25 mm×3 mm PBX 9205 pellet to explore the influence of dynamic Mode-I cracks in these materials. The crack was initiated by up to 0.24 g of Detasheet placed along a precursor 50 mm long notch, with a shield to contain the reaction products and prevent propagation along the fractured surfaces. The crack was studied by means of a streak camera and a Fourier-filter of the light reflecting off the newly minted surfaces. The sub-microsecond behavior of holes initiating, preceding and coalescing with the main crack were observed in the PMMA samples. The embedding and mechanical loading of explosives by this technique did not initiate a self-sustaining reaction in preliminary testing.
Combination of microsecond and nanosecond pulsed electric field treatments for inactivation of Escherichia coli in water samples.

Science.gov (United States)

Žgalin, Maj Kobe; Hodžić, Duša; Reberšek, Matej; Kandušer, Maša

2012-10-01

Inactivation of microorganisms with pulsed electric fields is one of the nonthermal methods most commonly used in biotechnological applications such as liquid food pasteurization and water treatment. In this study, the effects of microsecond and nanosecond pulses on inactivation of Escherichia coli in distilled water were investigated. Bacterial colonies were counted on agar plates, and the count was expressed as colony-forming units per milliliter of bacterial suspension. Inactivation of bacterial cells was shown as the reduction of colony-forming units per milliliter of treated samples compared to untreated control. According to our results, when using microsecond pulses the level of inactivation increases with application of more intense electric field strengths and with number of pulses delivered. Almost 2-log reductions in bacterial counts were achieved at a field strength of 30 kV/cm with eight pulses and a 4.5-log reduction was observed at the same field strength using 48 pulses. Extending the duration of microsecond pulses from 100 to 250 μs showed no improvement in inactivation. Nanosecond pulses alone did not have any detectable effect on inactivation of E. coli regardless of the treatment time, but a significant 3-log reduction was achieved in combination with microsecond pulses.
High power microwave emission and diagnostics of microsecond electron beams

Energy Technology Data Exchange (ETDEWEB)

Gilgenbach, R; Hochman, J M; Jayness, R; Rintamaki, J I; Lau, Y Y; Luginsland, J; Lash, J S [Univ. of Michigan, Ann Arbor, MI (United States). Intense Electron Beam Interaction Lab.; Spencer, T A [Air Force Phillips Lab., Kirtland AFB, NM (United States)

1997-12-31

Experiments were performed to generate high power, long-pulse microwaves by the gyrotron mechanism in rectangular cross-section interaction cavities. Long-pulse electron beams are generated by MELBA (Michigan Electron Long Beam Accelerator), which operates with parameters: -0.8 MV, 1-10 kA, and 0.5-1 microsecond pulse length. Microwave power levels are in the megawatt range. Polarization control is being studied by adjustment of the solenoidal magnetic field. Initial results show polarization power ratios up to a factor of 15. Electron beam dynamics (V{sub perp}/V{sub par}) are being measured by radiation darkening on glass plates. Computer modeling utilizes the MAGIC Code for electromagnetic waves and a single electron orbit code that includes a distribution of angles. (author). 4 figs., 4 refs.
Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

Directory of Open Access Journals (Sweden)

Zied Gaieb

Full Text Available Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7 bound to its ligand CCL21. Keywords: Molecular dynamics, Change-point detection, Side chain reorganization, Helical domain motion, Intramolecular network, Membrane proteins, GPCR, GPCR computational modeling, GPCR allostery
Molecular Docking, Molecular Dynamics, and Structure-Activity Relationship Explorations of 14-Oxygenated N-Methylmorphinan-6-ones as Potent μ-Opioid Receptor Agonists.

Science.gov (United States)

Noha, Stefan M; Schmidhammer, Helmut; Spetea, Mariana

2017-06-21

Among opioids, morphinans are of major importance as the most effective analgesic drugs acting primarily via μ-opioid receptor (μ-OR) activation. Our long-standing efforts in the field of opioid analgesics from the class of morphinans led to N-methylmorphinan-6-ones differently substituted at positions 5 and 14 as μ-OR agonists inducing potent analgesia and fewer undesirable effects. Herein we present the first thorough molecular modeling study and structure-activity relationship (SAR) explorations aided by docking and molecular dynamics (MD) simulations of 14-oxygenated N-methylmorphinan-6-ones to gain insights into their mode of binding to the μ-OR and interaction mechanisms. The structure of activated μ-OR provides an essential model for how ligand/μ-OR binding is encoded within small chemical differences in otherwise structurally similar morphinans. We reveal important molecular interactions that these μ-agonists share and distinguish them. The molecular docking outcomes indicate the crucial role of the relative orientation of the ligand in the μ-OR binding site, influencing the propensity of critical non-covalent interactions that are required to facilitate ligand/μ-OR interactions and receptor activation. The MD simulations point out minor differences in the tendency to form hydrogen bonds by the 4,5α-epoxy group, along with the tendency to affect the 3-7 lock switch. The emerged SARs reveal the subtle interplay between the substituents at positions 5 and 14 in the morphinan scaffold by enabling the identification of key structural elements that determine the distinct pharmacological profiles. This study provides a significant structural basis for understanding ligand binding and μ-OR activation by the 14-oxygenated N-methylmorphinan-6-ones, which should be useful for guiding drug design.
Ultrafast molecular dynamics illuminated with synchrotron radiation

International Nuclear Information System (INIS)

Bozek, John D.; Miron, Catalin

2015-01-01

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

International Nuclear Information System (INIS)

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

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs
An initial investigation of the sub-microsecond features of dynamic crack propagation in PMMA and the RDX-based explosive PBX 9205

Science.gov (United States)

Washabaugh, Peter; Hill, Larry

2007-06-01

A dynamic crack propagating in a brittle material releases enough thermal energy to produce visible light. The dynamic fracture of even macroscopically amorphous materials becomes unsteady as the crack propagation velocity approaches the material wave-speeds. The heat generated at a crack-tip, especially as it jumps, may be a mechanism to initiate a self-sustaining reaction in an energetic material. Experiments were conducted in specimens to simulate an infinite plate for 20 μs. The initial specimens were 152 mm square by 6 mm thick acrylic sheets, and were fabricated to study non-steady near-wave-speed crack propagation. A variant of this specimen embedded a 25 mm x 3 mm PBX 9205 pellet to explore the influence of dynamic Mode-I cracks in these materials. The crack was initiated by up to 0.2 g of Detasheet placed along a precursor 50 mm long notch, with a shield to contain the reaction products and prevent propagation along the fractured surfaces. The crack was studied by means of a streak camera and a Fourier-filter of the light reflecting off the newly minted surfaces. The sub-microsecond behavior of holes initiating, preceding and coalescing with the main crack were observed in the PMMA samples. The embedding and mechanical loading of explosives by this technique did not initiate a self-sustaining reaction in preliminary testing.
Charged-particle spectroscopy in the microsecond range following projectile fragmentation

CERN Document Server

Pfützner, M; Grzywacz, R; Janas, Z; Momayezi, M; Bingham, C; Blank, B; Chartier, M; Geissel, H; Giovinazzo, J; Hellström, M; Kurcewicz, J; Lalleman, A S; Mazzocchi, C; Mukha, I; Plettner, C; Roeckl, E; Rykaczewski, K; Schmidt, K; Simon, R S; Stanoiu, M; Thomas, J C

2002-01-01

We present a new approach to charged-particle spectroscopy of short-lived nuclei produced by relativistic projectile fragmentation. The system based on digital DGF-4C CAMAC modules and newly developed fast-reset preamplifiers was tested at the Fragment Separator of GSI. We were able to detect low-energy (approx 1 MeV) decay signals occurring a few microseconds after a heavy-ion implantation accompanied by a release of approx 1 GeV energy. Applications for the study of one- and two-proton radioactivity are discussed.
Wire Array Z-pinches on Sphinx Machine: Experimental Results and Relevant Points of Microsecond Implosion Physics

Science.gov (United States)

Calamy, H.; Hamann, F.; Lassalle, F.; Bayol, F.; Mangeant, C.; Morell, A.; Huet, D.; Bedoch, J. P.; Chittenden, J. P.; Lebedev, S. V.; Jennings, C. A.; Bland, S. N.

2006-01-01

Centre d'Etudes de Gramat (France) has developed an efficient long implosion time (800 ns) Aluminum plasma radiation source (PRS). Based on the LTD technology, the SPHINX facility is developed as a 1-3MJ, 1μs rise time, 4-10 MA current driver. In this paper, it was used in 1MJ, 4MA configuration to drive Aluminum nested wire arrays Z-pinches with K-shell yield up to 20 kJ and a FWHM of the x-ray pulse of about 50 ns. We present latest SPHINX experiments and some of the main physic issues of the microsecond regime. Experimental setup and results are described with the aim of giving trends that have been obtained. The main features of microsecond implosion of wire arrays can be analyzed thanks to same methods and theories as used for faster Z-pinches. The effect of load polarity was examined. The stability of the implosion , one of the critical point of microsecond wire arrays due to the load dimensions imposed by the time scale, is tackled. A simple scaling from 100 ns Z-pinch results to 800 ns ones gives good results and the use of nested arrays improves dramatically the implosion quality and the Kshell yield of the load. However, additional effects such as the impact of the return current can geometry on the implosion have to be taken into account on our loads. Axial inhomogeneity of the implosion the origin of which is not yet well understood occurs in some shots and impacts the radiation output. The shape of the radiative pulse is discussed and compared with the homogeneity of the implosion. Numerical 2D R-Z and R-θ simulations are used to highlight some experimental results and understand the plasma conditions during these microsecond wire arrays implosions.
Wire Array Z-pinches on Sphinx Machine: Experimental Results and Relevant Points of Microsecond Implosion Physics

International Nuclear Information System (INIS)

Calamy, H.; Hamann, F.; Lassalle, F.; Bayol, F.; Mangeant, C.; Morell, A.; Huet, D.; Bedoch, J.P.; Chittenden, J.P.; Lebedev, S.V.; Jennings, C.A.; Bland, S.N.

2006-01-01

Centre d'Etudes de Gramat (France) has developed an efficient long implosion time (800 ns) Aluminum plasma radiation source (PRS). Based on the LTD technology, the SPHINX facility is developed as a 1-3MJ, 1μs rise time, 4-10 MA current driver. In this paper, it was used in 1MJ, 4MA configuration to drive Aluminum nested wire arrays Z-pinches with K-shell yield up to 20 kJ and a FWHM of the x-ray pulse of about 50 ns. We present latest SPHINX experiments and some of the main physic issues of the microsecond regime. Experimental setup and results are described with the aim of giving trends that have been obtained. The main features of microsecond implosion of wire arrays can be analyzed thanks to same methods and theories as used for faster Z-pinches. The effect of load polarity was examined. The stability of the implosion , one of the critical point of microsecond wire arrays due to the load dimensions imposed by the time scale, is tackled. A simple scaling from 100 ns Z-pinch results to 800 ns ones gives good results and the use of nested arrays improves dramatically the implosion quality and the Kshell yield of the load. However, additional effects such as the impact of the return current can geometry on the implosion have to be taken into account on our loads. Axial inhomogeneity of the implosion the origin of which is not yet well understood occurs in some shots and impacts the radiation output. The shape of the radiative pulse is discussed and compared with the homogeneity of the implosion. Numerical 2D R-Z and R-θ simulations are used to highlight some experimental results and understand the plasma conditions during these microsecond wire arrays implosions
Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......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...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...
Molecular dynamics and Monte Carlo calculations in statistical mechanics

International Nuclear Information System (INIS)

Wood, W.W.; Erpenbeck, J.J.

1976-01-01

Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references
Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin.

Directory of Open Access Journals (Sweden)

Ayse Ozlem Aykut

Full Text Available We elucidate the mechanisms that lead to population shifts in the conformational states of calcium-loaded calmodulin (Ca(2+-CaM. We design extensive molecular dynamics simulations to classify the effects that are responsible for adopting occupied conformations available in the ensemble of NMR structures. Electrostatic interactions amongst the different regions of the protein and with its vicinal water are herein mediated by lowering the ionic strength or the pH. Amino acid E31, which is one of the few charged residues whose ionization state is highly sensitive to pH differences in the physiological range, proves to be distinctive in its control of population shifts. E31A mutation at low ionic strength results in a distinct change from an extended to a compact Ca(2+-CaM conformation within tens of nanoseconds, that otherwise occur on the time scales of microseconds. The kinked linker found in this particular compact form is observed in many of the target-bound forms of Ca(2+-CaM, increasing the binding affinity. This mutation is unique in controlling C-lobe dynamics by affecting the fluctuations between the EF-hand motif helices. We also monitor the effect of the ionic strength on the conformational multiplicity of Ca(2+-CaM. By lowering the ionic strength, the tendency of nonspecific anions in water to accumulate near the protein surface increases, especially in the vicinity of the linker. The change in the distribution of ions in the vicinal layer of water allows N- and C- lobes to span a wide variety of relative orientations that are otherwise not observed at physiological ionic strength. E31 protonation restores the conformations associated with physiological environmental conditions even at low ionic strength.
Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

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

2014-01-01

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

Energy Technology Data Exchange (ETDEWEB)

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

2010-06-01

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

Science.gov (United States)

Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

2011-12-01

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as

Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

Energy Technology Data Exchange (ETDEWEB)

Lambert, F

2007-08-15

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

Czech Academy of Sciences Publication Activity Database

Islam, B.; Sgobba, M.; Laughton, C.; Orozco, M.; Šponer, Jiří; Neidle, S.; Haider, S.

2013-01-01

Roč. 41, č. 4 (2013), s. 2723-2735 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GAP208/11/1822 Grant - others:GA ČR(CZ) ED1.1.00/02.0068 Program:ED Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS * CRYSTAL-STRUCTURE * B-DNA Subject RIV: BO - Biophysics Impact factor: 8.808, year: 2013
Kinetics from Replica Exchange Molecular Dynamics Simulations.

Science.gov (United States)

Stelzl, Lukas S; Hummer, Gerhard

2017-08-08

Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.
A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Fabrizio Marinelli

2009-08-01

Full Text Available Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.
Pulsed power inductive energy storage in the microsecond range

International Nuclear Information System (INIS)

Rix, W.; Miller, A.R.; Thompson, J.; Waisman, E.; Wilkinson, M.; Wilson, A.

1993-01-01

During the past five years Maxwell has developed a series of inductive energy storage (IES) pulsed power generators; ACE 1, ACE 2, ACE 3, and ACE 4, to drive electron-beam loads. They are all based on a plasma opening switch (POS) contained in a single vacuum envelope operating at conduction times of around one microsecond. They all employ fast capacitor bank technology to match this conduction time without intermediate power conditioning. Oil or air filled transmission lines transfer capacitor bank energy to a vacuum section where the final pulse compression is accomplished. Development of the ACE series is described, emphasizing capacitor bank and the opening switch technology for delivering high voltage, multimegampere pulses to electron beam loads
Lattice dynamics and molecular dynamics simulation of complex materials

International Nuclear Information System (INIS)

Chaplot, S.L.

1997-01-01

In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)
Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

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

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...
Powerful FEM-generator driven by microsecond sheet beam

Energy Technology Data Exchange (ETDEWEB)

Agafonov, M A; Arzhannikov, A V; Sinitskij, S L; Tarasov, A V [Institute of Nuclear Physics, Novosibirsk (Russian Federation); Ginzburg, N S; Peskov, N Yu [Institute of Applied Physics, Nizhny Novgorod (Russian Federation)

1997-12-31

The results of experimental and theoretical investigations in the creation of a powerful mm-band generator driven by a sheet beam are presented. A microsecond pulse of mm-radiation with a 200 J energy content was obtained in the experiments. The possibility of increasing this energy content up to tens of kJ was demonstrated. 3 figs., 8 refs.
Substructured multibody molecular dynamics.

Energy Technology Data Exchange (ETDEWEB)

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

2006-11-01

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

International Nuclear Information System (INIS)

Balucani, U.; Tognetti, V.; Vallauri, R.

1979-01-01

Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy
Reaction dynamics of molecular hydrogen on silicon surfaces

DEFF Research Database (Denmark)

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

1996-01-01

of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...
Decay of surface nanostructures via long-time-scale dynamics

International Nuclear Information System (INIS)

Voter, A.F.; Stanciu, N.

1998-01-01

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have developed a new approach for extending the time scale of molecular dynamics simulations. For infrequent-event systems, the category that includes most diffusive events in the solid phase, this hyperdynamics method can extend the simulation time by a few orders of magnitude compared to direct molecular dynamics. The trajectory is run on a potential surface that has been biased to raise the energy in the potential basins without affecting the transition state region. The method is described and applied to surface and bulk diffusion processes, achieving microsecond and millisecond simulation times. The authors have also developed a new parallel computing method that is efficient for small system sizes. The combination of the hyperdynamics with this parallel replica dynamics looks promising as a general materials simulation tool
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Science.gov (United States)

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.
Protein rotational dynamics investigated with a dual EPR/optical molecular probe. Spin-labeled eosin.

Science.gov (United States)

Cobb, C E; Hustedt, E J; Beechem, J M; Beth, A H

1993-01-01

An acyl spin-label derivative of 5-aminoeosin (5-SLE) was chemically synthesized and employed in studies of rotational dynamics of the free probe and of the probe when bound noncovalently to bovine serum albumin using the spectroscopic techniques of fluorescence anisotropy decay and electron paramagnetic resonance (EPR) and their long-lifetime counterparts phosphorescence anisotropy decay and saturation transfer EPR. Previous work (Beth, A. H., Cobb, C. E., and J. M. Beechem, 1992. Synthesis and characterization of a combined fluorescence, phosphorescence, and electron paramagnetic resonance probe. Society of Photo-Optical Instrumentation Engineers. Time-Resolved Laser Spectroscopy III. 504-512) has shown that the spin-label moiety only slightly altered the fluorescence and phosphorescence lifetimes and quantum yields of 5-SLE when compared with 5-SLE whose nitroxide had been reduced with ascorbate and with the diamagnetic homolog 5-acetyleosin. In the present work, we have utilized time-resolved fluorescence anisotropy decay and linear EPR spectroscopies to observe and quantitate the psec motions of 5-SLE in solution and the nsec motions of the 5-SLE-bovine serum albumin complex. Time-resolved phosphorescence anisotropy decay and saturation transfer EPR studies have been carried out to observe and quantitate the microseconds motions of the 5-SLE-albumin complex in glycerol/buffer solutions of varying viscosity. These latter studies have enabled a rigorous comparison of rotational correlation times obtained from these complementary techniques to be made with a single probe. The studies described demonstrate that it is possible to employ a single molecular probe to carry out the full range of fluorescence, phosphorescence, EPR, and saturation transfer EPR studies. It is anticipated that "dual" molecular probes of this general type will significantly enhance capabilities for extracting dynamics and structural information from macromolecules and their functional
Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-01

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

KAUST Repository

Sandberg, Mattias

2016-01-06

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

International Nuclear Information System (INIS)

Denisov, G.V.; Kuznetsov, D.L.; Novoselov, Yu.N.; Tkachenko, R.M.

2002-01-01

Flue gases of power plants realizing sulfur and nitrogen oxides into the atmosphere represent one of the environmental pollution sources. Paper presents the results of experimental investigations of conversion of sulfur and nitrogen oxides in the ionized gas mixture simulating composition of off-gases of thermal power stations. Pulse beam of microsecond duration electrons was used as a source of ionization. Mutual influence of both types of oxides on process of their conversion is shown. One studied possible kinetic mechanisms to remove sulfur and nitrogen oxides from gaseous mixture [ru
Polymer friction Molecular Dynamics

DEFF Research Database (Denmark)

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

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

International Nuclear Information System (INIS)

Alder, B.J.

1985-07-01

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-05-29

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

One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

Science.gov (United States)

Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

2018-04-12

The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two
Next generation extended Lagrangian first principles molecular dynamics.

