Molecular dynamics simulations of classical stopping power.
Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S
2013-11-22
Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results.
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...
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives...
Classical molecular dynamics simulation of electronically non-adiabatic processes.
Miller, William H; Cotton, Stephen J
2016-12-22
Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).
High temperature phonon dispersion in graphene using classical molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Anees, P., E-mail: anees@igcar.gov.in; Panigrahi, B. K. [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam-603102 (India); Valsakumar, M. C., E-mail: anees@igcar.gov.in [School of Engineering Sciences and Technology, University of Hyderabad, Hyderabad-500046 (India)
2014-04-24
Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 K the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.
The classical and quantum dynamics of molecular spins on graphene
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2015-01-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019
Energy conservation in molecular dynamics simulations of classical systems.
Toxvaerd, Søren; Heilmann, Ole J; Dyre, Jeppe C
2012-06-14
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 of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.
Adding quantum effects to the semi-classical molecular dynamics simulations
Yang, Siyang
2011-01-01
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using trajectories have achieved great successes in the computer simulations of various systems, but it is difficult to incorporate quantum effects in a robust way. Therefore, improving quantum wavepacket dynamics and incorporating nonadiabatic transitions and quantum effects into classical and semi-classical molecular dynamics is critical as well as challenging. In this paper, we present a MD scheme in which a new set of equations of motion (EOM) are proposed to effectively propagate nuclear trajectories while conserving quantum mechanical energy which is critical for describing quantum effects like tunneling. The new quantum EOM is tested on a one-state one-dimensional and a two-state two-dimensional model nonadiabatic systems. The global quantum force experienced by each trajecto...
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.
Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer
Directory of Open Access Journals (Sweden)
Casuyac Miqueas
2016-01-01
Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.
Classical and quantum dynamics of a model for atomic-molecular Bose--Einstein condensates
Santos Filho, Gilberto Nascimento; Tonel, Arlei Prestes; Foerster, Angela; Links, Jon(Centre for Mathematical Physics, School of Mathematics and Physics, The University of Queensland, 4072, Australia)
2005-01-01
We study a model for a two-mode atomic-molecular Bose--Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the coupling parameter space into four regions. The different regions give rise to qualitatively different dynamics. We then show that this classification holds true for the quantum dynamics.
Greenwood, Donald T
1997-01-01
Graduate-level text for science and technology students provides strong background in the more abstract and intellectually satisfying areas of dynamical theory. Topics include d'Alembert's principle and the idea of virtual work, Hamilton's equations, Hamilton-Jacobi theory, canonical transformations, more. Problems and references at chapter ends.
Vladimirov, P. V.; Borodin, V. A.
2017-02-01
Beryllium selected as a neutron multiplier material for the tritium breeding blanket of fusion reactor should withstand high doses of fast neutron irradiation. The damage produced by irradiation is usually evaluated assuming that the number of atomic displacements to the threshold displacement energy, Ed, which is considered as an intrinsic material parameter. In this work the value of Ed for hcp beryllium is estimated simultaneously from classical and first-principles molecular dynamics simulations. Quite similar quantitative pictures of defect production are observed in both simulation types, though the predicted displacement threshold values seem to be approximately two times higher in the first-principles approach. We expect that, after more detailed first-principles investigations, this approach can be used for scaling the damage prediction predictions by classical molecular dynamics, opening a way for more consistent calculations of displacement damage in materials.
Protocol for classical molecular dynamics simulations of nano-junctions in solution
Gkionis, Konstantinos
2012-10-19
Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite goldelectrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite goldsurfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the goldelectrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.
A new extension of classical molecular dynamics: An electron transfer algorithm.
Raskovalov, Anton
2017-05-05
The molecular dynamics is one of the most widely used methods for the simulation of the properties corresponding to ionic motion. Unfortunately, classical molecular dynamics cannot be applied for electron transfer simulation. Suggested modification of the molecular dynamics allows performing the electron transfer from one particle to another during simulation runtime. All additional data structure and the corresponding algorithms are presented in this article. The method can be applied to the systems with pair Van der Waals and Coulomb interactions. Moreover, it may be extended for many-bodied interatomic interactions. In addition, an algorithm of transference numbers calculation has been designed. This extension is not an independent method but it can be useful for simulating the systems with high concentration of electron donors and acceptors. © 2017 Wiley Periodicals, Inc.
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.
Craig, Ian R; Manolopoulos, David E
2004-08-22
We propose an approximate method for calculating Kubo-transformed real-time correlation functions involving position-dependent operators, based on path integral (Parrinello-Rahman) molecular dynamics. The method gives the exact quantum mechanical correlation function at time zero, exactly satisfies the quantum mechanical detailed balance condition, and for correlation functions of the form C(Ax)(t) and C(xB)(t) it gives the exact result for a harmonic potential. It also works reasonably well at short times for more general potentials and correlation functions, as we illustrate with some example calculations. The method provides a consistent improvement over purely classical molecular dynamics that is most apparent in the low-temperature regime.
Momentum-dependent potentials: Towards the molecular dynamics of fermionlike classical particles
Energy Technology Data Exchange (ETDEWEB)
Cordero, P. (Departamento de Fisica, Facultad de Ciencias Fisicas y Matematicas, Universidad de Chile, Casilla 487, Santiago 3 (Chile)); Hernandez, E.S. (Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina))
1995-03-01
We investigate classical Hamiltonian models for particles interacting with steep differential repulsive barriers both in coordinate and momentum space. The final aim is to define a classical system of many particles behaving as fermions in many respects. In this paper we examine the appearance of the phase portrait of one- or two-particle systems to skim the essential features that would later be transcribed to the basic rules of a molecular dynamics algorithm. One of the remarkable properties of the phase portrait is the flow from states that start far away with a wide range of momentum towards a narrow region in momentum---a virtual locking of momentum---in the vicinity of the steepest part of the barrier in momentum space. The central ideas are developed through two examples in one and two dimensions.