Science.gov (United States)

Niklasson, Anders M N

2017-08-07

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

African Journals Online (AJOL)

A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...
An electronic system for simulation of neural networks with a micro-second real time constraint

International Nuclear Information System (INIS)

Chorti, Arsenia; Granado, Bertrand; Denby, Bruce; Garda, Patrick

2001-01-01

Neural networks implemented in hardware can perform pattern recognition very quickly, and as such have been used to advantage in the triggering systems of certain high energy physics experiments. Typically, time constants of the order of a few microseconds are required. In this paper, we present a new system. MAHARADJA, for evaluating MLP and RBF neural network paradigms in real time. The system is tested on a possible ATLAS muon triggering application suggested by the Tel Aviv ATLAS group, consisting of a 4-8-8-4 MLP which must be evaluated in 10 microseconds. The inputs to the net are dx/dz, x(z=0), dy/dz, and y(z=0), whereas the outputs give pt, tan(phi), sin(theta), and q, the charge. With a 10 MHz clock, MAHARADJA calculates the result in 6.8 microseconds; at 20 MHz, which is readily attainable, this would be reduced to only 3.4 microseconds. The system can also handle RBF networks with 3 different distance metrics (Euclidean, Manhattan and Mahalanobis), and can simulate any MLP of 10 hidden layers or less. The electronic implementation is with FPGA's, which can be optimized for a specific neural network because the number of processing elements can be modified
Coalescence of silver unidimensional structures by molecular dynamics simulation

International Nuclear Information System (INIS)

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

2007-01-01

The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Drug delivery with microsecond laser pulses into gelatin

Science.gov (United States)

Shangguan, Hanqun; Casperson, Lee W.; Shearin, Alan; Gregory, Kenton W.; Prahl, Scott A.

1996-07-01

Photoacoustic drug delivery is a technique for localized drug delivery by laser-induced hydrodynamic pressure following cavitation bubble expansion and collapse. Photoacoustic drug delivery was investigated on gelatin-based thrombus models with planar and cylindrical geometries by use of one microsecond laser pulses. Solutions of a hydrophobic dye in mineral oil permitted monitoring of delivered colored oil into clear gelatin-based thrombus models. Cavitation bubble development and photoacoustic drug delivery were visualized with flash photography. This study demonstrated that cavitation is the governing mechanism for photoacoustic drug delivery, and the deepest penetration of colored oil in gels followed the bubble collapse. Spatial distribution measurements revealed that colored oil could be driven a few millimeters into the gels in both axial and radial directions, and the penetration was less than 500 mu m when the gelatin structure was not fractured. localized drug delivery, cavitation bubble, laser thrombolysis.
One-component plasma dynamical structure factor and the plasma dispersion: Method of moments

International Nuclear Information System (INIS)

Adamjan, S.V.; Tkachenko, I.M.; Meyer, T.

1989-01-01

The molecular dynamics data of Hansen, McDonald and Pollock on the dynamical properties of the classical one-component plasma (OCP) are compared with the results based on an approximation formula for the dielectric function satisfying all known sum rules and exact relations using HNC plasma static properties. (author)
Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

Science.gov (United States)

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

2017-12-01

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

International Nuclear Information System (INIS)

Fazio, M.V.; Carlsten, B.E.; Faehl, R.; Kwan, T.J.; Rickel, D.G.; Stringfield, R.M.; Tallerico, P.J.

1991-01-01

Los Alamos is extending the performance of the Friedman-type, high-current relativistic klystron amplifier (RKA) to the microsecond regime while attempting to achieve the gigawatt-level peak power capability that has been characteristic of the RKA at shorter pulse lengths. Currently the electron beam power into the device is about 1 GW in microsecond duration pulses, with an effort underway to increase the beam power to 2.5 GW. To data the device has yielded an rf modulated electron beam power of 350 MW, with up to 50 MW coupled into waveguide. Several aspects of RKA operation under investigation that affect RKA beam bunching efficiency and amplifier gain include cavity tuning, beam diameter, beam current, and input rf drive power, and the development of an output coupler that efficiently couples the microwave power from the low impedance beam into rectangular waveguide operating in the dominant mode. Current results from experimental testing and code modeling are presented
High-current relativistic klystron amplifier development for microsecond pulse lengths

International Nuclear Information System (INIS)

Fazio, M.V.; Carlsten, B.E.; Faehl, R.J.; Kwan, T.J.; Rickel, D.G.; Stringfield, R.M.; Tallerico, P.J.

1991-01-01

Los Alamos is extending the performance of the Friedman-type, high-current relativistic klystron amplifier (RKA) to the microsecond regime while attempting to achieve the gigawatt-level peak power capability that has been characteristic of the RKA at shorter pulse lengths. Currently the electron beam power into the device is about 1 GW in microsecond duration pulses, with an effort underway to increase the beam power to 2.5 GW. To date the device has yielded an rf modulated electron beam power of 350 MW, with up to 50 MW coupled into waveguide. Several aspects of RKA operation under investigation that affect RKA beam bunching efficiency and amplifier gain include cavity tuning, beam diameter, beam current, and input rf drive power, and the development of an output coupler that efficiently couples the microwave power from the low impedance beam into rectangular waveguide operating in the dominant mode. Current results from experimental testing and code modelling are presented. 5 refs., 5 figs
Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

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

2014-10-15

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

Science.gov (United States)

Negre, Christian

2017-06-01

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

International Nuclear Information System (INIS)

Rix, W.; Coleman, M.; Miller, A.R.; Parks, D.; Robertson, K.; Thompson, J.; Waisman, E.; Wilson, A.

1993-01-01

The authors describe a series of experiments carried out on ACE 2 and ACE 4 to elucidate the mechanisms controlling the conduction and opening phases on plasma opening switches in a radial geometry with conduction times on the order of a microsecond. The results indicate both conduction and opening physics are similar to that observed on lower current systems in a coaxial geometry
Thermally driven molecular linear motors - A molecular dynamics study

DEFF Research Database (Denmark)

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

2009-01-01

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

DEFF Research Database (Denmark)

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

1999-01-01

models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...
Towards the molecular bases of polymerase dynamics

International Nuclear Information System (INIS)

Chela Flores, J.

1991-03-01

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

International Nuclear Information System (INIS)

Massel, F; Kantian, A; Giamarchi, T; Daley, A J; Törmä, P

2013-01-01

We study the non-equilibrium dynamics of an impurity in a harmonic trap that is kicked with a well-defined quasi-momentum, and interacts with a bath of free fermions or interacting bosons in a one-dimensional lattice configuration. Using numerical and analytical techniques we investigate the full dynamics beyond linear response, which allows us to quantitatively characterize states of the impurity in the bath for different parameter regimes. These vary from a tightly bound molecular state in a strongly interacting limit to a polaron (dressed impurity) and a free particle for weak interactions, with composite behaviour in the intermediate regime. These dynamics and different parameter regimes should be readily realizable in systems of cold atoms in optical lattices. (paper)
Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

Science.gov (United States)

Martin, Daniel R.; Matyushov, Dmitry V.

2015-04-01

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ˜0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.
Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

International Nuclear Information System (INIS)

Martin, Daniel R.; Matyushov, Dmitry V.

2015-01-01

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc 1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins
Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

International Nuclear Information System (INIS)

Perez, Danny

2012-01-01

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Moving contact lines: linking molecular dynamics and continuum-scale modelling.

Science.gov (United States)

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-04

Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.
Exploring the dynamics about the glass transition by muon spin relaxation and muon spin rotation

International Nuclear Information System (INIS)

Bermejo, F J; Bustinduy, I; Cox, S F J; Lord, J S; Cabrillo, C; Gonzalez, M A

2006-01-01

The capability of muon spin rotation and muon spin relaxation to explore dynamics in the vicinity of the glass transition is illustrated by results pertaining to three materials exhibiting two different glass-forming abilities. Measurements under transverse magnetic fields enable us to monitor the dynamics of muonium-labelled closed-shell molecules within the microsecond range. The results display the onset of stochastic molecular motions taking place upon crossing from below the glass-transition temperature. In turn, the molecular dynamics of radicals formed by addition of atomic muonium to unsaturated organic molecules can also be explored up to far shorter times by means of relaxation measurements under longitudinal fields. The technique is then shown to be capable of singling out stochastic reorientational motions from others, which usually are strongly coupled to them and usually dominate the material response when measured using higher-frequency probes such as neutron and light scattering
Molecular dynamics simulations of solutions at constant chemical potential

Science.gov (United States)

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

2015-04-01

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

Science.gov (United States)

Lin, Jiajin; Yang, Jianhua; Zhang, Jiande; Zhang, Huibo; Yang, Xiao

2014-09-01

To solve the issue of operation instability for the trigatron switch in the application of tens of microseconds or even less charging time, a novel trigatron spark gap with slightly uneven electric field was presented. Compared with the conventional trigatron, the novel trigatron was constructed with an obvious field enhancement on the edge of the opposite electrode. The selection of the field enhancement was analyzed based on the theory introduced by Martin. A low voltage trigatron model was constructed and tested on the tens of microseconds charging time platform. The results show that the character of relative range was improved while the trigger character still held a high level. This slightly uneven electric field typed trigatron is willing to be employed in the Tesla transformer - pulse forming line system.
Current-driven dynamics in molecular-scale devices

International Nuclear Information System (INIS)

Seideman, Tamar

2003-01-01

We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)
Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

International Nuclear Information System (INIS)

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

2004-01-01

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

Directory of Open Access Journals (Sweden)

Godre Subodh S.

2015-01-01

Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.
Molecular Dynamics Studies of Nanofluidic Devices

DEFF Research Database (Denmark)

Zambrano Rodriguez, Harvey Alexander

of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding 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...... 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 MD simulation results indicate...
Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

Science.gov (United States)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project
Simulations of the structure and dynamics of nanoparticle-based ionic liquids

KAUST Repository

Hong, Bingbing

2012-01-01

We use molecular dynamics simulations over microsecond time scales to study the structure and dynamics of coarse-grained models for nanoparticle-based ionic liquids. The systems of interest consist of particles with charged surface groups and linear or three-arm counterions, which also act as the solvent. A comparable uncharged model of nanoparticles with tethered chains is also studied. The pair correlation functions display a rich structure resulting from the packing of cores and chains, as well as electrostatic effects. Even though electrostatic interactions between oppositely charged ions at contact are much greater than the thermal energy, we find that chain dynamics at intermediate time scales are dominated by chain hopping between core particles. The uncharged core particles with tethered chains diffuse faster than the ionic core particles. © 2012 The Royal Society of Chemistry.
Molecular dynamics studies of superionic conductors

International Nuclear Information System (INIS)

Rahman, A.; Vashishta, P.

1983-01-01

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

International Nuclear Information System (INIS)

Krennrich, F.; Le Bohec, S.; Weekes, T. C.

2000-01-01

Gamma-ray observations above 200 MeV are conventionally made by satellite-based detectors. The EGRET detector on the Compton Gamma Ray Observatory has provided good sensitivity for the detection of bursts lasting for more than 200 ms. Theoretical predictions of high-energy gamma-ray bursts produced by quantum mechanical decay of primordial black holes (Hawking) suggest the emission of bursts on shorter timescales. The final stage of a primordial black hole results in a burst of gamma rays, peaking around 250 MeV and lasting for 1/10 of a microsecond or longer depending on particle physics. In this work we show that there is an observational window using ground-based imaging Cerenkov detectors to measure gamma-ray burst emission at energies E>200 MeV. This technique, with a sensitivity for bursts lasting nanoseconds to several microseconds, is based on the detection of multiphoton-initiated air showers. (c) (c) 2000. The American Astronomical Society
Theoretical Concepts in Molecular Photodissociation Dynamics

DEFF Research Database (Denmark)

Henriksen, Niels Engholm

1995-01-01

This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
Analytical and molecular dynamical investigations of the influence of molecular vibrations upon the (e,2e) electron momentum distributions of furan

International Nuclear Information System (INIS)

Morini, F; Deleuze, M S; Watanabe, N; Takahashi, M

2015-01-01

The role of molecular vibrations has been theoretically investigated in the electronic ground state on the (e, 2e) valence orbital momentum profiles of furan by means of two complementary approaches. The first one relies upon the principles of Born-Oppenheimer Molecular Dynamics (BOMD), whereas the second one, referred as Harmonic Analytical Quantum Mechanical (HAQM) approach, includes on quantum-mechanical (paper)
Molecular dynamics of surfactant protein C

DEFF Research Database (Denmark)

Ramírez, Eunice; Santana, Alberto; Cruz, Anthony

2006-01-01

Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...
Extended Lagrangian Excited State Molecular Dynamics.

Science.gov (United States)

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).
Advances in molecular vibrations and collision dynamics molecular clusters

CERN Document Server

Bacic, Zatko

1998-01-01

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

Science.gov (United States)

Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

2015-04-21

This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP
Stability of molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren

2012-01-01

The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...
Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

Indian Academy of Sciences (India)

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

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

Czech Academy of Sciences Publication Activity Database

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

2016-01-01

Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016
Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc{sub 1} complex

Energy Technology Data Exchange (ETDEWEB)

Martin, Daniel R.; Matyushov, Dmitry V., E-mail: dmitrym@asu.edu [Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287 (United States)

2015-04-28

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc{sub 1} bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.
MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS

Directory of Open Access Journals (Sweden)

Paolo Ruggerone

2013-02-01

Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

Directory of Open Access Journals (Sweden)

Paolo Ruggerone

2013-02-01

Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Plasma Emission Spectra of Opuntia Nopalea Obtained with Microsecond Laser Pulses

International Nuclear Information System (INIS)

Ponce, L.; Flores, T.; Arronte, A.; Flores, A.

2008-01-01

Laser-induced Plasma Spectroscopy was performed during the spines ablation of Opuntia by using Nd:YAG microsecond laser pulses. The results show strong absorption in Glochids that causes the intense electronic noise on the spectra. This process is consider suitable for practical elimination of spines in alimentary products like opuntia
Measuring Dynamic and Kinetic Information in the Previously Inaccessible Supra-tc Window of Nanoseconds to Microseconds by Solution NMR Spectroscopy

Directory of Open Access Journals (Sweden)

Donghan Lee

2013-09-01

Full Text Available Nuclear Magnetic Resonance (NMR spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-τc window (defined as τc < supra-τc < 40 μs; in which τc is the overall tumbling time of a molecule from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD. The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τc window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τc scale by up to a factor of two (motion up to 25 ms. From the data obtained with these techniques and methodology, the importance of the supra-τ c scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τc scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.
Visualizing Energy on Target: Molecular Dynamics Simulations

Science.gov (United States)

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target
Production of an intense source of micro-second proton pulses; Recherche d'une intense source de protons pulsee a la micro-seconde

Energy Technology Data Exchange (ETDEWEB)

Belmont, J L [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

1965-02-01

In order to obtain micro-second proton pulses of 100 mA, we have built a duoplasmatron ion source and beam focusing equipment. The pulses of the ion-source were produced by a load discharge. The source operates as a hydrogen-thyratron. The particular geometry of the duoplasmatron was chosen in order that the ion emission be stable with a 10 A arc and with a gas-flow lower than 10 cm{sup 3}/h T.P.N. Studies of the beam showed preponderance of protons and the presence of heavy ions. The beam density is higher on the optic axis. (author) [French] Pour obtenir des impulsions d'une microseconde de 100 mA de protons, on a ete amene a construire une source 'duoplasmatron' et son optique de focalisation. La pulsation de la source a ete faite par decharge d'une ligne, la source fonctionnant elle-meme comme un thyratron a hydrogene. La geometrie de la source a ete etudiee pour que l'emission d'ions soit stable avec un arc de 10 amperes de crete et un debit de gaz de 10 cm{sup 3}/h T.P.N. Une analyse du faisceau a revele la preponderance des protons et l'existence d'ions lourds. La densite du faisceau est plus grande sur l'axe de l'optique.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

International Nuclear Information System (INIS)

Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.

2011-01-01

This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.
Nonadiabatic electron wavepacket dynamics behind molecular autoionization

Science.gov (United States)

Matsuoka, Takahide; Takatsuka, Kazuo

2018-01-01

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

International Nuclear Information System (INIS)

Hoover, W.G.

1982-10-01

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

International Nuclear Information System (INIS)

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

1989-01-01

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

International Nuclear Information System (INIS)

Karo, A.M.

1981-01-01

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

Science.gov (United States)

Levy, Dalit

2013-01-01

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

International Nuclear Information System (INIS)

Calamy, H.; Lassalle, F.; Loyen, A.; Zucchini, F.; Chittenden, J. P.; Hamann, F.; Maury, P.; Georges, A.; Bedoch, J. P.; Morell, A.

2008-01-01

The Sphinx machine [F. Lassalle et al., 'Status on the SPHINX machine based on the 1microsecond LTD technology'] based on microsecond linear transformer driver (LTD) technology is used to implode an aluminium wire array with an outer diameter up to 140 mm and maximum current from 3.5 to 5 MA. 700 to 800 ns implosion Z-pinch experiments are performed on this driver essentially with aluminium. Best results obtained before the improvement described in this paper were 1-3 TW radial total power, 100-300 kJ total yield, and 20-30 kJ energy above 1 keV. An auxiliary generator was added to the Sphinx machine in order to allow a multi microsecond current to be injected through the wire array load before the start of the main current. Amplitude and duration of this current prepulse are adjustable, with maxima ∼10 kA and 50 μs. This prepulse dramatically changes the ablation phase leading to an improvement of the axial homogeneity of both the implosion and the final radiating column. Total power was multiplied by a factor of 6, total yield by a factor of 2.5 with a reproducible behavior. This paper presents experimental results, magnetohydrodynamic simulations, and analysis of the effect of such a long current prepulse
Dynamics in ion-molecule collisions at high velocities: One- and two-electron processes

International Nuclear Information System (INIS)

Wang, Yudong.

1992-01-01

This dissertation addresses the dynamic interactions in ion-molecule collisions. Theoretical methods are developed for single and multiple electron transitions in fast collisions with diatomic molecules by heavy-ion projectiles. Various theories and models are developed to treat the three basic inelastic processes (excitation, ionization and charge transfer) involving one and more electrons. The development, incorporating the understanding of ion-atom collision theories with some unique characteristics for molecular targets, provides new insights into phenomena that are absent from collisions with atomic targets. The influence from the multiple scattering centers on collision dynamics is assessed. For diatomic molecules, effects due to a fixed molecular orientation or alignment are calculated and compared with available experimental observations. Compared with excitation and ionization, electron capture, which probes deeper into the target, presents significant two-center interference and strong orientation dependence. Attention has been given in this dissertation to exploring mechanisms for two-and multiple electron transitions. Application of independent electron approximation to transfer excitation from molecular hydrogen is studied. Electron-electron interaction originated from projectile and target nuclear centers is studied in conjunction with the molecular nature of target. Limitations of the present theories and models as well as possible new areas for future theoretical and experimental applications are also discussed. This is the first attempt to describe multi-electron processes in molecular dynamics involving fast highly charged ions
Microsecond-scale X-ray imaging with Controlled-Drift Detectors

International Nuclear Information System (INIS)

Castoldi, A.; Galimberti, A.; Guazzoni, C.; Rehak, P.; Strueder, L.

2006-01-01

The Controlled-Drift Detector is a fully-depleted silicon detector that allows 2-D position sensing and energy spectroscopy of X-rays in the range 0.5-20keV with excellent time resolution (few tens of μs) and limited readout channels. In this paper we review the Controlled-Drift Detector operating principle and we present the X-ray imaging and spectroscopic capabilities of Controlled Drift Detectors in microsecond-scale experiments and the more relevant applications fields
Physical adsorption and molecular dynamics

International Nuclear Information System (INIS)

Cohan, N.V.

1981-01-01

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

International Nuclear Information System (INIS)

Baranyai, Andras; Cummings, Peter T.

2000-01-01

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

International Nuclear Information System (INIS)

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

1992-01-01

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

Anomalous dependence of the lasing parameters of dye solutions on the spectrum of microsecond pump laser pulses

International Nuclear Information System (INIS)

Tarkovsky, V V; Kurstak, V Yu; Anufrik, S S

2003-01-01

The anomalous dependence of the lasing parameters of ethanol solutions of coumarin, rhodamine, oxazine, and laser dyes of other classes on the spectrum of microsecond pump laser pulses is found. The dependence is determined by the shape of the induced singlet - singlet absorption spectra and absorption spectra of short-lived photoproducts. The elucidation of the influence of these factors makes it possible to choose optimal pump spectra and to enhance the efficiency and stability of microsecond dye lasers. (active media)
Molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

2012-01-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to 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 about 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 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 the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)
Molecular dynamics for dense matter

Science.gov (United States)

Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

2012-08-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to 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 about 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 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 the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.
High-speed photography of dynamic photoelastic experiment with a highly accurate blasting machine

Science.gov (United States)

Katsuyama, Kunihisa; Ogata, Yuji; Wada, Yuji; Hashizume, K.

1995-05-01

A high accurate blasting machine which could control 1 microsecond(s) was developed. At first, explosion of a bridge wire in an electric detonator was observed and next the detonations of caps were observed with a high speed camera. It is well known that a compressed stress wave reflects at the free face, it propagates to the backward as a tensile stress wave, and cracks grow when the tensile stress becomes the dynamic tensile strength. The behavior of these cracks has been discussed through the observation of the dynamic photoelastic high speed photography and the three dimensional dynamic stress analysis.
The 2011 Dynamics of Molecular Collisions Conference

Energy Technology Data Exchange (ETDEWEB)

Nesbitt, David J. [JILA, NIST

2011-07-11

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

Science.gov (United States)

2014-01-01

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

International Nuclear Information System (INIS)

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

2015-01-01

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

International Nuclear Information System (INIS)

Kobayashi, Kazuya; Liang, Yunfeng; Matsuoka, Toshifumi; Sakka, Tetsuo

2014-01-01

The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules
Coalescence of silver unidimensional structures by molecular dynamics simulation; Coalescencia de estructuras unidimensionales de plata por simulacion dinamica molecular

Energy Technology Data Exchange (ETDEWEB)

Perez A, M.; Gutierrez W, C.E.; Mondragon, G. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico); Arenas, J. [IFUNAM, 04510 Mexico D.F. (Mexico)

2007-07-01

The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

Science.gov (United States)

Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

2008-12-01

Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the
Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

Science.gov (United States)

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

2016-10-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

Directory of Open Access Journals (Sweden)

Samuel Hertig

2016-06-01

Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.
Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy.

Science.gov (United States)

Ban, David; Sabo, T Michael; Griesinger, Christian; Lee, Donghan

2013-09-26

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-tc window (defined as τ(c) supra-τ(c) supra-τ(c) window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τ(c) scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τ(c) scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τ(c) scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.
Internal motion time scales of a small, highly stable and disulfide-rich protein: A 15N, 13C NMR and molecular dynamics study

International Nuclear Information System (INIS)

Guenneugues, Marc; Gilquin, Bernard; Wolff, Nicolas; Menez, Andre; Zinn-Justin, Sophie

1999-01-01

Motions of the backbone CαHα and threonine CβHβ bonds of toxin α were investigated using natural abundance 13C NMR and molecular dynamics. Measurement of the 13C longitudinal and transverse relaxation rates employed ACCORDION techniques together with coherence selection by pulsed field gradients and sensitivity enhancement through the use of preservation of equivalent pathway, thus allowing a considerable reduction of the required spectrometer time. 13C R1, R2, 1H → 13C NOE were obtained, as well as the variations of R1ρ(90 deg.) as a function of the rf field strength. These data were compared to those recorded by 1H and 15N NMR on a labelled sample of the toxin [Guenneugues et al. (1997) Biochemistry, 36, 16097-16108]. Both sets of data showed that picosecond to nanosecond time scale motions are well correlated to the secondary structure of the protein. This was further reinforced by the analysis of a 1 ns molecular dynamics simulation in water. Several CαHα and threonine CβHβ experimentally exhibit fast motions with a correlation time longer than 500 ps, that cannot be sampled along the simulation. In addition, the backbone exhibits motions on the microsecond to millisecond time scale on more than half of its length. Thus, toxin α, a highly stable protein (Tm=75 deg. C at acidic pH) containing 61 amino acids and 4 disulfides, shows important internal motions on time scales ranging from 0.1-0.5 ps, to 10-100 ps, 1 ns, and about 30 μs to 10 ms
Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-01-22

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

Directory of Open Access Journals (Sweden)

Renata De Paris

2015-01-01

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

Directory of Open Access Journals (Sweden)

Elena ePapaleo

2015-05-01

Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu(290)

DEFF Research Database (Denmark)

Khelashvili, George; Schmidt, Solveig Gaarde; Shi, Lei

2016-01-01

Na+ ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na+ in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu290, either charged or neutral......Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In recent microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K+ ions from the intracellular side toward...... the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na+. Here we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K+ binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both...
Hydration dynamics in water clusters via quantum molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

2014-05-28

We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

Density measurements of microsecond-conduction-time POS plasmas

International Nuclear Information System (INIS)

Hinshelwood, D.; Goodrich, P.J.; Weber, B.V.; Commisso, R.J.; Grossmann, J.M.; Kellogg, J.C.

1993-01-01

Measurements of the electron density in a coaxial microsecond conduction time plasma opening switch during switch operation are described. Current conduction is observed to cause a radial redistribution of the switch plasma. A local reduction in axial line density of more than an order of magnitude occurs by the time opening begins. This reduction, and the scaling of conduction current with plasma density, indicate that current conduction in this experiment is limited by hydrodynamic effects. It is hypothesized that the density reduction allows the switch to open by an erosion mechanism. Initial numerical modeling efforts have reproduced the principal observed results. A model that predicts accurately the conduction current is presented
A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

2009-01-01

Full text: At sub-nuclear densities of about 10 14 g/cm 3 , 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)
Dynamical photo-induced electronic properties of molecular junctions

Science.gov (United States)

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

2018-03-01

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

CERN Document Server

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
Microsecond pulsed optical parametric oscillator pumped by a Q-switched fiber laser

NARCIS (Netherlands)

Klein, M.E.; Adel, P.; Auerbach, M.; Fallnich, C.; Gross, P.; Boller, Klaus J.

2003-01-01

We report on what is to our knowledge the first optical parametric oscillator (OPO) pumped by microsecond pulses from a wavelength-tunable solid-state laser. The singly resonant OPO (SRO) is based on a periodically poled LiNbO3 crystal and pumped with 2.1-ms-long pulses from an actively Q-switched
First-principles molecular dynamics study of Al/Alq3 interfaces

Directory of Open Access Journals (Sweden)

Kousuke Takeuchi et al

2007-01-01

Full Text Available We have carried out first-principles molecular dynamics simulations of Al deposition on tris (8-hydroxyquinoline aluminum (Alq3 layers to investigate atomic geometries and electronic properties of Al/Alq3 interfaces. Al atoms were ejected to Alq3 one by one with the kinetic energy of 37.4 kJ/mol, which approximately corresponds to the average kinetic energy of Al at the boiling temperature of metal Al. The first Al atom interacts with two of the three O atoms of meridional Alq3. Following Al atoms interact with Alq3 rather weakly and they tend to aggregate each other to form Al clusters. During the deposition process, Alq3 was not broken and its molecular structure remained essentially intact. At the interface, weak bonds between deposited Al atoms and N and C atoms were formed. The projected density of states (PDOS onto the Alq3 molecular orbitals shows gap states in between the highest occupied molecular orbitals (HOMOs and the lowest unoccupied molecular orbitals (LUMOs, which were experimentally observed by ultraviolet photoelectron spectroscopy (UPS and metastable atom electron spectroscopy (MAES. Our results show that even though the Alq3 molecular structure is retained, weak N–Al and C–Al bonds induce gap states.
Theory and application of quantum molecular dynamics

CERN Document Server

Zeng Hui Zhang, John

1999-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Cahoon, James Francis [Univ. of California, Berkeley, CA (United States)

2008-12-01

One and two dimensional time-resolved vibrational spectroscopy has been used to investigate the elementary reactions of several prototypical organometallic complexes in room temperature solution. The electron transfer and ligand substitution reactions of photogenerated 17-electron organometallic radicals CpW(CO)₃ and CpFe(CO)₂ have been examined with one dimensional spectroscopy on the picosecond through microsecond time-scales, revealing the importance of caging effects and odd-electron intermediates in these reactions. Similarly, an investigation of the photophysics of the simple Fischer carbene complex Cr(CO)₅[CMe(OMe)] showed that this class of molecule undergoes an unusual molecular rearrangement on the picosecond time-scale, briefly forming a metal-ketene complex. Although time-resolved spectroscopy has long been used for these types of photoinitiated reactions, the advent of two dimensional vibrational spectroscopy (2D-IR) opens the possibility to examine the ultrafast dynamics of molecules under thermal equilibrium conditions. Using this method, the picosecond fluxional rearrangements of the model metal carbonyl Fe(CO)₅ have been examined, revealing the mechanism, time-scale, and transition state of the fluxional reaction. The success of this experiment demonstrates that 2D-IR is a powerful technique to examine the thermally-driven, ultrafast rearrangements of organometallic molecules in solution.
The Design, Synthesis, and Study of Solid-State Molecular Rotors: Structure/Function Relationships for Condensed-Phase Anisotropic Dynamics

Science.gov (United States)

Vogelsberg, Cortnie Sue

strong to direct an assembly of molecular machines, 3) the relative flexibility of the crystal environment proximate to a dynamic component may have a significant effect on its function, and, 4) molecular machines, which possess both solid-state photochemical reactivity and dynamics may show complex reaction kinetics if the correlation time of the dynamic process and the lifetime of the excited state occur on the same time scale and the dynamic moiety inherently participates as a reaction intermediate. The study of periodic mesoporous organosilica with hierarchical order probed molecular dynamics within 2D layers of molecular rotors, organized in only one dimension and with ca. 50% exposed to the mesopore free volume. From their study, it was discovered that: 1) molecular rotors, which comprise the layers of the mesopore walls, form a 2D rotational glass, 2) rotator dynamics within the 2D rotational glass undergo a transition to a 2D rotational fluid, and, 3) a 2D rotational glass transition may be exploited to develop hyper-sensitive thermally activated molecular machines. The study of a metal-organic framework assembled from molecular rotors probed dynamics in a periodic three-dimensional free-volume environment, without the presence of close contacts. From the study of this solid-state material, it was determined that: 1) the intrinsic electronic barrier is one of the few factors, which may affect functional dynamics in a true free-volume environment, and, 2) molecular machines with dynamic barriers <
Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study.

Directory of Open Access Journals (Sweden)

Nils A Berglund

2015-04-01

Full Text Available Antimicrobial peptides are small, cationic proteins that can induce lysis of bacterial cells through interaction with their membranes. Different mechanisms for cell lysis have been proposed, but these models tend to neglect the role of the chemical composition of the membrane, which differs between bacterial species and can be heterogeneous even within a single cell. Moreover, the cell envelope of Gram-negative bacteria such as E. coli contains two membranes with differing compositions. To this end, we report the first molecular dynamics simulation study of the interaction of the antimicrobial peptide, polymyxin B1 with complex models of both the inner and outer membranes of E. coli. The results of >16 microseconds of simulation predict that polymyxin B1 is likely to interact with the membranes via distinct mechanisms. The lipopeptides aggregate in the lipopolysaccharide headgroup region of the outer membrane with limited tendency for insertion within the lipid A tails. In contrast, the lipopeptides readily insert into the inner membrane core, and the concomitant increased hydration may be responsible for bilayer destabilization and antimicrobial function. Given the urgent need to develop novel, potent antibiotics, the results presented here reveal key mechanistic details that may be exploited for future rational drug development.
Microscopic study of nuclear 'pasta' by quantum molecular dynamics

International Nuclear Information System (INIS)

Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

2002-01-01

Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. and be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple 'pasta' phases in neutron star crusts. (author)
Molecular dynamics of liquid crystals

Science.gov (United States)

Sarman, Sten

1997-02-01

We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.
Power ion beam production in an accelerator with inductive microsecond storage and plasmaerosion switch

International Nuclear Information System (INIS)

Mesyats, G.A.; Didenko, A.N.; Abdullin, Eh.N.; Tomskij Politekhnicheskij Inst.

1986-01-01

Results of investigations into powerful ion beam (PIB) production in an accelerator with inductive microsecond storage and plasmaerosion switch (PES) are given. The storage consists of the 100 kJ high-voltage pulse generator, the inductive load as a vacuum coaxial line. Coaxial line was divided into two regions with PES plasma guns. Generation of converging PIB on switching of energy flux from the first region to the second was performed in the PES area itself as well as in an additional diode during its placing at different distances from PES. The investigations have shown that microsecond PES is an effective element providing PIB eneration with durations of an order of tens of nanoseconds. Total PIB energy contribution is in the range of 3-6 kJ which constitutes 40-50% of total energy release in PES
Progress toward a microsecond duration, repetitive, intense-ion beam for active spectroscopic measurements on ITER

International Nuclear Information System (INIS)

Davis, H.A.; Bartsch, R.R.; Barnes, C.W.

1996-01-01

The authors describe the design of an intense, pulsed, repetitive, neutral beam based on magnetically insulated diode technology for injection into ITER for spectroscopic measurements of thermalizing alpha particle and thermal helium density profiles, ion temperature, plasma rotation, and low Z impurity concentrations in the confinement region. The beam is being developed to enhance low signal-to-noise ratios expected with conventional steady-state ion beams because of severe beam attenuation and intense bremstrahlung emission. A 5 GW (e.g., 100 keV, 50 kA) one-microsecond-duration beam would increase the signal by 10 3 compared to a conventional 5 MW beam with signal-to-noise ratios comparable to those from a chopped conventional beam in one second
Dynamic signature of molecular association in methanol

International Nuclear Information System (INIS)

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

2016-01-01

Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.
Molecular dynamics for fermions

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

2000-02-01

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.)
Pattern recognition in molecular dynamics. [FORTRAN

Energy Technology Data Exchange (ETDEWEB)

Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

1977-07-01

An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.
Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results

Science.gov (United States)

Bertolini, Davide; Tani, Alessandro

1997-10-01

Equilibrium molecular dynamics simulations have been carried out in the microcanonical ensemble at 300 and 255 K on the extended simple point charge (SPC/E) model of water [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)]. In addition to a number of static and dynamic properties, thermal conductivity λ has been calculated via Green-Kubo integration of the heat current time correlation functions (CF's) in the atomic and molecular formalism, at wave number k=0. The calculated values (0.67+/-0.04 W/mK at 300 K and 0.52+/-0.03 W/mK at 255 K) are in good agreement with the experimental data (0.61 W/mK at 300 K and 0.49 W/mK at 255 K). A negative long-time tail of the heat current CF, more apparent at 255 K, is responsible for the anomalous decrease of λ with temperature. An analysis of the dynamical modes contributing to λ has shown that its value is due to two low-frequency exponential-like modes, a faster collisional mode, with positive contribution, and a slower one, which determines the negative long-time tail. A comparison of the molecular and atomic spectra of the heat current CF has suggested that higher-frequency modes should not contribute to λ in this temperature range. Generalized thermal diffusivity DT(k) decreases as a function of k, after an initial minor increase at k=kmin. The k dependence of the generalized thermodynamic properties has been calculated in the atomic and molecular formalisms. The observed differences have been traced back to intramolecular or intermolecular rotational effects and related to the partial structure functions. Finally, from the results we calculated it appears that the SPC/E model gives results in better agreement with experimental data than the transferable intermolecular potential with four points TIP4P water model [Jorgensen et al., J. Chem. Phys. 79, 926 (1983)], with a larger improvement for, e.g., diffusion, viscosities, and dielectric properties and a smaller one for thermal conductivity. The SPC/E model shares
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

International Nuclear Information System (INIS)

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

2010-01-01

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

International Nuclear Information System (INIS)

Ould-Kaddour, F.; Barrat, J.L.

1991-05-01

Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.
Classical and quantum molecular dynamics in NMR spectra

CERN Document Server

Szymański, Sławomir

2018-01-01

The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...
Multiscale equation-free algorithms for molecular dynamics

Science.gov (United States)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.
Parallel computing and molecular dynamics of biological membranes

International Nuclear Information System (INIS)

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

1998-01-01

In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)
Scalable Molecular Dynamics for Large Biomolecular Systems

Directory of Open Access Journals (Sweden)

Robert K. Brunner

2000-01-01

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

International Nuclear Information System (INIS)

Gupta, Moumita; Dastidar, Krishna Rai

2009-01-01

We study the dynamics of the atomic and molecular Bose-Einstein condensates (BECs) of 87 Rb in a spherically symmetric trap coupled by stimulated Raman photoassociation process. Considering the higher order nonlinearity in the atom-atom interaction we analyze the dynamics of the system using coupled modified Gross-Pitaevskii (MGP) equations and compare it with mean-field coupled Gross-Pitaevskii (GP) dynamics. Considerable differences in the dynamics are obtained in these two approaches at large scattering length, i.e., for large values of peak-gas parameter x pk ≥10 -3 . We show how the dynamics of the coupled system is affected when the atom-molecule and molecule-molecule interactions are considered together with the atom-atom interaction and also when the strengths of these three interactions are increased. The effect of detuning on the efficiency of conversion of atomic fractions into molecules is demonstrated and the feasibility of maximum molecular BEC formation by varying the Raman detuning parameter at different values of time is explored. Thus by varying the Raman detuning and the scattering length for atom-atom interaction one can control the dynamics of the coupled atomic-molecular BEC system. We have also solved coupled Gross-Pitaevskii equations for atomic to molecular condensate formation through magnetic Feshbach resonance in a BEC of 85 Rb. We found similar features for oscillations between atomic and molecular condensates noted in previous theoretical study and obtained fairly good agreement with the evolution of total atomic condensate observed experimentally.
Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

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

2015-05-01

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

International Nuclear Information System (INIS)

Apostol, M.; Cune, L.C.

2016-01-01

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

International Nuclear Information System (INIS)

Seppaelae, A.; Vaari, J.; Puhakka, E.; Tanhua-Tyrkkoe, M.; Olin, M.; Kasa, S.

2012-01-01

Document available in extended abstract form only. Bentonite is one of the main material components to be used in the KBS-3 concept for safe disposal of spent nuclear fuel. The functional material in bentonite giving its beneficial properties is montmorillonite mineral. Montmorillonite consists of two completely different components: one nano-metre thick and approximately 200-400 nano-metres wide mineral layers carrying constant charge and charge compensating cations very near the mineral surfaces. The first component is more of a passive component while the second can absorb water molecules and change the cationic composition. In addition to montmorillonite bentonite usually contains some salts dissolved into water and accessory minerals. Any bulk bentonite is formed from these components via many scales of which structure is not yet fully known to science. Therefore the beneficial macroscopic properties of bentonite are assumed to follow from the nano-level structure and reactions. In safety studies of spent fuel disposal the time span to be considered extends beyond a hundred thousand years making any straightforward experimenting impossible. However, by modelling it is possible to study even very long periods of time. Unfortunately the model data and reactions are at least implicitly based on our short term experiments and may therefore be biased in some way. One possible solution to this may be the application of molecular chemistry or dynamics to construct the basis for our modelling studies. We have applied molecular chemistry on surface properties of kaolinite clay and biotite mineral but molecular dynamics is a new type of modelling for us. We believe that (during the coming ten years) molecular dynamics could make it easier to understand for example the following topics: How do charge compensating (exchanged) and aqueous cations interact? Why does water expand montmorillonite during wetting? Exact mechanism? How does water leave montmorillonite during
A comparison between characteristics of atmospheric-pressure plasma jets sustained by nanosecond- and microsecond-pulse generators in helium

International Nuclear Information System (INIS)

Zhang, Cheng; Shao, Tao; Wang, Ruixue; Yan, Ping; Zhou, Zhongsheng; Zhou, Yixiao

2014-01-01

Power source is an important parameter that can affect the characteristics of atmospheric-pressure plasma jets (APPJs), because it can play a key role on the discharge characteristics and ionization process of APPJs. In this paper, the characteristics of helium APPJs sustained by both nanosecond-pulse and microsecond-pulse generators are compared from the aspects of plume length, discharge current, consumption power, energy, and optical emission spectrum. Experimental results showed that the pulsed APPJ was initiated near the high-voltage electrode with a small curvature radius, and then the stable helium APPJ could be observed when the applied voltage increased. Moreover, the discharge current of the nanosecond-pulse APPJ was larger than that of the microsecond-pulse APPJ. Furthermore, although the nanosecond-pulse generator consumed less energy than the microsecond-pulse generator, longer plume length, larger instantaneous power per pulse and stronger spectral line intensity could be obtained in the nanosecond-pulse excitation case. In addition, some discussion indicated that the rise time of the applied voltage could play a prominent role on the generation of APPJs
Molecular quantum dynamics. From theory to applications

International Nuclear Information System (INIS)

Gatti, Fabien

2014-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

2014-09-01

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

Directory of Open Access Journals (Sweden)

Morker Mitul R.