Equilibrium properties of the reaction H2 ⇌ 2H by classical molecular dynamics simulations.
Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe
2014-01-21
We have developed a classical molecular dynamics model for the hydrogen dissociation reaction, containing two- and three-particle potentials derived by Kohen, Tully and Stillinger. Two fluid densities were investigated for a wide range of temperatures, and 11 fluid densities were considered for one temperature. We report the temperature range where the degree of reaction is significant, and also where a stable molecule dominates the population in the energy landscape. The three-particle potential, which is essential for the reaction model and seldom studied, together with the two-particle interaction lead to a large effective excluded volume diameter of the molecules in the molecular fluid. The three-particle interaction was also found to give a large positive contribution to the pressure of the reacting mixture at high density and/or low temperatures. From knowledge of the dissociation constant of the reaction and the fluid pressure, we estimated the standard enthalpy of the dissociation reaction to be 430 kJ mol(-1) (ρ = 0.0695 g cm(-3)) and 380 kJ mol(-1) (ρ = 0.0191 g cm(-3)). These values are in good agreement with the experimental vaule of 436 kJ mol(-1) under ambient pressure. The model is consistent with a Lennard-Jones model of the molecular fluid, and may facilitate studies of the impact of chemical reactions on transport systems.
Dupuy, John L.; Lewis, Steven P.; Stancil, P. C.
2016-11-01
Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H2) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5-400 K] across seven different temperatures of dust grains [10-70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99-0.22.
Determination of thermal properties pure ThO2 using classical molecular dynamics simulations
Ghosh, Partha S.; Kaur, Karamvir; Ali, K.; Arya, A.; Dey, G. K.
2016-05-01
This paper calculates lattice thermal expansion (LTE), thermal conductivity (TC) and melting temperature (MT) of ThO2 using classical molecular dynamic simulations. In this study we consider two set of interatomic potential consisting of Coulomb-Buckingham (Buck) and Coulomb-Buckingham-Morse-Many body (BMM) potential form. The MD calculated LTE of 10.29 × 10-6 and 10.61 × 10-6 K-1 using BMM and Buck potential, respectively, is slightly higher than the experimentally determined values (9.54 - 9.86 × 10-6 K-1). The MD calculated TC values in the high temperature range (600 to 1200 K) accords very well with the experimental measurements and at the low temperature range (300-500 K) our results are slightly different from experimental results as our presumption that the dominant mechanism for phonon scattering is the Umklapp process. The MD calculated MT of ThO2 using Buck and BMM potential model is 3662.5±12.5 K and 3812.5±12.5 K, respectively, and these values are in reasonable agreement with previous experimental values.
Wang, B T; Shao, J L; Zhang, G C; Li, W D; Zhang, P
2010-11-03
By classical molecular dynamics simulations employing an embedded atom method potential, we have simulated the bcc to hcp/fcc structural transition in single-crystal iron under uniform compression. Results showed that the transition pressure is different from uniaxial compression and shock loading. The transformation occurs on a picosecond timescale and the transition time decreases along with the increase of pressure. The nucleation and growth of the hcp and fcc phases under constant pressure and temperature are analyzed in detail. The nucleation planes, all belonging to the {110}(bcc) family and parallel to the three compression directions [100], [010], and [001], have been observed. About 20% bcc atoms have transformed to fcc phase under pressure just over the critical point, and under higher pressure the fraction of the fcc phase increases steadily to exceed that of the hcp phase. We have investigated the transition mechanism of iron from initial bcc to hcp/fcc and found that the transition mainly consists of compression, rotation, and shuffle.
Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics.
Skelton, A A; Wesolowski, D J; Cummings, P T
2011-07-19
Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.
Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice.
Waheed, Qaiser; Edholm, Olle
2011-09-13
Classical simulations of simple water models reproduce many properties of the liquid and ice but overestimate the heat capacity by about 65% at ordinary temperatures and much more for low temperature ice. This is due to the fact that the atomic vibrations are quantum mechanical. The application of harmonic quantum corrections to the molecular motion results in good heat capacities for the liquid and for ice at low temperatures but a successively growing positive deviation from experimental results for ice above 200 K that reaches 15% just below melting. We suggest that this deviation is due to the lack of quantum corrections to the anharmonic motions. For the liquid, the anharmonicities are even larger but also softer and thus in less need of quantum correction. Therefore, harmonic quantum corrections to the classically calculated liquid heat capacities result in agreement with the experimental values. The classical model underestimates the heat of melting by 15%, while the application of quantum corrections produces fair agreement. On the other hand, the heat of vaporization is overestimated by 10% in the harmonically corrected classical model.
Bryan, W A; King, R B; Nemeth, G R A J; Greenwood, J B; Williams, I D; Newell, W R
2010-01-01
A quasi-classical model (QCM) of molecular dynamics in intense femtosecond laser fields has been developed, and applied to a study of the effect of an ultrashort `control' pulse on the vibrational motion of a deuterium molecular ion in its ground electronic state. A nonadiabatic treatment accounts for the initial ionization-induced vibrational population caused by an ultrashort `pump' pulse. In the QCM, the nuclei move classically on the molecular potential as it is distorted by the laser-induced Stark shift and transition dipole. The nuclei then adjust to the modified potential, non-destructively shifting the vibrational population and relative phase. This shift has been studied as a function of control pulse parameters. Excellent agreement is observed with predictions of time-dependent quantum simulations, lending confidence to the validity of the model and permitting new observations to be made. The applicability of the QCM to more complex multi-potential energy surface molecules (where a quantum treatment...