2015-01-01

Full Text Available A 3-body classical molecular dynamics approach for heavy-ion reactions involving weakly bound projectiles is developed. In this approach a weakly bound projectile is constructed as a two-body cluster of the constituent tightly bound nuclei in a configuration corresponding to the observed breakup energy. This 3-body system with their individual nucleon configuration in their ground state is dynamically evolved for given initial conditions using the three-stage classical molecular dynamics approach (3S-CMD. Various levels of rigidbody constraints on the projectile constituents and the target are considered at appropriate stages. This 3-dimensional approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but internal excitations and breakup probabilities at distances close to the barrier also. Dynamical simulations of 6Li+209Bi show all the possible reaction mechanism like complete fusion, incomplete fusion, scattering and breakup scattering. Complete fusion cross sections of 6Li+209Bi and 7Li+209Bi reactions are calculated in this approach with systematic relaxations of the rigid-body constraints on one or more constituent nuclei.
Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

Directory of Open Access Journals (Sweden)

Nivedita Rai

2015-01-01

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

International Nuclear Information System (INIS)

Pratt, S.T.

1995-01-01

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

International Nuclear Information System (INIS)

Burenin, A.V.

2002-01-01

The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru
GPI-anchored protein organization and dynamics at the cell surface.

Science.gov (United States)

Saha, Suvrajit; Anilkumar, Anupama Ambika; Mayor, Satyajit

2016-02-01

The surface of eukaryotic cells is a multi-component fluid bilayer in which glycosylphosphatidylinositol (GPI)-anchored proteins are an abundant constituent. In this review, we discuss the complex nature of the organization and dynamics of GPI-anchored proteins at multiple spatial and temporal scales. Different biophysical techniques have been utilized for understanding this organization, including fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single particle tracking, and a number of super resolution methods. Major insights into the organization and dynamics have also come from exploring the short-range interactions of GPI-anchored proteins by fluorescence (or Förster) resonance energy transfer microscopy. Based on the nanometer to micron scale organization, at the microsecond to the second time scale dynamics, a picture of the membrane bilayer emerges where the lipid bilayer appears inextricably intertwined with the underlying dynamic cytoskeleton. These observations have prompted a revision of the current models of plasma membrane organization, and suggest an active actin-membrane composite. Copyright © 2016 by the American Society for Biochemistry and Molecular Biology, Inc.
Molecular dynamics modeling of polymer flammability

International Nuclear Information System (INIS)

Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

1992-01-01

Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)
Electron-nuclear dynamics of molecular systems

International Nuclear Information System (INIS)

Diz, A.; Oehrn, Y.

1994-01-01

The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions
Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

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

Science.gov (United States)

Lu, Tao

2009-07-01

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

Energy Technology Data Exchange (ETDEWEB)

Craven, Galen T.; Popov, Alexander V.; Hernandez, Rigoberto, E-mail: hernandez@chemistry.gatech.edu [Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400 (United States)

2015-04-21

The dynamical properties of a system of soft rods governed by stochastic hard collisions (SHCs) have been determined over a varying range of softness using molecular dynamics simulations in one dimension and analytic theory. The SHC model allows for interpenetration of the system’s constituent particles in the simulations, generating overlapping clustering behavior analogous to the spatial structures observed in systems governed by deterministic bounded potentials. Through variation of an assigned softness parameter δ, the limiting ranges of intermolecular softness are bridged, connecting the limiting ensemble behavior from hard to ideal (completely soft). Various dynamical and structural observables are measured from simulation and compared to developed theoretical values. The spatial properties are found to be well predicted by theories developed for the deterministic penetrable-sphere model with a transformation from energetic to probabilistic arguments. While the overlapping spatial structures are complex, the dynamical properties can be adequately approximated through a theory built on impulsive interactions with Enskog corrections. Our theory suggests that as the softness of interaction is varied toward the ideal limit, correlated collision processes are less important to the energy transfer mechanism, and Markovian processes dominate the evolution of the configuration space ensemble. For interaction softness close to hard limit, collision processes are highly correlated and overlapping spatial configurations give rise to entanglement of single-particle trajectories.
Dynamics of molecular superrotors in an external magnetic field

Science.gov (United States)

Korobenko, Aleksey; Milner, Valery

2015-08-01

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

CERN Document Server

Douhal, Abderrazzak

2002-01-01

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

KAUST Repository

Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2011-01-01

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
Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

2010-01-01

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...
Breaking The Millisecond Barrier On SpiNNaker: Implementing Asynchronous Event-Based Plastic Models With Microsecond Resolution

Directory of Open Access Journals (Sweden)

Xavier eLagorce

2015-06-01

Full Text Available Spike-based neuromorphic sensors such as retinas and cochleas, change the way in which the world is sampled. Instead of producing data sampled at a constant rate, these sensors output spikes that are asynchronous and event driven. The event-based nature of neuromorphic sensors implies a complete paradigm shift in current perception algorithms towards those that emphasize the importance of precise timing. The spikes produced by these sensors usually have a time resolution in the order of microseconds. This high temporal resolution is a crucial factor in learning tasks. It is also widely used in the field of biological neural networks. Sound localization for instance relies on detecting time lags between the two ears which, in the barn owl, reaches a temporal resolution of 5 microseconds. Current available neuromorphic computation platforms such as SpiNNaker often limit their users to a time resolution in the order of milliseconds that is not compatible with the asynchronous outputs of neuromorphic sensors. To overcome these limitations and allow for the exploration of new types of neuromorphic computing architectures, we introduce a novel software framework on the SpiNNaker platform. This framework allows for simulations of spiking networks and plasticity mechanisms using a completely asynchronous and event-based scheme running with a microsecond time resolution. Results on two example networks using this new implementation are presented.
Dynamics of molecular superrotors in an external magnetic field

International Nuclear Information System (INIS)

Korobenko, Aleksey; Milner, Valery

2015-01-01

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

Science.gov (United States)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.
Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

DEFF Research Database (Denmark)

Papaleo, Elena

2015-01-01

that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....
AceCloud: Molecular Dynamics Simulations in the Cloud.

Science.gov (United States)

Harvey, M J; De Fabritiis, G

2015-05-26

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

Science.gov (United States)

Benhassine, M; Saiz, E; Tomsia, A P; De Coninck, J

2009-10-06

The spreading for Cu and Ag droplets on top of a rigid solid surface modeling Mo is herewith considered via molecular dynamics. The dynamics of the base radius and the contact angle are recorded and fitted using the molecular-kinetic theory. A method is described to determine for liquid metals at the microscopic level the parameters appearing in this theory. These microscopic parameters are calculated directly in the simulations and compared to the fitted values. The agreement between the fitted values and the calculated ones shows that the dissipation of energy within the drop is caused primarily by the friction of liquid atoms over the substrate. This validation supports the understanding of the mechanisms controlling the spreading of liquid metals which, up to now, were based on experimental data and fitting procedures.
Rapid freezing of water under dynamic compression

Science.gov (United States)

Myint, Philip C.; Belof, Jonathan L.

2018-06-01

Understanding the behavior of materials at extreme pressures is a central issue in fields like aerodynamics, astronomy, and geology, as well as for advancing technological grand challenges such as inertial confinement fusion. Dynamic compression experiments to probe high-pressure states often encounter rapid phase transitions that may cause the materials to behave in unexpected ways, and understanding the kinetics of these phase transitions remains an area of great interest. In this review, we examine experimental and theoretical/computational efforts to study the freezing kinetics of water to a high-pressure solid phase known as ice VII. We first present a detailed analysis of dynamic compression experiments in which water has been observed to freeze on sub-microsecond time scales to ice VII. This is followed by a discussion of the limitations of currently available molecular and continuum simulation methods in modeling these experiments. We then describe how our phase transition kinetics models, which are based on classical nucleation theory, provide a more physics-based framework that overcomes some of these limitations. Finally, we give suggestions on future experimental and modeling work on the liquid–ice VII transition, including an outline of the development of a predictive multiscale model in which molecular and continuum simulations are intimately coupled.
Molecular dynamics simulations of RNA motifs

Czech Academy of Sciences Publication Activity Database

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

2002-01-01

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

International Nuclear Information System (INIS)

Kawabata, C.; takeuchi, M.; Bishop, A.R.

1985-01-01

A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians
Role of Lipids in Spheroidal High Density Lipoproteins

NARCIS (Netherlands)

Vuorela, Timo; Catte, Andrea; Niemela, Perttu S.; Hall, Anette; Hyvonen, Marja T.; Marrink, Siewert-Jan; Karttunen, Mikko; Vattulainen, Ilpo

2010-01-01

We study the structure and dynamics of spherical high density lipoprotein (HDL) particles through coarse-grained multi-microsecond molecular dynamics simulations. We simulate both a lipid droplet without the apolipoprotein A-I (apoA-I) and the full HDL particle including two apoA-I molecules
Role of lipids in spheroidal high density lipoproteins

NARCIS (Netherlands)

Vuorela, T.A.; Catte, A.; Niemelä, P.S.; Hall, A.; Hyvönen, M.T.; Marrink, S.J.; Karttunen, M.E.J.; Vattulainen, I.

2010-01-01

We study the structure and dynamics of spherical high density lipoprotein (HDL) particles through coarse-grained multi-microsecond molecular dynamics simulations. We simulate both a lipid droplet without the apolipoprotein A-I (apoA-I) and the full HDL particle including two apoA-I molecules
Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

Czech Academy of Sciences Publication Activity Database

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

2015-01-01

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

NARCIS (Netherlands)

Solhjoo, Soheil

2017-01-01

This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:
A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Statistical properties of anti-symmetrized molecular dynamics

International Nuclear Information System (INIS)

Ohnishi, A.; Randrup, J.

1993-01-01

We study the statistical equilibrium properties of the recently developed anti-symmetrized molecular dynamics model for heavy-ion reactions. We consider A non-interacting fermions in one dimension, either bound in a common harmonic potential or moving freely within an interval, and perform a Metropolis sampling of the corresponding parameter space. Generally the average excitation and the specific heat, considered as functions of the imposed temperature, behave in a classical manner when the canonical weight is calculated in the mean-field approximation. However, it is possible to obtain results that are much closer to the quantal behavior by modifying the weight to take approximate account of the energy fluctuations within the individual wave packets. (orig.)
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

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

Science.gov (United States)

Skarmoutsos, Ioannis; Samios, Jannis

2006-11-02

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.
Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state.

Directory of Open Access Journals (Sweden)

Becka M Warfield

Full Text Available RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are
Production of an intense source of micro-second proton pulses

International Nuclear Information System (INIS)

Belmont, J.L.

1965-02-01

In order to obtain micro-second proton pulses of 100 mA, we have built a duoplasmatron ion source and beam focusing equipment. The pulses of the ion-source were produced by a load discharge. The source operates as a hydrogen-thyratron. The particular geometry of the duoplasmatron was chosen in order that the ion emission be stable with a 10 A arc and with a gas-flow lower than 10 cm 3 /h T.P.N. Studies of the beam showed preponderance of protons and the presence of heavy ions. The beam density is higher on the optic axis. (author) [fr
Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

Science.gov (United States)

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
Haptization of molecular dynamics simulation with thermal display

International Nuclear Information System (INIS)

Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki

2010-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

KAUST Repository

Neumann, Philipp; Tchipev, Nikola

2012-01-01

We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm
Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

Science.gov (United States)

Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

2018-05-01

For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.
Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

KAUST Repository

Yoon, Seyoon; Monteiro, Paulo J.M.

2013-01-01

The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current
Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

DEFF Research Database (Denmark)

Toxvaerd, Søren

2001-01-01

Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...
A molecular dynamics study of Lennard-Jones physisorption on W(100)

International Nuclear Information System (INIS)

Broughton, J.Q.

1980-01-01

The physisorption of Xe on W(100) was modeled by Lennard-Jones pair-wise interaction potentials and the dynamics of coverages ranging from one to four adlayers obtained by molecular dynamics simulation. At 115 K, the first two layers were well-ordered and each adsorbed with c(2 x 2) symmetry. Further adsorption produced a surface similar to that of a distorted Xe(100) face. In accord with the work of Broughton and Woodcock, the top layers of the three- and four-adlayer coverages were rough and had liquid-like diffusion coefficients. The potential energies of all layers other than the first were similar, thus corroborating one of the postulates of BET theory. Generally, the effect of adsorbing a layer was to reduce the entropy of all those beneath. (orig.)
molecular dynamics simulations and quantum chemical calculations

African Journals Online (AJOL)

ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.
Invariant molecular-dynamics approach to structural phase transitions

International Nuclear Information System (INIS)

Wentzcovitch, R.M.

1991-01-01

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

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology
Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

Science.gov (United States)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.
Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

Science.gov (United States)

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.
NMR investigations of molecular dynamics

Science.gov (United States)

Palmer, Arthur

2011-03-01

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

Science.gov (United States)

Dubey, Girija S.; Gumbs, Godfrey; Fessatidis, Vassilios

2018-05-01

Molecular dynamics simulation are used to examine the effect of a uniform perpendicular magnetic field on a two-dimensional interacting electron system. In this simulation we include the effect of the magnetic field classically through the Lorentz force. Both the Coulomb and the magnetic forces are included directly in the electron dynamics to study their combined effect on the dynamical properties of the 2D system. Results are presented for the velocity autocorrelation function and the diffusion constants in the presence and absence of an external magnetic field. Our simulation results clearly show that the external magnetic field has an effect on the dynamical properties of the system.

Molecular dynamics simulations of the melting curve of NiAl alloy under pressure

OpenAIRE

Wenjin Zhang; Yufeng Peng; Zhongli Liu

2014-01-01

The melting curve of B2-NiAl alloy under pressure has been investigated using molecular dynamics technique and the embedded atom method (EAM) potential. The melting temperatures were determined with two approaches, the one-phase and the two-phase methods. The first one simulates a homogeneous melting, while the second one involves a heterogeneous melting of materials. Both approaches reduce the superheating effectively and their results are close to each other at the applied pressures. By fit...
Excitation dynamics and relaxation in a molecular heterodimer

International Nuclear Information System (INIS)

Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

2012-01-01

Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
The nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1992-03-01

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

Energy Technology Data Exchange (ETDEWEB)

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

1993-12-01

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

International Nuclear Information System (INIS)

Pasichnyk, Igor; Duenweg, Burkhard

2004-01-01

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

DEFF Research Database (Denmark)

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

2012-01-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...
The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial
Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

Science.gov (United States)

Hu, Hao; Liu, Haiyan

2013-05-30

Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.
Structural investigation of water-acetonitrile mixtures: An ab initio, molecular dynamics and X-ray diffraction study

International Nuclear Information System (INIS)

Bako, Imre; Megyes, Tuende; Palinkas, Gabor

2005-01-01

In this work, we present a study on water-acetonitrile (AN) mixtures by molecular dynamics ab initio and X-ray diffraction techniques. Comparison of the experimental total G(r) functions of the mixtures with the results of molecular dynamics simulation shows an overall good agreement. The properties of hydrogen bonded clusters (water clusters, and water-AN clusters) in these mixtures have been determined. Two different types of AN-water dimers were identified by ab initio quantum chemical calculation. One of these structures proved to be a true H-bonded dimer and the other a dipole bound dimer
Molecular dynamics computer simulations based on NMR data

International Nuclear Information System (INIS)

Vlieg, J. de.

1989-01-01

In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs
Molecular dynamics simulations of ultrathin water film confined between flat diamond plates

Directory of Open Access Journals (Sweden)

A.V. Khomenko

2008-12-01

Full Text Available Molecular dynamics simulations of ultrathin water film confined between atomically flat rigid diamond plates are described. Films with thickness of one and two molecular diameters are concerned and TIP4P model is used for water molecules. Dynamical and equilibrium characteristics of the system for different values of the external load and shear force are investigated. An increase of the external load causes the transition of the film to a solidlike state. This is manifested in a decrease of the diffusion constant and in the ordering of the liquid molecules into quasidiscrete layers. For two-layer film under high loads, the molecules also become ordered parallel to the surfaces. Time dependencies of the friction force and the changes of its average value with the load are obtained. In general, the behaviour of the studied model is consistent with the experimental results obtained for simple liquids with spherical molecules.
Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

Science.gov (United States)

Yagasaki, Takuma; Saito, Shinji

2009-09-15

Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is
STROBE-X: X-ray Timing & Spectroscopy on Dynamical Timescales from Microseconds to Years

Science.gov (United States)

Wilson-Hodge, Colleen A.; Ray, Paul S.; Maccarone, Thomas J.; Chakrabarty, Deepto; Gendreau, Keith C.; Arzoumanian, Zaven; Jenke, Peter; Ballantyne, David; Bozzo, Enrico; Brandt, Soren; Brenneman, Laura; Christophersen, Marc; DeRosa, Alessandra; Feroci, Marco; Goldstein, Adam; Hartmann, Dieter; Hernanz, Margarita; McDonald, Michael; Phlips, Bernard; Remillard, Ronald; Stevens, Abigail; Tomsick, John; Watts, Anna; Wood, Kent S.; Zane, Silvia; STROBE-X Collaboration

2018-01-01

We describe a probe-class mission concept that provides an unprecedented view of the X-ray sky, performing timing and 0.2-30 keV spectroscopy over timescales from microseconds to years. The Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X) comprises three primary instruments. The first uses an array of lightweight optics (3-m focal length) that concentrate incident photons onto solid state detectors with CCD-level (85-130 eV) energy resolution, 100 ns time resolution, and low background rates to cover the 0.2-12 keV band. This technology is scaled up from NICER, with enhanced optics to take advantage of the longer focal length of STROBE-X. The second uses large-area collimated silicon drift detectors, developed for ESA's LOFT, to cover the 2-30 keV band. These two instruments each provide an order of magnitude improvement in effective area compared with its predecessor (NICER and RXTE, respectively). Finally, a sensitive sky monitor triggers pointed observations, provides high duty cycle, high time resolution, high spectral resolution monitoring of the X-ray sky with ~20 times the sensitivity of the RXTE ASM, and enables multi-wavelength and multi-messenger studies on a continuous, rather than scanning basis. We include updated instrument designs resulting from the GSFC IDL run in November 2017.For the first time, the broad coverage provides simultaneous study of thermal components, non-thermal components, iron lines, and reflection features from a single platform for accreting black holes at all scales. The enormous collecting area allows detailed studies of the dense matter equation of state using both thermal emission from rotation-powered pulsars and harder emission from X-ray burst oscillations. The combination of the wide-field monitor and the sensitive pointed instruments enables observations of potential electromagnetic counterparts to LIGO/Virgo and neutrino events. Extragalactic science, such as constraining bulk metalicity
Ab initio molecular dynamics in a finite homogeneous electric field.

Science.gov (United States)

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.
Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Bresme, F.; Armstrong, J.

2014-01-01

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation
Fermionic molecular dynamics for colliding and decaying nuclei

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

1993-11-01

Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)
Optical spectra and lattice dynamics of molecular crystals

CERN Document Server

Zhizhin, GN

1995-01-01

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

International Nuclear Information System (INIS)

De Leeuw, S.W.; Brakkee, M.J.D.

1990-01-01

Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

Science.gov (United States)

Cooke, Ben; Schmidler, Scott C

2008-10-28

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.
Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.

Science.gov (United States)

Okumura, Hisashi

2008-09-28

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

Orthonormal Wavelet Bases for Quantum Molecular Dynamics

International Nuclear Information System (INIS)

Tymczak, C.; Wang, X.

1997-01-01

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-04-04

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

NARCIS (Netherlands)

Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the
Molecular dynamics for reactions of heterogeneous catalysis

NARCIS (Netherlands)

Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

1991-01-01

An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.
Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

Science.gov (United States)

Wu, Bin

, at neutral condition, the exterior residues folding back into interior would necessarily lead to higher entropy and equivalently lower free energy and thereby is energetically favored. As one decreases the pH condition of PAMAM dendrimers, the constituent residues would carry positive charges. The resultant inter-residue Coulomb repulsion would naturally result in conformational evolution. We found from CVSANS analysis that when dendrimers are charged by different acids, this conformational evolution is not the same. For dendrimers charged by DCl, the mass is seen to relocate from molecular interior to periphery. Nevertheless, those acidified by D 2SO4 exhibit surprisingly minor structural change under variation of molecular charge. To explain the above observation, we performed MD simulations and calculated the excess free energy of Cl- and SO 42- counterions. The binding between sulfate ions and charged amines of PAMAM dendrimers are found to be much stronger than the case for chlorides. This more energetic binding would serve as better screening effect among charged residues. Consequently, electrostatic repulsion triggered outstretching tendency is effectively diminished. In order to make direct comparison between MD simulations and neutron scattering experiments, we proposed and implemented a rigorous method, which incorporates the contribution from those invasive water molecules, to calculate scattering functions of a single PAMAM dendrimer using equilibrium MD trajectories. The bridge between neutron scattering experiments and MD simulation is successfully established. Aside from structural comparisons between MD simulations and experiments, we utilized MD simulation to decipher the previously reported QENS experimental observation that the segmental dynamics of PAMAM dendrimer would enhance with increasing molecular charge. We pursued the mechanism from the perspective of hydrocarbon component of dendrimer and solvent (water) interaction as a form similar to
Molecular dynamics simulations on PGLa using NMR orientational constraints

Energy Technology Data Exchange (ETDEWEB)

Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

2015-11-15

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
Self-diffusion in monodisperse three-dimensional magnetic fluids by molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Dobroserdova, A.B. [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); Kantorovich, S.S., E-mail: alla.dobroserdova@urfu.ru [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); University of Vienna, Sensengasse 8, Vienna (Austria)

2017-06-01

In the present work we study the self-diffusion behaviour in the three-dimensional monodisperse magnetic fluids using the Molecular Dynamics Simulation and Density Functional Theory. The peculiarity of computer simulation is to study two different systems: dipolar and soft sphere ones. In the theoretical method, it is important to choose the approximation for the main structures, which are chains. We compare the theoretical results and the computer simulation data for the self-diffusion coefficient as a function of the particle volume fraction and magnetic dipole-dipole interaction parameter and find the qualitative and quantitative agreement to be good. - Highlights: • The paper deals with the study of the self-diffusion in monodisperse three-dimensional magnetic fluids. • The theoretical approach contains the free energy density functional minimization. • Computer simulations are performed by the molecular dynamics method. • We have a good qualitative and quantitative agreement between the theoretical results and computer simulation data.
A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

NARCIS (Netherlands)

Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.

2010-01-01

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose
A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

NARCIS (Netherlands)

van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,
A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

NARCIS (Netherlands)

van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,
Reaction dynamics in polyatomic molecular systems

Energy Technology Data Exchange (ETDEWEB)

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

1993-12-01

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

DEFF Research Database (Denmark)

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

2012-01-01

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...
Implementation of surface hopping molecular dynamics using semiempirical methods

International Nuclear Information System (INIS)

Fabiano, E.; Keal, T.W.; Thiel, W.

2008-01-01

A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained
Ab Initio molecular dynamics with excited electrons

NARCIS (Netherlands)

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

1994-01-01

A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.
Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

Science.gov (United States)

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.
Isolating strong-field dynamics in molecular systems

Science.gov (United States)

Orenstein, Gal; Pedatzur, Oren; Uzan, Ayelet J.; Bruner, Barry D.; Mairesse, Yann; Dudovich, Nirit

2017-05-01

Strong-field ionization followed by recollision provides a unique pump-probe measurement which reveals a range of electronic processes, combining sub-Angstrom spatial and attosecond temporal resolution. A major limitation of this approach is imposed by the coupling between the spatial and temporal degrees of freedom. In this paper we focus on the study of high harmonic generation and demonstrate the ability to isolate the internal dynamics—decoupling the temporal information from the spatial one. By applying an in situ approach we reveal the universality of the intrinsic pump-probe measurement and establish its validity in molecular systems. When several orbitals are involved we identify the fingerprint of the transition from the single-channel case into the multiple-channel dynamics, where complex multielectron phenomena are expected to be observed.
Experimental investigation of the ion current distribution in microsecond plasma opening switch

Energy Technology Data Exchange (ETDEWEB)

Bystritskij, V; Grigor` ev, S; Kharlov, A; Sinebryukhov, A [Russian Academy of Sciences, Tomsk (Russian Federation). Institute of Electrophysics

1997-12-31

This paper is devoted to the investigations of properties of the microsecond plasma opening switch (MPOS) as an ion beam source for surface modification. Two plasma sources were investigated: flash-board and cable guns. The detailed measurements of axial and azimuthal distributions of ion current density in the switch were performed. It was found that the azimuthal inhomogeneity of the ion beam increases from the beginning to the end of MPOS. The advantages and problems of this approach are discussed. (author). 5 figs., 2 refs.
Molecular dynamics coupled with a virtual system for effective conformational sampling.

Science.gov (United States)

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

DEFF Research Database (Denmark)

Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

2007-01-01

The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...
Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

Science.gov (United States)

Shekhar, Adarsh

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

In silico modelling and molecular dynamics simulation studies of thiazolidine based PTP1B inhibitors.

Science.gov (United States)

Mahapatra, Manoj Kumar; Bera, Krishnendu; Singh, Durg Vijay; Kumar, Rajnish; Kumar, Manoj

2018-04-01

Protein tyrosine phosphatase 1B (PTP1B) has been identified as a negative regulator of insulin and leptin signalling pathway; hence, it can be considered as a new therapeutic target of intervention for the treatment of type 2 diabetes. Inhibition of this molecular target takes care of both diabetes and obesity, i.e. diabestiy. In order to get more information on identification and optimization of lead, pharmacophore modelling, atom-based 3D QSAR, docking and molecular dynamics studies were carried out on a set of ligands containing thiazolidine scaffold. A six-point pharmacophore model consisting of three hydrogen bond acceptor (A), one negative ionic (N) and two aromatic rings (R) with discrete geometries as pharmacophoric features were developed for a predictive 3D QSAR model. The probable binding conformation of the ligands within the active site was studied through molecular docking. The molecular interactions and the structural features responsible for PTP1B inhibition and selectivity were further supplemented by molecular dynamics simulation study for a time scale of 30 ns. The present investigation has identified some of the indispensible structural features of thiazolidine analogues which can further be explored to optimize PTP1B inhibitors.
Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

Science.gov (United States)

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.
Molecular dynamics simulations of cluster fission and fusion processes

DEFF Research Database (Denmark)

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

2004-01-01

Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...
Molecular dynamics simulation of self-diffusion coefficients for liquid metals

International Nuclear Information System (INIS)

Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu

2013-01-01

The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)
Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

Science.gov (United States)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of
Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Federica Chiappori

Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.
Catalysis and communication in dynamic molecular networks

NARCIS (Netherlands)

Fanlo Virgos, Hugo

2015-01-01

The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity
Molecular dynamics study of atomic displacements in disordered solid alloys

Science.gov (United States)

Puzyrev, Yevgeniy S.

The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.
Bridging the gap between molecular dynamics simulations and phase-field modelling: dynamics of a [NixZr1-x]liquid-Zrcrystal solidification front

International Nuclear Information System (INIS)

Danilov, Denis; Nestler, Britta; Guerdane, Mohammed; Teichler, Helmar

2009-01-01

Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal-liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates.
Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

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

CERN Document Server

Lathouwers, L

1992-01-01

From March 30th to April 3rd, 1992, a NATO Advanced Research workshop entitled "Time Dependent Quantum Molecular Dynamics: Theory and Experiment" was held at Snowbird, Utah. The organizing committee consisted of J. BROECKHOVE (Antwerp, Belgium), L. CEDERBAUM (Heidelberg, Germany), L. LATHOUWERS (Antwerp, Belgium), N. OHRN (Gainesville, Florida) and J. SIMONS (Salt Lake City, Utah). Fifty-two participants from eleven different countries attended the meeting at which thirty-three talks and one poster session were held. Twenty-eight participants submitted contributions to the proceedings of the meeting, which are reproduced in this volume. The workshop brought together experts in different areas 0 f molecular quantum dynamics, all adhering to the time dependent approach. The aim was to discuss and compare methods and applications. The ~amiliarityo~ the aUdience with the concepts o~ time dependent approaches greatly facilitated topical discussions and probing towards new applications. A broad area of subject matt...
Laser Controlled Molecular Orientation Dynamics

International Nuclear Information System (INIS)

Atabek, O.

2004-01-01

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

Science.gov (United States)

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

2012-01-01

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

Science.gov (United States)

Lombardi, Andrea; Palazzetti, Federico

2018-02-01

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

Directory of Open Access Journals (Sweden)

Sposito Garrison

2002-09-01

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

Science.gov (United States)

Sutton, Rebecca; Sposito, Garrison

2002-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Bystritskij, V; Grigor` ev, S; Kharlov, A; Sinebryukhov, A [Russian Academy of Sciences, Tomsk (Russian Federation). Institute of Electrophysics; Burkov, P [Russian Academy of Scinces, Tomsk (Russian Federation). Institute of Strength Physics and Materials Control; Grigorev, V; Koval, T [Institute of Nuclear Physics, Tomsk (Russian Federation)

1997-12-31

The paper is devoted to the investigations of the material surface modification by high power ion beam generated in microsecond plasma opening switch (MPOS). Various types of steels were investigated: stainless steel 17-4PH, carbon steel C1020, pure iron. For all these materials, the optimal regimes for irradiation were defined. A significant increase in microhardness (1.5 to 2-fold) was obtained for these materials. Numerical calculations and theoretical estimations of the ion beam-matter interaction were also performed. The advantages and problems of this approach are discussed. (author). 8 figs., 3 refs.
Dynamical quenching of tunneling in molecular magnets

International Nuclear Information System (INIS)

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

2015-01-01

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-12-15

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

Directory of Open Access Journals (Sweden)

Huiding Xie

2015-11-01

Full Text Available In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD simulation and binding free energy (ΔGbind calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA, and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik

2010-03-17

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

KAUST Repository

von Schwerin, Erik; Szepessy, Anders

2010-01-01

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.
Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein

Science.gov (United States)

Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin

2017-10-01

Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins.
Efficient molecular dynamics simulations with many-body potentials on graphics processing units

Science.gov (United States)

Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari

2017-09-01

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).
The limiting dynamics of a bistable molecular switch with and without noise.

Science.gov (United States)

Mackey, Michael C; Tyran-Kamińska, Marta

2016-08-01

We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the steady state distribution in the population can range from a single unimodal distribution through a bimodal distribution and give the explicit analytic form for the invariant stationary density which is globally asymptotically stable. Rather remarkably, the behaviour of the stationary density with respect to the parameters characterizing the molecular behaviour of the bistable switch is qualitatively identical in the presence of noise coming from bursting as well as in the presence of Gaussian noise in the degradation rate. This implies that one cannot distinguish between either the dominant source or nature of noise based on the stationary molecular distribution in a population of cells. We finally show that the switch model with bursting but two dominant slow genes has an asymptotically stable stationary density.
Dynamics of relaxation to a stationary state for interacting molecular motors

Science.gov (United States)

Gomes, Luiza V. F.; Kolomeisky, Anatoly B.

2018-01-01

Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscle contraction. It is known that these biological molecular motors usually perform their cellular tasks by acting collectively, and there are interactions between individual motors that specify the overall collective behavior. One of the fundamental issues related to the collective dynamics of motor proteins is the question if they function at stationary-state conditions. To investigate this problem, we analyze a relaxation to the stationary state for the system of interacting molecular motors. Our approach utilizes a recently developed theoretical framework, which views the collective dynamics of motor proteins as a totally asymmetric simple exclusion process of interacting particles, where interactions are taken into account via a thermodynamically consistent approach. The dynamics of relaxation to the stationary state is analyzed using a domain-wall method that relies on a mean-field description, which takes into account some correlations. It is found that the system quickly relaxes for repulsive interactions, while attractive interactions always slow down reaching the stationary state. It is also predicted that for some range of parameters the fastest relaxation might be achieved for a weak repulsive interaction. Our theoretical predictions are tested with Monte Carlo computer simulations. The implications of our findings for biological systems are briefly discussed.
Molecular beam studies of adsorption dynamics

International Nuclear Information System (INIS)

Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.

1991-01-01

We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential
Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

Science.gov (United States)

Lee, Hui Sun; Qi, Yifei; Im, Wonpil

2015-03-09

N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.
The use of molecular dynamics for the thermodynamic properties of simple and transition metals

International Nuclear Information System (INIS)

Straub, G.K.

1987-04-01

The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated
Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach

Energy Technology Data Exchange (ETDEWEB)

Shamloo, Amir, E-mail: shamloo@sharif.edu; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria, E-mail: aalasti@sharif.edu

2016-07-15

Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted. - Highlights: • Molecular dynamics simulation of crossing nano-particles through the BBB membrane at different velocities. • Recording the position of nano-particle and the membrane-NP interaction force profile. • Identification of a frequency domain model for the membrane. • Calculating the diffusion coefficient based on MD simulation and identified model. • Obtaining a relation between continuum medium and discrete medium.
Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

Energy Technology Data Exchange (ETDEWEB)

Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2015-02-14

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

Science.gov (United States)

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

2015-02-14

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

NARCIS (Netherlands)

AHLSTROM, P; BERENDSEN, HJC

1993-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Bousige, Colin; Boţan, Alexandru; Coasne, Benoît, E-mail: coasne@mit.edu [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Ulm, Franz-Josef [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Pellenq, Roland J.-M. [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); CINaM, CNRS/Aix Marseille Université, Campus de Luminy, 13288 Marseille Cedex 09 (France)

2015-03-21

We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.
Correlations and symmetry of interactions influence collective dynamics of molecular motors

International Nuclear Information System (INIS)

Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

2015-01-01

Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)
Molecular dynamics simulation of impact test

International Nuclear Information System (INIS)

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

1998-01-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamics simulation of impact test

Energy Technology Data Exchange (ETDEWEB)

Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

1998-11-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Electronic structure and molecular dynamics of Na2Li

Science.gov (United States)

Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s
First principles molecular dynamics of metal/water interfaces under bias potential

Science.gov (United States)

Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi

2014-03-01

Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.
The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

Energy Technology Data Exchange (ETDEWEB)

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

2015-06-28

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

Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

DEFF Research Database (Denmark)

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

Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...
Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription.

Science.gov (United States)

Wu, Shaogui

2017-06-01

Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PP i )? This problem still remains obscure. In this work, we studied the problem using all-atom molecular dynamics simulation combined with steered molecular dynamics and umbrella sampling simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups. One ion makes weaker contacts with PP i than the whole protein. Hence, PP i release is less likely to take it away. The other one forms tighter contacts with PP i relative to the protein. The formed (Mg 2+ -PP i ) 2- complex is found to break the contacts with surrounding protein residues one by one so as to dissociate from the active site. This effectively avoids the coexistence of two ions in the active site after PP i release and guarantees a reasonable Mg 2+ ion number in the active site for the next NAC. The observations from this work can provide valuable information for comprehensively understanding the molecular mechanism of transcription. Proteins 2017; 85:1002-1007. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

Science.gov (United States)

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.
Molecular dynamics simulation of a phospholipid membrane

NARCIS (Netherlands)

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

We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in
Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

International Nuclear Information System (INIS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-01-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective
Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Science.gov (United States)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

International Nuclear Information System (INIS)

Smith, R.W.

1991-01-01

Molecular dynamics has been used with a Lenard-Jones (6-12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined as E=(E tot -E gnd )/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission. (orig.)
Backbone dynamics of the human CC-chemokine eotaxin

Energy Technology Data Exchange (ETDEWEB)

Ye Jiqing; Mayer, Kristen L.; Stone, Martin J. [Indiana University, Department of Chemistry (United States)

1999-10-15

Eotaxin is a CC chemokine with potent chemoattractant activity towards eosinophils. {sup 15}N NMR relaxation data have been used to characterize the backbone dynamics of recombinant human eotaxin. {sup 15}N longitudinal (R{sub 1}) and transverse (R{sub 2}) auto relaxation rates, heteronuclear {sup 1}H-{sup 15}N steady-state NOEs, and transverse cross-relaxation rates ({eta}{sub xy}) were obtained at 30 deg. C for all resolved backbone secondary amide groups using {sup 1} H-detected two-dimensional NMR experiments. Ratios of transverse auto and cross relaxation rates were used to identify NH groups influenced by slow conformational rearrangement. Relaxation data were fit to the extended model free dynamics formalism, yielding parameters describing axially symmetric molecular rotational diffusion and the internal dynamics of each NH group. The molecular rotational correlation time ({tau}{sub m}) is 5.09{+-}0.02 ns, indicating that eotaxin exists predominantly as a monomer under the conditions of the NMR study. The ratio of diffusion rates about unique and perpendicular axes (D{sub parallel}/D{sub perpendicular}) is 0.81{+-}0.02. Residues with large amplitudes of subnanosecond motion are clustered in the N-terminal region (residues 1-19), the C-terminus (residues 68-73) and the loop connecting the first two {beta}-strands (residues 30-37). N-terminal flexibility appears to be conserved throughout the chemokine family and may have implications for the mechanism of chemokine receptor activation. Residues exhibiting significant dynamics on the microsecond-millisecond time scale are located close to the two conserved disulfide bonds, suggesting that these motions may be coupled to disulfide bond isomerization.
Shapiro like steps reveals molecular nanomagnets’ spin dynamics

International Nuclear Information System (INIS)

Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

2015-01-01

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

DEFF Research Database (Denmark)

Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...
Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

2015-06-09

The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.
Electron-nuclear corellations for photoinduced dynamics in molecular dimers

Science.gov (United States)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).
Vectorization, parallelization and implementation of Quantum molecular dynamics codes (QQQF, MONTEV)

Energy Technology Data Exchange (ETDEWEB)

Kato, Kaori [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Kunugi, Tomoaki; Kotake, Susumu; Shibahara, Masahiko

1998-03-01

This report describes parallelization, vectorization and implementation for two simulation codes, Quantum molecular dynamics simulation code QQQF and Photon montecalro molecular dynamics simulation code MONTEV, that have been developed for the analysis of the thermalization of photon energies in the molecule or materials. QQQF has been vectorized and parallelized on Fujitsu VPP and has been implemented from VPP to Intel Paragon XP/S and parallelized. MONTEV has been implemented from VPP to Paragon and parallelized. (author)
An analysis of hydrated proton diffusion in ab initio molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Tse, Ying-Lung Steve; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Knight, Chris [Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

2015-01-07

A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions
Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

Science.gov (United States)

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

NARCIS (Netherlands)

JUFFER, AH; BERENDSEN, HJC

1993-01-01

A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the
Thermal transport in semicrystalline polyethylene by molecular dynamics simulation

Science.gov (United States)

Lu, Tingyu; Kim, Kyunghoon; Li, Xiaobo; Zhou, Jun; Chen, Gang; Liu, Jun

2018-01-01

Recent research has highlighted the potential to achieve high-thermal-conductivity polymers by aligning their molecular chains. Combined with other merits, such as low-cost, corrosion resistance, and light weight, such polymers are attractive for heat transfer applications. Due to their quasi-one-dimensional structural nature, the understanding on the thermal transport in those ultra-drawn semicrystalline polymer fibers or films is still lacking. In this paper, we built the ideal repeating units of semicrystalline polyethylene and studied their dependence of thermal conductivity on different crystallinity and interlamellar topology using the molecular dynamics simulations. We found that the conventional models, such as the Choy-Young's model, the series model, and Takayanagi's model, cannot accurately predict the thermal conductivity of the quasi-one-dimensional semicrystalline polyethylene. A modified Takayanagi's model was proposed to explain the dependence of thermal conductivity on the bridge number at intermediate and high crystallinity. We also analyzed the heat transfer pathways and demonstrated the substantial role of interlamellar bridges in the thermal transport in the semicrystalline polyethylene. Our work could contribute to the understanding of the structure-property relationship in semicrystalline polymers and shed some light on the development of plastic heat sinks and thermal management in flexible electronics.
Molecular dynamics simulations and quantum chemical calculations ...

African Journals Online (AJOL)

Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...
Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

NARCIS (Netherlands)

Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

2007-01-01

A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which

Droplet spreading driven by van der Waals force: a molecular dynamics study

KAUST Repository

Wu, Congmin

2010-07-07

The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.
Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.

Science.gov (United States)

Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei

2018-06-05

The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.
Constant-pH molecular dynamics using stochastic titration

Science.gov (United States)

Baptista, António M.; Teixeira, Vitor H.; Soares, Cláudio M.