Indian Academy of Sciences (India)
Y Pathania; P K Ahluwalla
2005-09-01
We have carried out a molecular dynamics simulation of two- and three- dimensional double Yukawa fluids near the triple point. We have compared some of the static and dynamic correlation functions with those of Lennard{Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good agreement. However, when repulsive and attractive parameters occurring in double Yukawa potential are varied, we found distinct differences in static and dynamic correlation functions. We have also compared the two-dimensional correlation functions with those of three-dimensional to study the effect of dimensionality, near the triple point region.
Whitfield, T. W.; Crain, J.; Martyna, G. J.
2006-03-01
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
Marsalek, Ondrej; Markland, Thomas E
2016-02-07
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
Institute of Scientific and Technical Information of China (English)
LI Chao-Hong; DUAN Yi-Wu; Wing-Ki Liu; Jian-Min Yuan
2001-01-01
Within Born-Oppenheimer approximation, by using the classical trajectory theory, a description for the high order harmonic generation of the hydrogen molecular ion interacting with ultrashort laser pulses has been pre sented. The Coulomb singularities have been remedied by the regularization. The action-angle variables have been used to generate the initial inversion symmetry microcanonical distribution. Within a proper intensity range, a harmonic plateau with only odd harmonics appears. For a larger intensity, because of the existence of chaos, the harmonic spectra become noisier. For a large enough intensity, the ionization takes place and the harmonics disappear. So the chaos causes the noises, the ionization suppresses the harmonic generation, and the onset of the ionization follows the onset of chaos.
Energy Technology Data Exchange (ETDEWEB)
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: paul.tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)
2015-03-14
Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10{sup 3}-10{sup 5} molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.
A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants
Directory of Open Access Journals (Sweden)
James P. Ewen
2016-08-01
Full Text Available For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i accurately predict important properties of long-chain, linear molecules; and (ii reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP, allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-tom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are
Chagarov, Evgueni Anatolievich
Chemical-mechanical polishing (CMP) is a widely accepted process in the semiconductor industry. Despite intense theoretical and experimental research on CMP, there is a serious lack of fundamental understanding of the physical-chemical processes of polishing. The present work is intended to investigate these fundamental processes on an atomistic level. To model CMP on the atomic scale, a model of the amorphous silica is prepared by applying Design of Experiments (DOE) techniques to systematically investigate molecular dynamics preparation. These simulations yield high-quality models of amorphous silica, which are in excellent agreement with experimental results and are defect-free. Molecular dynamics simulations are performed to investigate the mechanical deformation during CMP of silica for different geometries and relative velocities. The simulations clarify asperity shape evolution during the process of shear and reveal temperature distributions as a function of time. It is found that the ratio of radii of a particle and asperity strongly affects the amount of the material removed whereas the relative velocity has a weaker affect on it. During shear, a significant local temperature increase occurs. This temperature increase lasts for a short time (picoseconds), but it can have a major impact on the amount of material removed. It is found that there could be significant deposition of the material from the particle to the slab, which can fill surface trenches and thereby make the surface smoother. An analytic model is developed for describing the amount of material removed as a function of asperity and particle radii and relative velocity. Density-functional calculations of different surfaces of two silica polymorphs, alpha-quartz and beta-cristobalite, are performed. The surface energies are calculated as a function of oxygen partial pressure for several different surface reconstructions and terminations. The case of hydrogen passivation is investigated to
Classical and molecular genetic mapping
A brief history of classical genetic mapping in soybean [Glycine max (L.) Merr.] is described. Detailed descriptions are given of the development of molecular genetic linkage maps based upon various types of DNA markers Like many plant and animal species, the first molecular map of soybean was bas...
Bayse, Craig A; Merz, Kenneth M
2014-08-05
Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.
Dynamical Symmetries in Classical Mechanics
Boozer, A. D.
2012-01-01
We show how symmetries of a classical dynamical system can be described in terms of operators that act on the state space for the system. We illustrate our results by considering a number of possible symmetries that a classical dynamical system might have, and for each symmetry we give examples of dynamical systems that do and do not possess that…
Reif, Maria M; Oostenbrink, Chris
2014-01-30
The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.
Dupuy, John L; Stancil, P C
2016-01-01
Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g. a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H$_2$) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics (MD) simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking ...
Classical dynamics a modern perspective
Sudarshan, Ennackal Chandy George
2016-01-01
Classical dynamics is traditionally treated as an early stage in the development of physics, a stage that has long been superseded by more ambitious theories. Here, in this book, classical dynamics is treated as a subject on its own as well as a research frontier. Incorporating insights gained over the past several decades, the essential principles of classical dynamics are presented, while demonstrating that a number of key results originally considered only in the context of quantum theory and particle physics, have their foundations in classical dynamics.Graduate students in physics and practicing physicists will welcome the present approach to classical dynamics that encompasses systems of particles, free and interacting fields, and coupled systems. Lie groups and Lie algebras are incorporated at a basic level and are used in describing space-time symmetry groups. There is an extensive discussion on constrained systems, Dirac brackets and their geometrical interpretation. The Lie-algebraic description of ...