2002-09-01

A new method is proposed for performing constant-pH molecular dynamics (MD) simulations, that is, MD simulations where pH is one of the external thermodynamic parameters, like the temperature or the pressure. The protonation state of each titrable site in the solute is allowed to change during a molecular mechanics (MM) MD simulation, the new states being obtained from a combination of continuum electrostatics (CE) calculations and Monte Carlo (MC) simulation of protonation equilibrium. The coupling between the MM/MD and CE/MC algorithms is done in a way that ensures a proper Markov chain, sampling from the intended semigrand canonical distribution. This stochastic titration method is applied to succinic acid, aimed at illustrating the method and examining the choice of its adjustable parameters. The complete titration of succinic acid, using constant-pH MD simulations at different pH values, gives a clear picture of the coupling between the trans/gauche isomerization and the protonation process, making it possible to reconcile some apparently contradictory results of previous studies. The present constant-pH MD method is shown to require a moderate increase of computational cost when compared to the usual MD method.
Molecular dynamics simulations of melting behavior of alkane as phase change materials slurry

International Nuclear Information System (INIS)

Rao Zhonghao; Wang Shuangfeng; Wu Maochun; Zhang Yanlai; Li Fuhuo

2012-01-01

Highlights: ► The melting behavior of phase change materials slurry was investigated by molecular dynamics simulation method. ► Four different PCM slurry systems including pure water and water/n-nonadecane composite were constructed. ► Amorphous structure and periodic boundary conditions were used in the molecular dynamics simulations. ► The simulated melting temperatures are very close to the published experimental values. - Abstract: The alkane based phase change materials slurry, with high latent heat storage capacity, is effective to enhance the heat transfer rate of traditional fluid. In this paper, the melting behavior of composite phase change materials slurry which consists of n-nonadecane and water was investigated by using molecular dynamics simulation. Four different systems including pure water and water/n-nonadecane composite were constructed with amorphous structure and periodic boundary conditions. The results showed that the simulated density and melting temperature were very close to the published experimental values. Mixing the n-nonadecane into water decreased the mobility but increased the energy storage capacity of composite systems. To describe the melting behavior of alkane based phase change materials slurry on molecular or atomic scale, molecular dynamics simulation is an effective method.
Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann

Energy Technology Data Exchange (ETDEWEB)

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

2017-06-01

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

Science.gov (United States)

Hanna, Hanna; Andre, Franck M; Mir, Lluis M

2017-04-20

Human mesenchymal stem cells are promising tools for regenerative medicine due to their ability to differentiate into many cellular types such as osteocytes, chondrocytes and adipocytes amongst many other cell types. These cells present spontaneous calcium oscillations implicating calcium channels and pumps of the plasma membrane and the endoplasmic reticulum. These oscillations regulate many basic functions in the cell such as proliferation and differentiation. Therefore, the possibility to mimic or regulate these oscillations might be useful to regulate mesenchymal stem cells biological functions. One or several electric pulses of 100 μs were used to induce Ca 2+ spikes caused by the penetration of Ca 2+ from the extracellular medium, through the transiently electropermeabilized plasma membrane, in human adipose mesenchymal stem cells from several donors. Attached cells were preloaded with Fluo-4 AM and exposed to the electric pulse(s) under the fluorescence microscope. Viability was also checked. According to the pulse(s) electric field amplitude, it is possible to generate a supplementary calcium spike with properties close to those of calcium spontaneous oscillations, or, on the contrary, to inhibit the spontaneous calcium oscillations for a very long time compared to the pulse duration. Through that inhibition of the oscillations, Ca 2+ oscillations of desired amplitude and frequency could then be imposed on the cells using subsequent electric pulses. None of the pulses used here, even those with the highest amplitude, caused a loss of cell viability. An easy way to control Ca 2+ oscillations in mesenchymal stem cells, through their cancellation or the addition of supplementary Ca 2+ spikes, is reported here. Indeed, the direct link between the microsecond electric pulse(s) delivery and the occurrence/cancellation of cytosolic Ca 2+ spikes allowed us to mimic and regulate the Ca 2+ oscillations in these cells. Since microsecond electric pulse delivery
Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

Directory of Open Access Journals (Sweden)

Dirk-Sören Lühmann

2015-08-01

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

Science.gov (United States)

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

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

Directory of Open Access Journals (Sweden)

Ji-Long Zhang

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

Science.gov (United States)

Lach, Joanna; Goclon, Jakub; Rodziewicz, Pawel

2016-04-05

Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum. Copyright © 2015 Elsevier B.V. All rights reserved.
Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

International Nuclear Information System (INIS)

More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

2012-01-01

Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)
Thermophysical properties of hydrogen-helium mixtures: re-examination of the mixing rules via quantum molecular dynamics simulations.

Science.gov (United States)

Wang, Cong; He, Xian-Tu; Zhang, Ping

2013-09-01

Thermophysical properties of hydrogen, helium, and hydrogen-helium mixtures have been investigated in the warm dense matter regime at electron number densities ranging from 6.02 × 10^{29} ∼ 2.41 × 10^{30} m^{-3} and temperatures from 4000 to 20000 K via quantum molecular dynamics simulations. We focus on the dynamical properties such as the equation of states, diffusion coefficients, and viscosity. Mixing rules (density matching, pressure matching, and binary ionic mixing rules) have been validated by checking composite properties of pure species against that of the fully interacting mixture derived from quantum molecular dynamics simulations. These mixing rules reproduce pressures within 10% accuracy, while it is 75% and 50% for the diffusion and viscosity, respectively. The binary ionic mixing rule moves the results into better agreement. Predictions from one component plasma model are also provided and discussed.
Nonequilibrium molecular dynamics theory, algorithms and applications

CERN Document Server

Todd, Billy D

2017-01-01

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

NARCIS (Netherlands)

Marrink, SJ; Mark, AE

2003-01-01

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

NARCIS (Netherlands)

Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

2007-01-01

We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated
Quantum molecular dynamics study of the Su-Schrieffer-Heeger model

NARCIS (Netherlands)

Michielsen, Kristel; Raedt, Hans De

A quantum molecular dynamics technique is presented to compute the static and dynamic properties of a system of fermions coupled to classical degrees of freedom. The method is employed to investigate the properties of the Su-Schrieffer-Heeger model, an electron-phonon model which is often used to
A comparative molecular dynamics study of diffusion of n-decane ...

Indian Academy of Sciences (India)

Administrator

Abstract. Molecular dynamics simulations are reported on the structure and dynamics of n-decane and. 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We.
Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

National Research Council Canada - National Science Library

Johnston, K

1998-01-01

.... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...
Friction in Carborane-Based Molecular Rotors Driven by Gas Flow or Electric Field: Classical Molecular Dynamics

Czech Academy of Sciences Publication Activity Database

Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

2012-01-01

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

Directory of Open Access Journals (Sweden)

Rong Shen

2015-10-01

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

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Zeynab Mohammad Hosseini Naveh

Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.
Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions

International Nuclear Information System (INIS)

Verkhovtsev, A.; Korol, A.V.; Solovyov, A.V.

2017-01-01

We present the results of classical molecular dynamics simulations of collision-induced fusion and fragmentation of C 60 fullerenes, performed by means of the MBN Explorer software package. The simulations provide information on structural differences of the fused compound depending on kinematics of the collision process. The analysis of fragmentation dynamics at different initial conditions shows that the size distributions of produced molecular fragments are peaked for dimers, which is in agreement with a well-established mechanism of C 60 fragmentation via preferential C 2 emission. Atomic trajectories of the colliding particles are analyzed and different fragmentation patterns are observed and discussed. On the basis of the performed simulations, characteristic time of C 2 emission is estimated as a function of collision energy. The results are compared with experimental time-of-flight distributions of molecular fragments and with earlier theoretical studies. Considering the widely explored case study of C 60 -C 60 collisions, we demonstrate broad capabilities of the MBN Explorer software, which can be utilized for studying collisions of a broad variety of nano-scale and bio-molecular systems by means of classical molecular dynamics. (authors)
Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

Czech Academy of Sciences Publication Activity Database

Chocholoušová, Jana; Feig, M.

2006-01-01

Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006
Molecular dynamics investigation on adsorption layer of alcohols at the air/brine interface.

Science.gov (United States)

Nguyen, Cuong V; Phan, Chi M; Ang, Ha M; Nakahara, Hiromichi; Shibata, Osamu; Moroi, Yoshikiyo

2015-01-01

Alcohols are a significant group of surfactants which have been employed extensively in industry to improve the interfacial effects. Recently, the change in surface potential (ΔV) of two isomeric hexanols, methyl isobutyl carbinol (MIBC) and 1-hexanol, was investigated by using an ionizing (241)Am electrode. It clearly showed the opposite effects between MIBC and 1-hexanol in the interfacial zone: one enhanced the presence of cations, whereas the other enhanced the presence of anions. This study employs molecular dynamics simulation to provide new insights into the interactions between alcohol molecules and ions as well as water at the molecular level. The results qualitatively agreed with the experimental data and verified the significance of MIBC branching structure on the molecular arrangement within the interfacial zone. The results also highlighted the role of the second water layer on the interfacial properties.
High-pressure microscopy for tracking dynamic properties of molecular machines.

Science.gov (United States)

Nishiyama, Masayoshi

2017-12-01

High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo. This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa. Application of pressure could change polymerization and depolymerization processes of the microtubule cytoskeleton, suggesting a modulation of the intermolecular interaction between tubulin molecules. A novel motility assay demonstrated that high hydrostatic pressure induces counterclockwise (CCW) to clockwise (CW) reversals of the Escherichia coli flagellar motor. The present techniques could be extended to study how molecular machines in complicated systems respond to mechanical stimuli. Copyright © 2017 Elsevier B.V. All rights reserved.
Structural, dynamic, electronic, and vibrational properties of flexible, intermediate, and stressed rigid As-Se glasses and liquids from first principles molecular dynamics

International Nuclear Information System (INIS)

Bauchy, M.; Kachmar, A.; Micoulaut, M.

2014-01-01

The structural, vibrational, electronic, and dynamic properties of amorphous and liquid As x Se 1-x (0.10 Molecular Dynamics. Within the above range of compositions, thresholds, and anomalies are found in the behavior of reciprocal and real space properties that can be correlated to the experimental location of the Boolchand intermediate phase in these glassy networks, observed at 0.27 dynamical atomic-scale fingerprints for the onset of rigidity within the network, while also providing a much more complex picture than the one derived from mean-field approaches of stiffness transitions
Mechanisms of molecular transport through the urea channel of Helicobacter pylori

Science.gov (United States)

McNulty, Reginald; Ulmschneider, Jakob P.; Luecke, Hartmut; Ulmschneider, Martin B.

2013-12-01

Helicobacter pylori survival in acidic environments relies on cytoplasmic hydrolysis of gastric urea into ammonia and carbon dioxide, which buffer the pathogen’s periplasm. Urea uptake is greatly enhanced and regulated by HpUreI, a proton-gated inner membrane channel protein essential for gastric survival of H. pylori. The crystal structure of HpUreI describes a static snapshot of the channel with two constriction sites near the center of the bilayer that are too narrow to allow passage of urea or even water. Here we describe the urea transport mechanism at atomic resolution, revealed by unrestrained microsecond equilibrium molecular dynamics simulations of the hexameric channel assembly. Two consecutive constrictions open to allow conduction of urea, which is guided through the channel by interplay between conserved residues that determine proton rejection and solute selectivity. Remarkably, HpUreI conducts water at rates equivalent to aquaporins, which might be essential for efficient transport of urea at small concentration gradients.
Molecular dynamics simulation of potentiometric sensor response: the effect of biomolecules, surface morphology and surface charge.

Science.gov (United States)

Lowe, B M; Skylaris, C-K; Green, N G; Shibuta, Y; Sakata, T

2018-05-10

The silica-water interface is critical to many modern technologies in chemical engineering and biosensing. One technology used commonly in biosensors, the potentiometric sensor, operates by measuring the changes in electric potential due to changes in the interfacial electric field. Predictive modelling of this response caused by surface binding of biomolecules remains highly challenging. In this work, through the most extensive molecular dynamics simulation of the silica-water interfacial potential and electric field to date, we report a novel prediction and explanation of the effects of nano-morphology on sensor response. Amorphous silica demonstrated a larger potentiometric response than an equivalent crystalline silica model due to increased sodium adsorption, in agreement with experiments showing improved sensor response with nano-texturing. We provide proof-of-concept that molecular dynamics can be used as a complementary tool for potentiometric biosensor response prediction. Effects that are conventionally neglected, such as surface morphology, water polarisation, biomolecule dynamics and finite-size effects, are explicitly modelled.
Sex speeds adaptation by altering the dynamics of molecular evolution.

Science.gov (United States)

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

2016-03-10

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

Science.gov (United States)

Lehmann, Kevin K.

2003-03-01

Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.
The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

Science.gov (United States)

Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

2016-09-07

Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.
Accelerating convergence of molecular dynamics-based structural relaxation

DEFF Research Database (Denmark)

Christensen, Asbjørn

2005-01-01

We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...
Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

Indian Academy of Sciences (India)

Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...
DyNet: visualization and analysis of dynamic molecular interaction networks.

Science.gov (United States)

Goenawan, Ivan H; Bryan, Kenneth; Lynn, David J

2016-09-01

: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). david.lynn@sahmri.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces

International Nuclear Information System (INIS)

Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.

2011-01-01

The use of accelerators such as general-purpose graphics processing units (GPGPUs) have become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - (1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory, (2) minimizing the amount of code that must be ported for efficient acceleration, (3) utilizing the available processing power from both many-core CPUs and accelerators, and (4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPGPUs and 180 CPU cores.
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

KAUST Repository

Neumann, Philipp

2012-06-01

We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.
Molecular electron recollision dynamics in intense circularly polarized laser pulses

Science.gov (United States)

Bandrauk, André D.; Yuan, Kai-Jun

2018-04-01

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

Science.gov (United States)

Foroutan, Masumeh; Fatemi, S Mahmood; Esmaeilian, Farshad

2017-02-01

During the past decade, the research on fluids in nanoconfined geometries has received considerable attention as a consequence of their wide applications in different fields. Several nanoconfined systems such as water and ionic liquids, together with an equally impressive array of nanoconfining media such as carbon nanotube, graphene and graphene oxide have received increasingly growing interest in the past years. Water is the first system that has been reviewed in this article, due to its important role in transport phenomena in environmental sciences. Water is often considered as a highly nanoconfined system, due to its reduction to a few layers of water molecules between the extended surface of large macromolecules. The second system discussed here is ionic liquids, which have been widely studied in the modern green chemistry movement. Considering the great importance of ionic liquids in industry, and also their oil/water counterpart, nanoconfined ionic liquid system has become an important area of research with many fascinating applications. Furthermore, the method of molecular dynamics simulation is one of the major tools in the theoretical study of water and ionic liquids in nanoconfinement, which increasingly has been joined with experimental procedures. In this way, the choice of water and ionic liquids in nanoconfinement is justified by applying molecular dynamics simulation approaches in this review article.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

2015-12-07

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

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Science.gov (United States)

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

2018-04-24

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

International Nuclear Information System (INIS)

Kent, P R C

2008-01-01

Plane wave density functional calculations have traditionally been able to use the largest available supercomputing resources. We analyze the scalability of modern projector-augmented wave implementations to identify the challenges in performing molecular dynamics calculations of large systems containing many thousands of electrons. Benchmark calculations on the Cray XT4 demonstrate that global linear-algebra operations are the primary reason for limited parallel scalability. Plane-wave related operations can be made sufficiently scalable. Improving parallel linear-algebra performance is an essential step to reaching longer timescales in future large-scale molecular dynamics calculations
Molecular dynamics study of silver

International Nuclear Information System (INIS)

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

1995-03-01

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

Science.gov (United States)

Zhu, You-Liang; Pan, Deng; Li, Zhan-Wei; Liu, Hong; Qian, Hu-Jun; Zhao, Yang; Lu, Zhong-Yuan; Sun, Zhao-Yan

2018-04-01

We describe the algorithm of employing multi-GPU power on the basis of Message Passing Interface (MPI) domain decomposition in a molecular dynamics code, GALAMOST, which is designed for the coarse-grained simulation of soft matters. The code of multi-GPU version is developed based on our previous single-GPU version. In multi-GPU runs, one GPU takes charge of one domain and runs single-GPU code path. The communication between neighbouring domains takes a similar algorithm of CPU-based code of LAMMPS, but is optimised specifically for GPUs. We employ a memory-saving design which can enlarge maximum system size at the same device condition. An optimisation algorithm is employed to prolong the update period of neighbour list. We demonstrate good performance of multi-GPU runs on the simulation of Lennard-Jones liquid, dissipative particle dynamics liquid, polymer and nanoparticle composite, and two-patch particles on workstation. A good scaling of many nodes on cluster for two-patch particles is presented.
Crystal structure and pair potentials: A molecular-dynamics study

Energy Technology Data Exchange (ETDEWEB)

Parrinello, M.; Rahman, A.

1980-10-06

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

Indian Academy of Sciences (India)

aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.
Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

International Nuclear Information System (INIS)

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

1980-01-01

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

DEFF Research Database (Denmark)

Euro, Liliya; Haapanen, Outi; Róg, Tomasz

2017-01-01

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

Directory of Open Access Journals (Sweden)

Christian Mücksch

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

Science.gov (United States)

Sneha, P; Doss, C George Priya

2016-01-01

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

Science.gov (United States)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

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

International Nuclear Information System (INIS)

Wang Xiaojing; Wang Wei; Han Peilin; Kubo, Momoji; Miyamoto, Akira

2008-01-01

An accelerated quantum chemical molecular dynamical code 'Colors-Excite' was used to investigate the photolysis of alkyl nitrites series, RONO (R=CH 3 and C(CH 3 ) 3 ) on copper surfaces. Our calculations showed that the photo-dissociated processes are associated with the alkyl substituents of RONO when adsorbed on copper surfaces. For R=CH 3 , a two-step photolysis reaction occurred, yielding diverse intermediate products including RO radical, NO, and HNO, consistent with those reported in gas phase. While for R=C(CH 3 ) 3 , only one-step photolysis reaction occurred and gave intermediate products of RO radical and NO. Consequently, pure RO species were achieved to adsorb on metal surfaces by removing the NO species in photolysis reaction. The detailed photo-dissociated behaviors of RONO on copper surfaces with different alkyl substituents which are uncovered by the present simulation can be extended to explain the diverse dissociative mechanism experimentally observed. The quantum chemical molecular dynamical code 'Colors-Excite' is proved to be highly applicable to the photo-dissociations on metal surfaces
Self-assembly formation of palm-based esters nano-emulsion: A molecular dynamics study

Science.gov (United States)

Abdul Rahman, Mohd. Basyaruddin; Huan, Qiu-Yi; Tejo, Bimo A.; Basri, Mahiran; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Abdul

2009-10-01

Palm-oil esters (POEs) are unsaturated and non-ionic esters that can be prepared by enzymatic synthesis from palm oil. Their nano-emulsion properties possess great potential to act as drug carrier for transdermal drug delivery system. A ratio of 75:5:20 (water/POEs/Span20) was chosen from homogenous region in the phase diagram of our previous experimental work to undergo molecular dynamics simulation. A 15 ns molecular dynamics simulation of nano-emulsion system (water/POEs/Span20) was carried out using OPLS-AA force field. The aggregations of the oil and surfactant molecules are observed throughout the simulation. After 8 ns of simulation, the molecules start to aggregate to form one spherical micelle where the POEs molecules are surrounded by the non-ionic surfactant (Span20) molecules with an average size of 4.2 ± 0.05 nm. The size of the micelle and the ability of palm-based nano-emulsion to self-assemble suggest that this nano-emulsion can potentially use in transdermal drug delivery system.
Microsecond-scale electric field pulses in cloud lightning discharges

Science.gov (United States)

Villanueva, Y.; Rakov, V. A.; Uman, M. A.; Brook, M.

1994-01-01

From wideband electric field records acquired using a 12-bit digitizing system with a 500-ns sampling interval, microsecond-scale pulses in different stages of cloud flashes in Florida and New Mexico are analyzed. Pulse occurrence statistics and waveshape characteristics are presented. The larger pulses tend to occur early in the flash, confirming the results of Bils et al. (1988) and in contrast with the three-stage representation of cloud-discharge electric fields suggested by Kitagawa and Brook (1960). Possible explanations for the discrepancy are discussed. The tendency for the larger pulses to occur early in the cloud flash suggests that they are related to the initial in-cloud channel formation processes and contradicts the common view found in the atmospheric radio-noise literature that the main sources of VLF/LF electromagnetic radiation in cloud flashes are the K processes which occur in the final, or J type, part of the cloud discharge.
Molecular dynamics simulations of elasto-hydrodynamic lubrication and boundary lubrication for automotive tribology

International Nuclear Information System (INIS)

Washizu, Hitoshi; Sanda, Shuzo; Hyodo, Shi-aki; Ohmori, Toshihide; Nishino, Noriaki; Suzuki, Atsushi

2007-01-01

Friction control of machine elements on a molecular level is a challenging subject in vehicle technology. We describe the molecular dynamics studies of friction in two significant lubrication regimes. As a case of elastohydrodynamic lubrication, we introduce the mechanism of momentum transfer related to the molecular structure of the hydrocarbon fluids, phase transition of the fluids under high pressure, and a submicron thickness simulation of the oil film using a tera-flops computer. For boundary lubrication, the dynamic behavior of water molecules on hydrophilic and hydrophobic silicon surfaces under a shear condition is studied. The dynamic structure of the hydrogen bond network on the hydrophilic surface is related to the low friction of the diamond-like carbon containing silicon (DLC-Si) coating
Dynamic analysis of electron density in the course of the internal motion of molecular system

International Nuclear Information System (INIS)

Tachibana, A.; Hori, K.; Asai, Y.; Yamabe, T.