Panek, Jarosław J; Mazzarello, Riccardo; Novič, Marjana; Jezierska-Mazzarello, Aneta
2011-02-01
Mercury(II) has a strong affinity for the thiol groups in proteins often resulting in the disruption of their biological functions. In this study we present classical and first-principles, DFT-based molecular dynamics (MD) simulations of a complex of Hg(II) and proteinase K, a well-known serine protease with a very broad and diverse enzymatic activity. It contains a catalytic triad formed by Asp39, His69, and Ser224, which is responsible for its biological activity. It was found previously by X-ray diffraction experiments that the presence of Hg(II) inhibits the enzymatic action of proteinase K by affecting the stereochemistry of the triad. Our simulations predict that (i) the overall structure as well as the protein backbone dynamics are only slightly affected by the mercury cation, (ii) depending on the occupied mercury site, the hydrogen bonds of the catalytic triad are either severely disrupted (both bonds for mercury at site 1, and the His69-Ser224 contact for mercury at site 2) or slightly strengthened (the Asp39-His69 bond when mercury is at site 2), (iii) the network of hydrogen bonds of the catalytic triad is not static but undergoes constant fluctuations, which are significantly modified by the presence of the Hg(II) cation, influencing in turn the triad's ability to carry out the enzymatic function--these facts explain the experimental findings on the inhibition of proteinase K by Hg(II).
Pérez-Conesa, Sergio; Torrico, Francisco; Martínez, José M.; Pappalardo, Rafael R.; Sánchez Marcos, Enrique
2016-12-01
A new ab initio interaction potential based on the hydrated ion concept has been developed to obtain the structure, energetics, and dynamics of the hydration of uranyl in aqueous solution. It is the first force field that explicitly parameterizes the interaction of the uranyl hydrate with bulk water molecules to accurately define the second-shell behavior. The [UO2(H2O)5 ] 2 + presents a first hydration shell U-O average distance of 2.46 Å and a second hydration shell peak at 4.61 Å corresponding to 22 molecules using a coordination number definition based on a multisite solute cavity. The second shell solvent molecules have longer mean residence times than those corresponding to the divalent monatomic cations. The axial regions are relatively de-populated, lacking direct hydrogen bonding to apical oxygens. Angle-solved radial distribution functions as well as the spatial distribution functions show a strong anisotropy in the ion hydration. The [UO2(H2O)5 ] 2 + solvent structure may be regarded as a combination of a conventional second hydration shell in the equatorial and bridge regions, and a clathrate-like low density region in the axial region. Translational diffusion coefficient, hydration enthalpy, power spectra of the main vibrational modes, and the EXAFS spectrum simulated from molecular dynamics trajectories agree fairly well with the experiment.
Directory of Open Access Journals (Sweden)
Collings Matthew D
2002-11-01
Full Text Available Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H2O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust. In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m NaCl–water mixtures under ambient (25°C, 1 bar, hydrothermal (325°C, 1 kbar and deep crustal (625°C, 15 kbar conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757. With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (NanClmn-m clusters in addition to simple NaCl ion pairs. Large polyatomic (NanClmn-m clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions.
Ensemble simulations with discrete classical dynamics
DEFF Research Database (Denmark)
Toxværd, Søren
2013-01-01
For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exist a shadow Hamiltonian $\\tilde{H}$ with energy $\\tilde{E}(h)$, for which the discrete particle positions lie on the analytic trajectories for $\\tilde{H}$. $\\tilde...
Bergstra, J.A.; Bethke, I.
2002-01-01
Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model
Energy Technology Data Exchange (ETDEWEB)
Pham, V.T. [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Tavernelli, I. [Ecole Polytechnique Federale de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Milne, C.J.; van der Veen, R.M. [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); D' Angelo, P. [Dipartimento di Chimica, Universita di Roma ' La Sapienza' , Ple A. Moro 5, 00185 Roma (Italy); Bressler, Ch. [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Chergui, M., E-mail: Majed.Chergui@epfl.ch [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland)
2010-05-25
Graphical abstract: The L{sub 3}-edge EXAFS spectra of aqueous iodide are compared to classical, QM/MM and DFT-based molecular dynamics simulations. The QM/MM simulations reproduce best the experimental data. An anisotropy of the solvation shell is also identified. - Abstract: The L{sub 3} X-ray absorption spectrum of aqueous iodide is reported, and its EXAFS is compared to theoretical spectra reconstructed from the radial distribution function of the iodide hydration obtained from classical, hybrid Quantum Mechanics Molecular Mechanics, (QM/MM) and full quantum (density functional theory, DFT) molecular dynamics simulations. Since EXAFS is mainly sensitive to short distances around the iodide ion, it is a direct probe of the local solvation structure. The comparison shows that QM/MM simulations deliver a satisfactory description of the EXAFS signal, while nonpolarizable classical simulations are somewhat less satisfactory and DFT-based simulations perform poorly. We also identify a weak anisotropy of the water solvation shell around iodide, which may be of importance in electron photoejection experiments.
Agarwal, Animesh
2015-01-01
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however computationally this technique is very demanding. The abovementioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One possible solution to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this ...
Viridi, Sparisoma; Waris, Abdul; Perkasa, Yudha Satya
2011-01-01
Molecular dynamics in 2-D accompanied by granular model provides an opportunity to investigate binding between nuclei particles and its properties that arises during collision in a fusion reaction. A fully classical approach is used to observe the influence of initial angle of nucleus orientation to the product yielded by the reaction. As an example, a simplest fusion reaction between 1H2 and 1H3 is observed. Several products of the fusion reaction have been obtained, even the unreported ones, including temporary 2He4 nucleus.
Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations
Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei
2017-02-01
Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.
Energy Technology Data Exchange (ETDEWEB)
Ganster, P
2004-10-15
A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
Rajput, Nav Nidhi; Qu, Xiaohui; Sa, Niya; Burrell, Anthony K; Persson, Kristin A
2015-03-11
In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg(2+) → Mg(+)), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI(-) exhibits a significant bond weakening while paired with the transient, partially reduced Mg(+). In contrast, BH4(-) and BF4(-) are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.
Cwiklik, Lukasz; Aquino, Adelia J A; Vazdar, Mario; Jurkiewicz, Piotr; Pittner, Jiří; Hof, Martin; Lischka, Hans
2011-10-20
Absorption and fluorescence spectra of PRODAN (6-propionyl-2-dimethylaminonaphthalene) were studied by means of the time-dependent density functional theory and the algebraic diagrammatic construction method. The influence of environment, a phosphatidylcholine lipid bilayer and water, was taken into account employing a combination of quantum chemical calculations with empirical force-field molecular dynamics simulations. Additionally, experimental absorption and emission spectra of PRODAN were measured in cyclohexane, water, and lipid vesicles. Both planar and twisted configurations of the first excited state of PRODAN were taken into account. The twisted structure is stabilized in both water and a lipid bilayer, and should be considered as an emitting state in polar environments. Orientation of the excited dye in the lipid bilayer significantly depends on configuration. In the bilayer, the fluorescence spectrum can be regarded as a combination of emission from both planar and twisted structures.
Wohlert, Jakob
2014-05-22
In this paper, we report the calculation of the enthalpy of sublimation, Δ(sub)H, as a function of temperature of crystalline β-cellobiose from molecular dynamics (MD) simulations, using two popular carbohydrate force fields. Together with the entropy difference between the solid and the vapor, ΔS, evaluated at atmospheric pressure, Δ(sub)H gives the vapor pressure of cellobiose over the solid phase as a function of T. It is found that when quantum mechanical corrections to the enthalpy calculated from the distribution of normal modes is applied both force fields give Δ(sub)H close to experiments. The entropy change, ΔS, which is calculated within a harmonic approximation becomes too small, leading to vapor pressures that are too low. These findings are relevant to MD simulations of crystalline carbohydrates in general, e.g., native cellulose.
Govers, K.; Verwerft, M.
2013-07-01
The High Burnup Structure (HBS) observed at pellet periphery in conventional Light Water Reactor nuclear fuels and around spots presenting high plutonium content in mixed (U, Pu) oxide fuel - MOX fuel - consists of a restructuration of the original grains into smaller ones. The process is often postulated to occur because of the accumulation of irradiation damage and the retention of fission products in the matrix. The computing power nowadays available enables for simulating larger systems at the atomic scale up to the point that nano-polycrystalline material can now be investigated by empirical potential molecular dynamics. Simulations of nano-polycrystalline UO2 structures have been carried out at various temperatures to investigate atom mobility close to grain boundaries. The variation of Arrhénius parameters for the diffusion coefficient of oxygen, uranium and xenon as a function of the distance from a grain boundary was studied, leading to the distinction of three zones: the grain boundary layers (up to 1 nm depth) presenting enhanced diffusion, an intermediate zone (1 to roughly 2 nm depth) with intermediate diffusion values and the bulk of the grains. The following Arrhénius relations for grain boundary diffusion were derived:
Sardar, Subhankar; Paul, Amit Kumar; Mondal, Padmabati; Sarkar, Biplab; Adhikari, Satrajit
2008-11-14
We are investigating the molecular dynamics of the butatriene cation after excitation from the ground state (X(2)B(2g)) to the first excited electronic state (A(2)B(2u)) by using the time-dependent discrete variable representation (TDDVR) method. The investigation is being carried out with a realistic 18-mode model Hamiltonian consisting of all the vibrational degrees of freedom of the butatriene molecule. First, we perform the simulation on a basic five mode model, and then by including additional thirteen modes as bath on the basic model. This sequential inclusion of bath modes demonstrates the effect of so called weak modes on the subsystem, where the calculations of energy and population transfer from the basic model to the bath quantify the same effect. The spectral profile obtained by using the TDDVR approach shows reasonably good agreement with the results calculated by the quantum mechanical approach/experimental measurement. It appears that the TDDVR approach for those large systems where quantum mechanical description is needed in a restricted region, is a good compromise between accuracy and speed.
Directory of Open Access Journals (Sweden)
Xiaolei Wang
2013-12-01
Full Text Available We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand–Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein–Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm.
Energy Technology Data Exchange (ETDEWEB)
Tran, H., E-mail: ha.tran@lisa.u-pec.fr [Laboratoire Interuniversitaire des Systèmes Atmosphériques, UMR CNRS 7583, Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France); Domenech, J.-L. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, (IEM-CSIC), Serrano 123, 28006 Madrid (Spain)
2014-08-14
Spectral shapes of isolated lines of HCl perturbed by Ar are investigated for the first time using classical molecular dynamics simulations (CMDS). Using reliable intermolecular potentials taken from the literature, these CMDS provide the time evolution of the auto-correlation function of the dipole moment, whose Fourier-Laplace transform leads to the absorption spectrum. In order to test these calculations, room temperature spectra of various lines in the fundamental band of HCl diluted in Ar are measured, in a large pressure range, with a difference-frequency laser spectrometer. Comparisons between measured and calculated spectra show that the CMDS are able to predict the large Dicke narrowing effect on the shape of HCl lines and to satisfactorily reproduce the shapes of HCl spectra at different pressures and for various rotational quantum numbers.
Durdagi, Serdar; Reis, Heribert; Papadopoulos, Manthos G; Mavromoustakos, Thomas
2008-08-01
The C-1'-dithiolane Delta(8)-tetrahydrocannabinol (Delta(8)-THC) amphiphilic analogue (-)-2-(6a,7,10,10a-tetrahydro-6,6,9-trimethylhydroxy-6H-dibenzo[b,d]pyranyl)-2-hexyl-1,3-dithiolane (AMG3) is considered as one of the most potent synthetic analgesic cannabinoid (CB) ligands. Its structure is characterized by rigid tricyclic and flexible alkyl chain segments. Its conformational properties have not been fully explored. Structure-activity relationship (SAR) studies on classical CBs showed that the alkyl side chain is the most critical structural part for the receptor activation. However, reported low energy conformers of classical CB analogues vary mainly in the conformation of their alkyl side chain segment. Therefore, comparative molecular dynamics (MD) simulations of low energy conformers of AMG3 were performed in order to investigate its structural and dynamical properties in two different systems. System-I includes ligand and amphoteric solvent DMSO, simulating the biological environment and system-II includes ligand at active site of the homology models of CB1 and CB2 receptors in the solvent. The trajectory analysis results are compared for the systems I and II. In system-I, the dihedral angle defined between aromatic ring and dithiolane ring of AMG3 shows more resistance to be transformed into another torsional angle and the dihedral angle adjacent to dithiolane ring belonging in the alkyl chain has flexibility to adopt gauche+/- and trans dihedral angles. The rest of the dihedral angles within the alkyl chain are all trans. These results point out that wrapped conformations are dynamically less favored in solution than linear conformations. Two possible plane angles defined between the rigid and flexible segments are found to be the most favored and adopting values of approximately 90 degrees and approximately 140 degrees. In system-II, these values are approximately 90 degrees and approximately 120 degrees. Conformers of AMG3 at the CB1 receptor favor to
Shkrob, I A; Larsen, R E; Schwartz, B J; Glover, William J.; Larsen, Ross E.; Schwartz, Benjamin J.; Shkrob, Ilya A.
2006-01-01
Adiabatic mixed quantum/classical molecular dynamics simulations were used to generate snapshots of the hydrated electron (e-) in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the e- were extracted from these simulations and embedded in a matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory and single-excitation configuration interaction methods were then applied to these embedded clusters. The salient feature of these hybrid calculations is significant transfer (ca. 0.18) of the excess electron's charge density into the O 2p orbitals in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfc) tensors, and the IR and Raman spectra of the e-. The calculated hfc tensors were used to compute the EPR and ESEEM spectra for the ...
Ngo, N. H.; Tran, H.; Gamache, R. R.; Bermejo, D.; Domenech, J.-L.
2012-08-01
The modeling of the shape of H2O lines perturbed by N2 (and air) using the Keilson-Storer (KS) kernel for collision-induced velocity changes is revisited with classical molecular dynamics simulations (CMDS). The latter have been performed for a large number of molecules starting from intermolecular-potential surfaces. Contrary to the assumption made in a previous study [H. Tran, D. Bermejo, J.-L. Domenech, P. Joubert, R. R. Gamache, and J.-M. Hartmann, J. Quant. Spectrosc. Radiat. Transf. 108, 126 (2007)], 10.1016/j.jqsrt.2007.03.009, the results of these CMDS show that the velocity-orientation and -modulus changes statistically occur at the same time scale. This validates the use of a single memory parameter in the Keilson-Storer kernel to describe both the velocity-orientation and -modulus changes. The CMDS results also show that velocity- and rotational state-changing collisions are statistically partially correlated. A partially correlated speed-dependent Keilson-Storer model has thus been used to describe the line-shape. For this, the velocity changes KS kernel parameters have been directly determined from CMDS, while the speed-dependent broadening and shifting coefficients have been calculated with a semi-classical approach. Comparisons between calculated spectra and measurements of several lines of H2O broadened by N2 (and air) in the ν3 and 2ν1 + ν2 + ν3 bands for a wide range of pressure show very satisfactory agreement. The evolution of non-Voigt effects from Doppler to collisional regimes is also presented and discussed.
Chaos in effective classical and quantum dynamics
Casetti, L; Modugno, M; Casetti, Lapo; Gatto, Raoul; Modugno, Michele
1998-01-01
We investigate the dynamics of classical and quantum N-component phi^4 oscillators in presence of an external field. In the large N limit the effective dynamics is described by two-degree-of-freedom classical Hamiltonian systems. In the classical model we observe chaotic orbits for any value of the external field, while in the quantum case chaos is strongly suppressed. A simple explanation of this behaviour is found in the change in the structure of the orbits induced by quantum corrections. Consistently with Heisenberg's principle, quantum fluctuations are forced away from zero, removing in the effective quantum dynamics a hyperbolic fixed point that is a major source of chaos in the classical model.
Classical and quantum dynamics from classical paths to path integrals
Dittrich, Walter
2016-01-01
Graduate students who want to become familiar with advanced computational strategies in classical and quantum dynamics will find here both the fundamentals of a standard course and a detailed treatment of the time-dependent oscillator, Chern-Simons mechanics, the Maslov anomaly and the Berry phase, to name a few. Well-chosen and detailed examples illustrate the perturbation theory, canonical transformations, the action principle and demonstrate the usage of path integrals. This new edition has been revised and enlarged with chapters on quantum electrodynamics, high energy physics, Green’s functions and strong interaction.