1984-01-01

The general dynamic aspect of electron density of a molecular system is studied on the basis of the general equation of the electron orbital which is formulated for the dynamic study of electronic motion. The newly defined electron orbital incorporates the dynamics of molecular vibration into the electronic structures. In this scheme, the change of electron distribution caused by excitation of vibrational state is defined as the ''dynamic electron transfer.'' The dynamic electron density is found to have the remarkable ''additive'' property. The time-dependent aspect of the dynamic electron redistribution is also analyzed on the basis of the ''coherent state.'' The new method relates the classical vibrational amplitude to the quantum number of the vibrational state. As a preliminary application of the present treatment, the dynamic electron densities of H 2 , HD, HT, HF, and HCl molecules are calculated by use of ab initio molecular orbital method
Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

Science.gov (United States)

Skolnick, Jeffrey

2016-09-01

An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes.
Molecular dynamic analysis of the structure of dendrimers

Energy Technology Data Exchange (ETDEWEB)

Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.
Molecular dynamic analysis of the structure of dendrimers

International Nuclear Information System (INIS)

Canetta, E.; Maino, G.

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques
Free energy from molecular dynamics with multiple constraints

NARCIS (Netherlands)

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

2000-01-01

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

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

African Journals Online (AJOL)

Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations

Directory of Open Access Journals (Sweden)

Cedrix J. Dongmo Foumthuim

2018-01-01

Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
The chaos and order in nuclear molecular dynamics

International Nuclear Information System (INIS)

Srokowski, T.

1995-01-01

The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12 C, 16 O and 20 Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs
Dynamics of Oxidation of Aluminum Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers

Science.gov (United States)

Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen

1999-06-01

Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.
Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies

Science.gov (United States)

Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.

2017-03-01

We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
Fermionic molecular dynamics for ground states and collisions of nuclei

International Nuclear Information System (INIS)

Feldmeier, H.; Bieler, K.; Schnack, J.

1994-08-01

The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)
Structural, dynamic, electronic, and vibrational properties of flexible, intermediate, and stressed rigid As-Se glasses and liquids from first principles molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Bauchy, M. [Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095-1593 (United States); Kachmar, A. [Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05 (France); Qatar Environment and Energy Research Institute, Qatar Foundation, P.O. Box 5825, Doha (Qatar); Micoulaut, M., E-mail: mmi@lptl.jussieu.fr [Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05 (France)

2014-11-21

The structural, vibrational, electronic, and dynamic properties of amorphous and liquid As{sub x}Se{sub 1-x} (0.10 Molecular Dynamics. Within the above range of compositions, thresholds, and anomalies are found in the behavior of reciprocal and real space properties that can be correlated to the experimental location of the Boolchand intermediate phase in these glassy networks, observed at 0.27 dynamical atomic-scale fingerprints for the onset of rigidity within the network, while also providing a much more complex picture than the one derived from mean-field approaches of stiffness transitions.
A molecular dynamics study of the structure and inter-particle interactions of polyethylene glycol-conjugated PAMAM dendrimers

OpenAIRE

Lee, Hwankyu; Larson, Ronald G.

2009-01-01

We performed molecular dynamics (MD) simulations of one or two copies of polyethylene glycol of molecular weight 550 (PEG550) and 5000 (PEG5000) Daltons, conjugated to generation 3 (G3) to 5 (G5) polyamidoamine (PAMAM) dendrimers with explicit water using a coarse-grained model. We found the radii of gyration of these dendrimer-PEG molecules to be close to those measured in experiments by Hedden and Bauer (Macromolecules 2003, 36, 1829). Densely grafted PEG ligands (>50% of the dendrimer surf...
Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: a molecular dynamics simulation study.

Directory of Open Access Journals (Sweden)

Amit Kumar

Full Text Available Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide. In particular we focused on the MHC peptide binding groove dynamics. The predisposing allele was found to form a stable complex with both the peptides, while the protective allele displayed stability only when bound with myelin peptide. The local flexibility of the MHC was probed dividing the binding groove into four compartments covering the well known peptide anchoring pockets. The predisposing allele in the first half cleft exhibits a narrower and more rigid groove conformation in the presence of myelin peptide. The protective allele shows a similar behavior, while in the second half cleft it displays a narrower and more flexible groove conformation in the presence of viral peptide. We further characterized these dynamical differences by evaluating H-bonds, hydrophobic and stacking interaction networks, finding striking similarities with super-type patterns emerging in other autoimmune diseases. The protective allele shows a defined preferential binding to myelin peptide, as confirmed by binding free energy calculations. All together, we believe the presented molecular analysis could help to design experimental assays, supports the molecular mimicry hypothesis and suggests that propensity to multiple sclerosis in Sardinia could be partly linked to distinct peptide-MHC interaction and binding characteristics of the antigen presentation mechanism.
Emission spectroscopic studies on dynamics of molecular excitation and dissociation by controlled electron impact

International Nuclear Information System (INIS)

Ogawa, Teiichiro

1986-01-01

Emission spectrum by controlled electron impact has been a successful technique for the investigation of molecular dynamics. (1) Molecular excitation. Aromatic molecules give an optical emission similar to fluorescence. However, as is shown by the vibrational structure and the electron energy dependence of benzene emission, its excitation process is not necessarily optical. Some aliphatic molecules also exhibit an emission band at the ultraviolet region. (2) Molecular dissociation. Analysis of the Doppler profile, the threshold energy, the excitation function and the isotope effect of the atomic emission produced in electron-molecule collisions has clarified the dynamics of the molecular dissociation. Especially the Doppler profile has given the translational energy distribution of the fragment atom, which is very useful to disclose the potential energy curve. Its angular dependence has recently found to allow determination of the symmetry of the intermediate excited state and the magnetic sublevel distribution of the fragment atom. These finding has revealed detailed state-to-state dynamics of the molecular dissociation. (author)
Effects of temperature and isotopic substitution on electron attachment dynamics of guanine–cytosine base pair: Ring-polymer and classical molecular dynamics simulations

International Nuclear Information System (INIS)

Minoshima, Yusuke; Seki, Yusuke; Takayanagi, Toshiyuki; Shiga, Motoyuki

2016-01-01

Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: 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.
Effects of temperature and isotopic substitution on electron attachment dynamics of guanine–cytosine base pair: Ring-polymer and classical molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Minoshima, Yusuke; Seki, Yusuke [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takayanagi, Toshiyuki, E-mail: tako@mail.saitama-u.ac.jp [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Shiga, Motoyuki [Center for Computational Science and E-Systems, Japan Atomic Energy Agency, 148-4, Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871 (Japan)

2016-06-15

Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: 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.
Molecular dynamics simulation of a chemical reaction

International Nuclear Information System (INIS)

Gorecki, J.; Gryko, J.

1988-06-01

Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Photocatalytic oxidation dynamics of acetone on TiO2: tight-binding quantum chemical molecular dynamics study

International Nuclear Information System (INIS)

Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

2005-01-01

The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed
Atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

Science.gov (United States)

Pabst, Stefan

2013-04-01

Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in recent years made it possible to generate ultrashort pulses, which can be used to trigger, to watch, and to control atomic and molecular motion. This tutorial focuses on experimental and theoretical advances which are used to study the dynamics of electrons and molecules in the presence of ultrashort pulses. In the first part, the rotational dynamics of molecules, which happens on picosecond and femtosecond time scales, is reviewed. Well-aligned molecules are particularly suitable for angle-dependent investigations like x-ray diffraction or strong-field ionization experiments. In the second part, the ionization dynamics of atoms is studied. The characteristic time scale lies, here, in the attosecond to few-femtosecond regime. Although a one-particle picture has been successfully applied to many processes, many-body effects do constantly occur. After a broad overview of the main mechanisms and the most common tools in attosecond physics, examples of many-body dynamics in the attosecond world (e.g., in high-harmonic generation and attosecond transient absorption spectroscopy) are discussed.
Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

International Nuclear Information System (INIS)

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

2016-01-01

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

Science.gov (United States)

Zhao, Lei; Cheng, Jiangtao

2017-09-07

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

Directory of Open Access Journals (Sweden)

Freddolino Peter L

2011-05-01

Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.
In situ diffraction profile analysis during tensile deformation motivated by molecular dynamics

International Nuclear Information System (INIS)

Van Swygenhoven, H.; Budrovic, Z.; Derlet, P.M.; Froseth, A.G.; Van Petegem, S.

2005-01-01

Molecular dynamics simulations can provide insight into the slip mechanism at the atomic scale and suggest that in nanocrystalline metals dislocations are nucleated and absorbed by the grain boundaries. However, this technique is limited by very short simulation times. Using suggestions from molecular dynamics, we have developed a new in situ X-ray diffraction technique wherein the profile analysis of several Bragg diffraction peaks during tensile deformation is possible. Combining experiment and careful structural analysis the results confirm the suggestions from atomistic simulations
Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

Science.gov (United States)

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

2017-03-01

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

A molecular dynamics algorithm for simulation of field theories in the canonical ensemble

International Nuclear Information System (INIS)

Kogut, J.B.; Sinclair, D.K.

1986-01-01

We add a single scalar degree of freedom (''demon'') to the microcanonical ensemble which converts its molecular dynamics into a simulation method for the canonical ensemble (euclidean path integral) of the underlying field theory. This generalization of the microcanonical molecular dynamics algorithm simulates the field theory at fixed coupling with a completely deterministic procedure. We discuss the finite size effects of the method, the equipartition theorem and ergodicity. The method is applied to the planar model in two dimensions and SU(3) lattice gauge theory with four species of light, dynamical quarks in four dimensions. The method is much less sensitive to its discrete time step than conventional Langevin equation simulations of the canonical ensemble. The method is a straightforward generalization of a procedure introduced by S. Nose for molecular physics. (orig.)
Semiquantum molecular dynamics simulation of thermal properties and heat transport in low-dimensional nanostructures

Science.gov (United States)

Savin, Alexander V.; Kosevich, Yuriy A.; Cantarero, Andres

2012-08-01

We present a detailed description of semiquantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian equations of motion in which the effects of phonon quantum statistics are introduced through random Langevin-like forces with a specific power spectral density (the color noise). The color noise describes the interaction of the molecular system with the thermostat. We apply this technique to the simulation of thermal properties and heat transport in different low-dimensional nanostructures. We describe the determination of temperature in quantum lattice systems, to which the equipartition limit is not applied. We show that one can determine the temperature of such a system from the measured power spectrum and temperature- and relaxation-rate-independent density of vibrational (phonon) states. We simulate the specific heat and heat transport in carbon nanotubes, as well as the heat transport in molecular nanoribbons with perfect (atomically smooth) and rough (porous) edges, and in nanoribbons with strongly anharmonic periodic interatomic potentials. We show that the effects of quantum statistics of phonons are essential for the carbon nanotube in the whole temperature range T<500K, in which the values of the specific heat and thermal conductivity of the nanotube are considerably less than that obtained within the description based on classical statistics of phonons. This conclusion is also applicable to other carbon-based materials and systems with high Debye temperature like graphene, graphene nanoribbons, fullerene, diamond, diamond nanowires, etc. We show that the existence of rough edges and quantum statistics of phonons change drastically the low-temperature thermal conductivity of the nanoribbon in comparison with that of the nanoribbon with perfect edges and classical phonon dynamics and statistics. The semiquantum molecular
Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

Directory of Open Access Journals (Sweden)

Jenny Farmer

2017-11-01

Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.
Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

Science.gov (United States)

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-02-22

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.
Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

International Nuclear Information System (INIS)

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

2016-01-01

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

International Nuclear Information System (INIS)

Milano, Giuseppe; De Nicola, Antonio; Kawakatsu, Toshihiro

2013-01-01

This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle–field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle–field models. This feature makes these models very promising ones in the exploration of several problems in biophysics. (paper)
Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics.

Science.gov (United States)

van den Broek, Karina; Kuhn, Hubert; Zielesny, Achim

2018-05-21

Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated "all-in-one" simulation systems.
Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

Science.gov (United States)

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

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821
Molecular dynamics simulation of ribosome jam

KAUST Repository

Matsumoto, Shigenori

2011-09-01

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

International Nuclear Information System (INIS)

Dellerue, Serge

2000-01-01

Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

Science.gov (United States)

Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

2011-01-01

The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525
POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

Science.gov (United States)

Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

2015-12-01

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.
Molecular Dynamics with Helical Periodic Boundary Conditions

Czech Academy of Sciences Publication Activity Database

Kessler, Jiří; Bouř, Petr

2014-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Okumura, Hisashi [Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585 (Japan); Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 (Japan)

2015-12-31

Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting

National Research Council Canada - National Science Library

Low, Tammy K

2006-01-01

.... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...
Modification of -Adenosyl--Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

Directory of Open Access Journals (Sweden)

Usman Sumo Friend Tambunan

2017-04-01

Full Text Available Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5 methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S -adenosyl- l -methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S -adenosyl- l -homocysteine (SAH. The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity test. The 2 simulations were performed using Molecular Operating Environment (MOE 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356 based on ΔG binding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.
Challenges for energy dispersive X-ray absorption spectroscopy at the ESRF: microsecond time resolution and Mega-bar pressures

International Nuclear Information System (INIS)

Aquilanti, G.

2002-01-01

This Thesis concerns the development of two different applications of energy-dispersive X-ray absorption spectroscopy at the ESRF: time-resolved studies pushed to the microsecond time resolution and high-pressure studies at the limit of the Mega-bar pressures. The work has been developed in two distinct parts, and the underlying theme has been the exploitation of the capabilities of an X-ray absorption spectrometer in dispersive geometry on a third generation synchrotron source. For time-resolved studies, the study of the triplet excited state following a laser excitation of Pt 2 (P 2 O 5 H 2 ) 4 4- has been chosen to push the technique to the microsecond time resolution. In the high-pressure part, the suitability of the energy dispersive X-ray absorption spectrometer for high-pressure studies using diamond anvils cell is stressed. Some technical developments carried out on beamline ID24 are discussed. Finally, the most extensive scientific part concerns a combined X-ray absorption and diffraction study of InAs under pressure. (author)
Physical properties of Cu nanoparticles: A molecular dynamics study

International Nuclear Information System (INIS)

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

2014-01-01

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

KAUST Repository

Watanabe, Hiroshi

2013-12-01

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.
High-performance modeling of CO2 sequestration by coupling reservoir simulation and molecular dynamics

KAUST Repository

Bao, Kai

2013-01-01

The present work describes a parallel computational framework for CO2 sequestration simulation by coupling reservoir simulation and molecular dynamics (MD) on massively parallel HPC systems. In this framework, a parallel reservoir simulator, Reservoir Simulation Toolbox (RST), solves the flow and transport equations that describe the subsurface flow behavior, while the molecular dynamics simulations are performed to provide the required physical parameters. Numerous technologies from different fields are employed to make this novel coupled system work efficiently. One of the major applications of the framework is the modeling of large scale CO2 sequestration for long-term storage in the subsurface geological formations, such as depleted reservoirs and deep saline aquifers, which has been proposed as one of the most attractive and practical solutions to reduce the CO2 emission problem to address the global-warming threat. To effectively solve such problems, fine grids and accurate prediction of the properties of fluid mixtures are essential for accuracy. In this work, the CO2 sequestration is presented as our first example to couple the reservoir simulation and molecular dynamics, while the framework can be extended naturally to the full multiphase multicomponent compositional flow simulation to handle more complicated physical process in the future. Accuracy and scalability analysis are performed on an IBM BlueGene/P and on an IBM BlueGene/Q, the latest IBM supercomputer. Results show good accuracy of our MD simulations compared with published data, and good scalability are observed with the massively parallel HPC systems. The performance and capacity of the proposed framework are well demonstrated with several experiments with hundreds of millions to a billion cells. To our best knowledge, the work represents the first attempt to couple the reservoir simulation and molecular simulation for large scale modeling. Due to the complexity of the subsurface systems

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

African Journals Online (AJOL)

The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...
Membrane potential and microsecond to millisecond delayed light emission after a single excitation flash in isolated chloroplasts

International Nuclear Information System (INIS)

Jursinic, P.; Govindjee; Wraight, C.A.

1978-01-01

The effect of light-induced and salt-jump induced membrane potential on microsecond and millisecond delayed light emission from chloroplasts, following a single 10 ns flash, have been studied. Microsecond delayed light emission is shown to be independent of the membrane potential contrary to proposals that the activation energy for delayed light emission can be modulated by transmembrane electric fields. This result is discussed in terms of the possible origin of this short-lived emission. Millisecond delayed light after a single excitation flash is enhanced by membrane potential only if a proton gradient is present. By measuring changes in ms delayed light caused by simultaneous injection of KCl and Na-benzoate (which creates a proton gradient) in the presence of valinomycin, the light-induced potential generated across the thylakoid membrane by a single excitation flash was calibrated and found to be 128 +- 10 mV in agreement with the recent measurements of Zickler and Witt, (FEBS Lett. 66, 142-148 (1976)), based on voltage-dependent ionophores. It is concluded that the secondary charges that give rise to ms delayed light, after a single flash, do not fully span the membrane. (author)
Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

Science.gov (United States)

Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

2018-04-01

Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.
Lipid Configurations from Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek

2018-01-01

of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...
Molecular dynamics studies of actinide nitrides

International Nuclear Information System (INIS)

Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo

2004-01-01

The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)
Constant pressure and temperature discrete-time Langevin molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Grønbech-Jensen, Niels [Department of Mechanical and Aerospace Engineering, University of California, Davis, California 95616 (United States); Department of Mathematics, University of California, Davis, California 95616 (United States); Farago, Oded [Department of Biomedical Engineering, Ben Gurion University of the Negev, Be' er Sheva 84105 (Israel); Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Be' er Sheva 84105 (Israel)

2014-11-21

We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are built on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems—a one-dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three-dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb and Dünweg [J. Chem. Phys. 111, 4453 (1999)], show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.
The dance of molecules: new dynamical perspectives on highly excited molecular vibrations.

Science.gov (United States)

Kellman, Michael E; Tyng, Vivian

2007-04-01

At low energies, molecular vibrational motion is described by the normal modes model. This model breaks down at higher energy, with strong coupling between normal modes and onset of chaotic dynamics. New anharmonic modes are born in bifurcations, or branchings of the normal modes. Knowledge of these new modes is obtained through the window of frequency-domain spectroscopy, using techniques of nonlinear classical dynamics. It may soon be possible to "watch" molecular rearrangement reactions spectroscopically. Connections are being made with reaction rate theories, condensed phase systems, and motions of electrons in quantum dots.
Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

Science.gov (United States)

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

2015-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Car, R.; Parrinello, M.

1988-01-18

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

Science.gov (United States)

Hasan, Mohammad Nasim; Shavik, Sheikh Mohammad; Rabbi, Kazi Fazle; Haque, Mominul

2016-07-01

Molecular dynamics simulation has been carried out to explore the evaporation characteristics of thin liquid argon film in nano-scale confinement. The present study has been conducted to realize the nano-scale physics of simultaneous evaporation and condensation inside a confined space for a three phase system with particular emphasis on the effect of surface wetting conditions. The simulation domain consisted of two parallel platinum plates; one at the top and another at the bottom. The fluid comprised of liquid argon film at the bottom plate and vapor argon in between liquid argon and upper plate of the domain. Considering hydrophilic and hydrophobic nature of top and bottom surfaces, two different cases have been investigated: (i) Case A: Both top and bottom surfaces are hydrophilic, (ii) Case B: both top and bottom surfaces are hydrophobic. For all cases, equilibrium molecular dynamics (EMD) was performed to reach equilibrium state at 90 K. Then the lower wall was set to four different temperatures such as 110 K, 120 K, 130 K and 140 K to perform non-equilibrium molecular dynamics (NEMD). The variation of temperature and density as well as the variation of system pressure with respect to time were closely monitored for each case. The heat fluxes normal to top and bottom walls were estimated and discussed to illuminate the effectiveness of heat transfer in both hydrophilic and hydrophobic confinement at various boundary temperatures of the bottom plate.
Molecular dynamics study of the silica-water-SDA interactions

NARCIS (Netherlands)

Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.