Classical dynamics of particles and systems
Marion, Jerry B
1965-01-01
Classical Dynamics of Particles and Systems presents a modern and reasonably complete account of the classical mechanics of particles, systems of particles, and rigid bodies for physics students at the advanced undergraduate level. The book aims to present a modern treatment of classical mechanical systems in such a way that the transition to the quantum theory of physics can be made with the least possible difficulty; to acquaint the student with new mathematical techniques and provide sufficient practice in solving problems; and to impart to the student some degree of sophistication in handl
General linear dynamics - quantum, classical or hybrid
Elze, H-T; Vallone, F
2011-01-01
We describe our recent proposal of a path integral formulation of classical Hamiltonian dynamics. Which leads us here to a new attempt at hybrid dynamics, which concerns the direct coupling of classical and quantum mechanical degrees of freedom. This is of practical as well as of foundational interest and no fully satisfactory solution of this problem has been established to date. Related aspects will be observed in a general linear ensemble theory, which comprises classical and quantum dynamics in the form of Liouville and von Neumann equations, respectively, as special cases. Considering the simplest object characterized by a two-dimensional state-space, we illustrate how quantum mechanics is special in several respects among possible linear generalizations.
Dynamics of Non-Classical Interval Exchanges
Gadre, Vaibhav S
2009-01-01
Train tracks with a single vertex are a generalization of interval exchange maps. Here, we consider non-classical interval exchanges: complete train tracks with a single vertex. These can be studied as a dynamical system by considering Rauzy induction in this context. This gives a refinement process on the parameter space similar to Kerckhoff's simplicial systems. We show that the refinement process gives an expansion that has a key dynamical property called uniform distortion. We use uniform distortion to prove normality of the expansion. Consequently we prove an analog of Keane's conjecture: almost every non-classical interval exchange is uniquely ergodic.
Quantum-Classical Correspondence: Dynamical Quantization and the Classical Limit
Energy Technology Data Exchange (ETDEWEB)
Turner, L [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)
2004-11-12
In only 150 pages, not counting appendices, references, or the index, this book is one author's perspective of the massive theoretical and philosophical hurdles in the no-man's-land separating the classical and quantum domains of physics. It ends with him emphasizing his own theoretical contribution to this area. In his own words, he has attempted to answer: 1. How can we obtain the quantum dynamics of open systems initially described by the equations of motion of classical physics (quantization process) 2. How can we retrieve classical dynamics from the quantum mechanical equations of motion by means of a classical limiting process (dequantization process). However, this monograph seems overly ambitious. Although the publisher's description refers to this book as an accessible entre, we find that this author scrambles too hastily over the peaks of information that are contained in his large collection of 272 references. Introductory motivating discussions are lacking. Profound ideas are glossed over superficially and shoddily. Equations morph. But no new convincing understanding of the physical world results. The author takes the viewpoint that physical systems are always in interaction with their environment and are thus not isolated and, therefore, not Hamiltonian. This impels him to produce a method of quantization of these stochastic systems without the need of a Hamiltonian. He also has interest in obtaining the classical limit of the quantized results. However, this reviewer does not understand why one needs to consider open systems to understand quantum-classical correspondence. The author demonstrates his method using various examples of the Smoluchowski form of the Fokker--Planck equation. He then renders these equations in a Wigner representation, uses what he terms an infinitesimality condition, and associates with a constant having the dimensions of an action. He thereby claims to develop master equations, such as the Caldeira
Shkrob, Ilya A; Glover, William J; Larsen, Ross E; Schwartz, Benjamin J
2007-06-21
Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess
Energy Technology Data Exchange (ETDEWEB)
Shkrob, I. A.; Glover, W. J.; Larsen, R. E.; Schwartz, B. J.; Chemistry; Univ. of California at Los Angeles
2007-06-21
Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Angstrom x 18 Angstrom x 18 Angstrom matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer ({approx}18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not
Geometry from dynamics, classical and quantum
Cariñena, José F; Marmo, Giuseppe; Morandi, Giuseppe
2015-01-01
This book describes, by using elementary techniques, how some geometrical structures widely used today in many areas of physics, like symplectic, Poisson, Lagrangian, Hermitian, etc., emerge from dynamics. It is assumed that what can be accessed in actual experiences when studying a given system is just its dynamical behavior that is described by using a family of variables ("observables" of the system). The book departs from the principle that ''dynamics is first'', and then tries to answer in what sense the sole dynamics determines the geometrical structures that have proved so useful to describe the dynamics in so many important instances. In this vein it is shown that most of the geometrical structures that are used in the standard presentations of classical dynamics (Jacobi, Poisson, symplectic, Hamiltonian, Lagrangian) are determined, though in general not uniquely, by the dynamics alone. The same program is accomplished for the geometrical structures relevant to describe quantum dynamics. Finall...
Quantum dynamical entropies in discrete classical chaos
Energy Technology Data Exchange (ETDEWEB)
Benatti, Fabio [Dipartimento di Fisica Teorica, Universita di Trieste, Strada Costiera 11, 34014 Trieste (Italy); Cappellini, Valerio [Dipartimento di Fisica Teorica, Universita di Trieste, Strada Costiera 11, 34014 Trieste (Italy); Zertuche, Federico [Instituto de Matematicas, UNAM, Unidad Cuernavaca, AP 273-3, Admon. 3, 62251 Cuernavaca, Morelos (Mexico)
2004-01-09
We discuss certain analogies between quantization and discretization of classical systems on manifolds. In particular, we will apply the quantum dynamical entropy of Alicki and Fannes to numerically study the footprints of chaos in discretized versions of hyperbolic maps on the torus.