2009-01-01

In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species
Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

Science.gov (United States)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.
On R factors for dynamic structure crystallography

DEFF Research Database (Denmark)

Coppens, Philip; Kaminski, Radoslaw; Schmøkel, Mette Stokkebro

2010-01-01

In studies of dynamic changes in crystals in which induced metastable species may have lifetimes of microseconds or less, refinements are most sensitive if based on the changes induced in the measured intensities. Agreement factors appropriate for such refinements, based on the ratios of the inte...... of the intensities before and after the external perturbation is applied, are discussed and compared with R factors commonly applied in static structure crystallography....
Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

International Nuclear Information System (INIS)

Sanz-Navarro, Carlos F.

2002-01-01

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

Science.gov (United States)

Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

2017-10-01

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

Directory of Open Access Journals (Sweden)

Jinxiang Xi

2018-03-01

Full Text Available Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of
Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses.

Science.gov (United States)

Xi, Jinxiang; Hu, Qin; Zhao, Linlin; Si, Xiuhua April

2018-03-27

Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

International Nuclear Information System (INIS)

Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.

1991-01-01

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
Statistical ensembles and molecular dynamics studies of anisotropic solids. II

International Nuclear Information System (INIS)

Ray, J.R.; Rahman, A.

1985-01-01

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

International Nuclear Information System (INIS)

Li, M.; Chu, W.Y.; Qian, C.F.; Gao, K.W.; Qiao, L.J.

2003-01-01

The molecular dynamics method is used to simulate dislocation intersection in aluminum containing 1.6x10 6 atoms using embedded atom method (EAM) potential. The results show that after intersection between two right-hand screw dislocations of opposite sign there are an extended jog corresponding to a row of 1/3 vacancies in the intersected dislocation, and a trail of vacancies behind the moving dislocation. After intersection between screw dislocations of same sign, there are an extended jog corresponding to a row of 1/3 interstitials in the intersected dislocation, and a trail of interstitials behind the moving dislocation. After intersection between screw and edge dislocations with different Burgers vector, there are a constriction corresponding to one 1/3 vacancy in the edge dislocation, and no point-defects behind the screw dislocation. When a moving screw dislocation intersects an edge dislocation with the same Burgers vector, the point of intersection will split into two constrictions corresponding to one 1/3 vacancy and 1/3 interstitial, respectively. The moving screw dislocation can pass the edge dislocation only after the two constrictions, which can move along the line of intersection of the two slip planes, meet and annihilate

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

Science.gov (United States)

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

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.
Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

Directory of Open Access Journals (Sweden)

Wei Zhang

2017-07-01

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

Science.gov (United States)

Malau, N. D.; Sianturi, M.

2017-03-01

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

International Nuclear Information System (INIS)

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

1993-01-01

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

International Nuclear Information System (INIS)

Doan, N.V.; Tietze, H.

1995-01-01

We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)
Ultrafast dissociation: An unexpected tool for probing molecular dynamics

International Nuclear Information System (INIS)

Morin, Paul; Miron, Catalin

2012-01-01

Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.
Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

Science.gov (United States)

Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

2011-03-01

The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.
Molecular Dynamics Analyses on Microscopic Contact Angle - Effect of Wall Atom Configuration

International Nuclear Information System (INIS)

Takahiro Ito; Yosuke Hirata; Yutaka Kukita

2006-01-01

Boiling or condensing phenomena of liquid on the solid surface is greatly affected by the wetting condition of the liquid to the solid. Although the contact angle is one of the most important parameter to represent the wetting condition, the behavior of the contact angle is not understood well, especially in the dynamic condition. In this study we made molecular dynamics simulations to investigate the microscopic contact angle behavior under several conditions on the numerical density of the wall atoms. In the analyses, when the number density of the wall is lower, the changing rate of the dynamics contact angles for the variation of ΔV was higher than those for the case where the wall density is higher. This is mainly due to the crystallization of the fluid near the wall and subsequent decrease in the slip between the fluid and the wall. The analyses also show that the static contact angle decreases with increase in the number density of the wall. This was mainly induced by the increase in the number density of the wall itself. (authors)
Crystallisation of a Lennard-Jones fluid by large scale molecular dynamics simulation

International Nuclear Information System (INIS)

Snook, I.

1998-01-01

Full text: The evolution of the structure of a large system of atoms interacting via a Lennard-Jones pair potential was simulated by the use of the Molecular Dynamics computer simulation technique. The system was initially equilibrated in the one phase region of the phase diagram at a temperature above critical then a temperature quench was performed which placed the system in a region were the single fluid phase was unstable. Quenches to below the triple point temperature gave rise to crystallisation The mechanism and final morphology is shown to depend strongly on the starting conditions e.g. the starting density
Molecular C dynamics downstream: the biochemical decomposition sequence and its impact on soil organic matter structure and function.

Science.gov (United States)

Grandy, A Stuart; Neff, Jason C

2008-10-15

Advances in spectroscopic and other chemical methods have greatly enhanced our ability to characterize soil organic matter chemistry. As a result, the molecular characteristics of soil C are now known for a range of ecosystems, soil types, and management intensities. Placing this knowledge into a broader ecological and management context is difficult, however, and remains one of the fundamental challenges of soil organic matter research. Here we present a conceptual model of molecular soil C dynamics to stimulate inter-disciplinary research into the ecological implications of molecular C turnover and its management- and process-level controls. Our model describes three properties of soil C dynamics: 1) soil size fractions have unique molecular patterns that reflect varying degrees of biological and physical control over decomposition; 2) there is a common decomposition sequence independent of plant inputs or other ecosystem properties; and 3) molecular decomposition sequences, although consistent, are not uniform and can be altered by processes that accelerate or slow the microbial transformation of specific molecules. The consequences of this model include several key points. First, lignin presents a constraint to decomposition of plant litter and particulate C (>53 microm) but exerts little influence on more stable mineral-associated soil fractions stabilized onto mineral fractions has a distinct composition related more to microbially processed organic matter than to plant-related compounds. Third, disturbances, such as N fertilization and tillage, which alter decomposition rates, can have "downstream effects"; that is, a disturbance that directly alters the molecular dynamics of particulate C may have a series of indirect effects on C stabilization in silt and clay fractions.
Molecular beam studies of reaction dynamics

International Nuclear Information System (INIS)

Lee, Yuan T.

1991-03-01

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

Energy Technology Data Exchange (ETDEWEB)

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

1993-12-01

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

KAUST Repository

Tsuda, Shin-ichi; Komatsu, Taiga; Takagi, Shu; Matsumoto, Yoichiro

2011-01-01

The growth of cavitation bubble nuclei in a metastable state in liquid argon, as one of cryogenic fluids, was investigated using a Molecular Dynamics (MD) simulation with a Nosé-Hoover chain thermostat. We observed rapid growth of bubble nuclei with weak inter-bubble interaction in the early stage, while observed a competing coarsening that looks like Ostwald ripening in the late stage and its growth exponent n became 0.51. We compared the present MD result with that in an adiabatic simulation (Energy-constant MD without any thermostats), and the influence of the field temperature was discussed. Also, we compared the present MD results with a coarsening theory for droplets, and discussed the characteristics of the coarsening mechanism of bubble nuclei. Copyright © 2011 by ASME.
A molecular dynamics calculation of solid phase of malonic acid ...

Indian Academy of Sciences (India)

Sathya S R R Perumal

Keywords. Hydrogen bond chain; elastic constants; molecular dynamics. 1. Introduction ... theory - a probabilistic model to determine the hydro- gen bonds within the .... compares poorly with the experimental value of 108.5. Similarly β and γ ...
On the molecular dynamics in the hurricane interactions with its environment

Science.gov (United States)

Meyer, Gabriel; Vitiello, Giuseppe

2018-06-01

By resorting to the Burgers model for hurricanes, we study the molecular motion involved in the hurricane dynamics. We show that the Lagrangian canonical formalism requires the inclusion of the environment degrees of freedom. This also allows the description of the motion of charged particles. In view of the role played by moist convection, cumulus and cloud water droplets in the hurricane dynamics, we discuss on the basis of symmetry considerations the role played by the molecular electrical dipoles and the formation of topologically non-trivial structures. The mechanism of energy storage and dissipation, the non-stationary time dependent Ginzburg-Landau equation and the vortex equation are studied. Finally, we discuss the fractal self-similarity properties of hurricanes.
MOLECULAR DYNAMICS SIMULATIONS OF DISPLACEMENT CASCADES IN MOLYBDENUM

International Nuclear Information System (INIS)

Smith, Richard Whiting

2003-01-01

Molecular dynamics calculations have been employed to simulate displacement cascades in neutron irradiated Mo. A total of 90 simulations were conducted for PKA energies between 1 and 40 keV and temperatures from 298 to 923K. The results suggest very little effect of temperature on final defect count and configuration, but do display a temperature effect on peak defect generation prior to cascade collapse. Cascade efficiency, relative to the NRT model, is computed to lie between 1/4 and 1/3 in agreement with simulations performed on previous systems. There is a tendency for both interstitials and vacancies to cluster together following cascade collapse producing vacancy rich regions surrounded by interstitials. Although coming to rest in close proximity, the point defects comprising the clusters generally do not lie within the nearest neighbor positions of one another, except for the formation of dumbbell di-interstitials. Cascades produced at higher PKA energies (20 or 40 keV) exhibit the formation of subcascades
Estimating Arrhenius parameters using temperature programmed molecular dynamics

International Nuclear Information System (INIS)

Imandi, Venkataramana; Chatterjee, Abhijit

2016-01-01

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.
Estimating Arrhenius parameters using temperature programmed molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Imandi, Venkataramana; Chatterjee, Abhijit, E-mail: abhijit@che.iitb.ac.in [Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076 (India)

2016-07-21

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.
Structure of HI-6*sarin-acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: reactivator mechanism and design.

Directory of Open Access Journals (Sweden)

Fredrik Ekström

2009-06-01

Full Text Available Organophosphonates such as isopropyl metylphosphonofluoridate (sarin are extremely toxic as they phosphonylate the catalytic serine residue of acetylcholinesterase (AChE, an enzyme essential to humans and other species. Design of effective AChE reactivators as antidotes to various organophosphonates requires information on how the reactivators interact with the phosphonylated AChEs. However, such information has not been available hitherto because of three main challenges. First, reactivators are generally flexible in order to change from the ground state to the transition state for reactivation; this flexibility discourages determination of crystal structures of AChE in complex with effective reactivators that are intrinsically disordered. Second, reactivation occurs upon binding of a reactivator to the phosphonylated AChE. Third, the phosphorous conjugate can develop resistance to reactivation. We have identified crystallographic conditions that led to the determination of a crystal structure of the sarin(nonaged-conjugated mouse AChE in complex with [(E-[1-[(4-carbamoylpyridin-1-ium-1-ylmethoxymethyl]pyridin-2-ylidene]methyl]-oxoazanium dichloride (HI-6 at a resolution of 2.2 A. In this structure, the carboxyamino-pyridinium ring of HI-6 is sandwiched by Tyr124 and Trp286, however, the oxime-pyridinium ring is disordered. By combining crystallography with microsecond molecular dynamics simulation, we determined the oxime-pyridinium ring structure, which shows that the oxime group of HI-6 can form a hydrogen-bond network to the sarin isopropyl ether oxygen, and a water molecule is able to form a hydrogen bond to the catalytic histidine residue and subsequently deprotonates the oxime for reactivation. These results offer insights into the reactivation mechanism of HI-6 and design of better reactivators.
Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

International Nuclear Information System (INIS)

Wang, J.; Gutierre, M.S.

2010-01-01

This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

Theoretical study of molecular vibrations in electron momentum spectroscopy experiments on furan: An analytical versus a molecular dynamical approach

International Nuclear Information System (INIS)

Morini, Filippo; Deleuze, Michael S.; Watanabe, Noboru; Takahashi, Masahiko

2015-01-01

The influence of thermally induced nuclear dynamics (molecular vibrations) in the initial electronic ground state on the valence orbital momentum profiles of furan has been theoretically investigated using two different approaches. The first of these approaches employs the principles of Born-Oppenheimer molecular dynamics, whereas the so-called harmonic analytical quantum mechanical approach resorts to an analytical decomposition of contributions arising from quantized harmonic vibrational eigenstates. In spite of their intrinsic differences, the two approaches enable consistent insights into the electron momentum distributions inferred from new measurements employing electron momentum spectroscopy and an electron impact energy of 1.2 keV. Both approaches point out in particular an appreciable influence of a few specific molecular vibrations of A 1 symmetry on the 9a 1 momentum profile, which can be unravelled from considerations on the symmetry characteristics of orbitals and their energy spacing
Metal cluster fission: jellium model and Molecular dynamics simulations

DEFF Research Database (Denmark)

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

2004-01-01

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

Science.gov (United States)

Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica

2012-10-09

NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.
Clumpy molecular clouds: A dynamic model self-consistently regulated by T Tauri star formation

International Nuclear Information System (INIS)

Norman, C.; Silk, J.

1980-01-01

A new model is proposed which can account for the longevity, energetics, and dynamical structure of dark molecular clouds. It seems clear that the kinetic and gravitational energy in macroscopic cloud motions cannot account for the energetic of many molecular clouds. A stellar energy source must evidently be tapped, and infrared observations indicate that one cannot utilize massive stars in dark clouds. Recent observations of a high space density of T Tauri stars in some dark clouds provide the basis for our assertion that high-velocity winds from these low-mass pre--main-sequence stars provide a continuous dynamic input into molecular clouds. The T Tauri winds sweep up shells of gas, the intersections or collisions of which form dense clumps embedded in a more rarefied interclump medium. Observations constrain the clumps to be ram-pressure confined, but at the relatively low Mach numbers, continuous leakage occurs. This mass input into the interclump medium leads to the existence of two phases; a dense, cold phase (clumps of density approx.10 4 --10 5 cm -3 and temperature approx.10 K) and a warm, more diffuse, interclump medium (ICM, of density approx.10 3 --10 4 cm -3 and temperature approx.30 K). Clump collisions lead to coalescence, and the evolution of the mass spectrum of clumps is studied
Rheology of liquid n-triacontane: Molecular dynamics simulation

International Nuclear Information System (INIS)

Kondratyuk, N D; Norman, G E; Stegailov, V V

2016-01-01

Molecular dynamics is applied to calculate diffusion coefficients of n-triacontane C 30 H 62 using Einstein-Smoluchowski and Green-Kubo relations. The displacement 〈Δr 2 〉( t ) has a subdiffusive part 〈Δr 2 〉 ∼ t α , caused by molecular crowding at low temperatures. Longtime asymptotes of 〈v(0)v(t)〉 are collated with the hydrodynamic tail t -3/2 demonstrated for atomic liquids. The influence of these asymptotes on the compliance of Einstein-Smoluchowski and Green-Kubo methods is analyzed. The effects of the force field parameters on the diffusion process are treated. The results are compared with experimental data. (paper)
A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

Energy Technology Data Exchange (ETDEWEB)

Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

2014-12-09

The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.
Viscosity calculations at molecular dynamics simulations

International Nuclear Information System (INIS)

Kirova, E M; Norman, G E

2015-01-01

Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)
Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.

Science.gov (United States)

Zheng, Mo; Li, Xiaoxia; Guo, Li

2013-04-01

Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. Copyright © 2013 Elsevier Inc. All rights reserved.
Recording the dynamic endocytosis of single gold nanoparticles by AFM-based force tracing.

Science.gov (United States)

Ding, Bohua; Tian, Yongmei; Pan, Yangang; Shan, Yuping; Cai, Mingjun; Xu, Haijiao; Sun, Yingchun; Wang, Hongda

2015-05-07

We utilized force tracing to directly record the endocytosis of single gold nanoparticles (Au NPs) with different sizes, revealing the size-dependent endocytosis dynamics and the crucial role of membrane cholesterol. The force, duration and velocity of Au NP invagination are accurately determined at the single-particle and microsecond level unprecedentedly.
Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated......Many questions about the nature of aggregation and the proteins that are involved in these events are still left unanswered. One of the proteins that is known to form amyloids is Transthyretine (TTR), the secondary transporter of thyroxine and transporter of retinol-binding-protein. Several...
Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations

International Nuclear Information System (INIS)

Kim, Woongkee; Kaviany, Massoud; Shim, J. H.

2014-01-01

It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments
Charge Carrier Dynamics at Silver Nanocluster-Molecular Acceptor Interfaces

KAUST Repository

Almansaf, Abdulkhaleq

2017-07-01

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

International Nuclear Information System (INIS)

Niss, Kristine; Dalle-Ferrier, Cecile; Frick, Bernhard; Russo, Daniela; Dyre, Jeppe; Alba-Simionesco, Christiane

2010-01-01

The mean-square displacement (MSD) was measured by neutron scattering at various temperatures and pressures for a number of molecular glass-forming liquids. The MSD is invariant along the glass-transition line at the pressure studied, thus establishing an 'intrinsic' Lindemann criterion for any given liquid. A one-to-one connection between the MSD's temperature dependence and the liquid's fragility is found when the MSD is evaluated on a time scale of ∼4 ns, but does not hold when the MSD is evaluated at shorter times. The findings are discussed in terms of the elastic model and the role of relaxations, and the correlations between slow and fast dynamics are addressed.
Petascale molecular dynamics simulation using the fast multipole method on K computer

KAUST Repository

Ohno, Yousuke; Yokota, Rio; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda; Narumi, Tetsu; Taiji, Makoto

2014-01-01

In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
Petascale molecular dynamics simulation using the fast multipole method on K computer

KAUST Repository

Ohno, Yousuke

2014-10-01

In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

Science.gov (United States)

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.
Molecular dynamics of interfacial water and cations associated with clay minerals

International Nuclear Information System (INIS)

Cygan, Randall T.; Greathouse, Jeffery A.; Teich-McGoldrick, Stephanie L.; Nenoff, Tina M.; Daemen, Luke L.

2012-01-01

Document available in extended abstract form only. Clay mineral interfaces, including interlayer and external surfaces, play an essential role in many geochemical processes. Adsorption, dissolution, precipitation, nucleation, and growth mechanisms, in particular, are controlled by the interplay of structure, thermodynamics, kinetics, and transport at clay mineral-water interfaces. Molecular details of these geochemical processes are especially important in evaluating the fate of radionuclide waste in the environment. Such details are typically beyond the sensitivity of experimental and analytical methods and therefore require accurate models and simulations. Also, the basal surfaces and interlayers of clay minerals offer structurally constrained interfacial environments to better evaluate the local molecular chemistry. We have developed and used classical and quantum methods to examine the complex behavior of clay mineral-water interfaces and dynamics of interlayer species. Bulk structures, swelling behavior, diffusion, and adsorption processes are evaluated and compared to experimental and spectroscopic findings. In particular, inelastic neutron scattering methods provide a successful probe of vibrational behavior of interlayer species to help guide the simulations. Librations involving rock, wag, and twist motions of water molecules are particularly sensitive to the interlayer environment of smectite minerals such as montmorillonite and beidellite. Trends in librational modes for interlayer water as a function of clay structure and cation hydration energy are readily explained using structural and vibrational analysis derived from molecular simulation. Molecular dynamics simulations of virtual phases, including hydrated pyrophyllite, help to explain the behavior of interlayer water that is not associated with cation species. Additionally, we use large-scale molecular dynamics simulations of other layered minerals, such as muscovite, to evaluate adsorption
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

Energy Technology Data Exchange (ETDEWEB)

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

2007-02-14

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

Indian Academy of Sciences (India)

2017-08-31

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

Energy Technology Data Exchange (ETDEWEB)

Yamaguchi, H.; Siebers, G.; Furukawa, A.; Otagiri, N.; Osman, R

2002-07-01

Molecular dynamics simulations were performed for a dodecamer DNA containing a single strand break (SSB), which has been represented by a 3'-OH deoxyribose and 5'-OH phosphate in the middle of the strand. Molecular force field parameters of the 5'-OH phosphate region were determined from an ab initio calculation at the HF/6-31G level using the program package GAMESS. The DNA was placed in a periodic boundary box with water molecules and Na+ counter-ions to produce a neutralised system. After minimisation, the system was heated to 300 K, equilibrated and a production run at constant NTP was executed for 1 ns using AMBER 4.1. Snapshots of the SSB-containing DNA and a detailed analysis of the equilibriated average structure revealed surprisingly small conformational changes compared to normal DNA. However, dynamic properties calculated using the essential dynamics method showed some features that may be important for the recognition of this damage by repair enzymes. (author)

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