Dynamics of the classical planar spin chain
Raedt, Bart De; Raedt, Hans De
1978-01-01
In this paper we pay attention to the classical one-dimensional planar spin system and, in particular, to the dynamics of such a model. We use the Monte Carlo method to calculate the static correlation functions, needed to determine the relaxation functions completely. We are then able to give the r
Effective dynamics of a classical point charges
Polonyi, Janos
2013-01-01
The effective Lagrangian of a point charge is derived by eliminating the electromagnetic field within the framework of the classical closed time path formalism. The short distance singularity of the electromagnetic field is regulated by an UV cutoff. The Abraham-Lorentz force is recovered and its similarity to anomalies is underlined. The full cutoff-dependent linearized equation of motion is obtained, no runaway trajectories are found but the effective dynamics shows acausality if the cutoff is beyond the classical charge radius. The strength of the radiation reaction force displays a pole in its cutoff-dependence in a manner reminiscent of the Landau-pole of perturbative QED. Similarity between the dynamical breakdown of the time reversal invariance and dynamical symmetry breaking is pointed out.
Point vortex dynamics: A classical mathematics playground
DEFF Research Database (Denmark)
Aref, Hassan
2007-01-01
The idealization of a two-dimensional, ideal flow as a collection of point vortices embedded in otherwise irrotational flow yields a surprisingly large number of mathematical insights and connects to a large number of areas of classical mathematics. Several examples are given including the integr...... participation in the exploration of this intriguing dynamical system from the mathematical physics community.......The idealization of a two-dimensional, ideal flow as a collection of point vortices embedded in otherwise irrotational flow yields a surprisingly large number of mathematical insights and connects to a large number of areas of classical mathematics. Several examples are given including...
Dynamics of Coupled Quantum-Classical Oscillators
Institute of Scientific and Technical Information of China (English)
HE Wei-Zhong; XU Liu-Su; ZOU Feng-Wu
2004-01-01
@@ The dynamics of systems consisting of coupled quantum-classical oscillators is numerically investigated. It is shown that, under certain conditions, the quantum oscillator exhibits chaos. When the mass of the classical oscillator increases, the chaos will be suppressed; if the energy of the system and/or the coupling strength between the two oscillators increases, chaotic behaviour of the system appears. This result will be helpful to understand the probability of the emergence of quantum chaos and may be applied to explain the spectra of complex atoms qualitatively.
Simulation of molecular transitions using classical trajectories
Energy Technology Data Exchange (ETDEWEB)
Donoso, A.; Martens, C. C. [University of California, California (United States)
2001-03-01
In the present work, we describe the implementation of a semiclassical method to study physical-chemical processes in molecular systems where electronic state transitions and quantum coherence play a dominant role. The method is based on classical trajectory propagation on the underlying coupled electronic surfaces and is derived from the semiclassical limit of the quantum Liouville equation. Unlike previous classical trajectory-based methods, quantum electronic coherence are treated naturally within this approach as complex weighted trajectory ensembles propagating on the average electronic surfaces. The method is tested on a model problem consisting of one-dimensional motion on two crossing electronic surfaces. Excellent agreement is obtained when compared to the exact results obtained by wave packet propagation. The method is applied to model quantum wave packet interferometry, where two wave packets, differing only in a relative phase, collide in the region where the two electronic surfaces cross. The dependence of the resulting population transfer on the initial relative phase of the wave packets is perfectly captured by our classical trajectory method. Comparison with an alternative method, surface hopping, shows that our approach is appropriate for modelling quantum interference phenomena. [Spanish] En este trabajo se describe la implementacion de un metodo semiclasico para estudiar procesos fisicos-quimicos en sistemas moleculares donde las transiciones entre estados electronicos y las coherencias cuanticas juegan un papel predominante. El metodo se basa en la propagacion de trayectorias clasicas sobre las correspondientes superficies electronicas acopladas y se deriva a partir del limite semiclasico de la ecuacion cuantica de Liouville. A diferencia de metodos previos basados en trayectoria clasica, dentro de este esquema, las coherencias electronicas cuanticas son tratadas de manera natural como ensamble de trayectorias con pesos complejos, moviendose en
On the classical theory of molecular optical activity
Frolov, Alexei M
2010-01-01
The basic principles of classical and semi-classical theories of molecular optical activity are discussed. These theories are valid for dilute solutions of optically active organic molecules. It is shown that all phenomena known in the classical theory of molecular optical activity can be described with the use of one pseudo-scalar which is a uniform function of the incident light frequency $\\omega$. The relation between optical rotation and circular dichroism is derived from the basic Kramers-Kronig relations. In our discussion of the general theory of molecular optical activity we introduce the tensor of molecular optical activity. It is shown that to evaluate the optical rotation and circular dichroism at arbitrary frequencies one needs to know only nine (3 + 6) molecular tensors. The quantum (or semi-classical) theory of molecular optical activity is also briefly discussed. We also raise the possibility of measuring the optical rotation and circular dichroism at wavelengths which correspond to the vacuum ...
State-Dependent Molecular Dynamics
Directory of Open Access Journals (Sweden)
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Energy Technology Data Exchange (ETDEWEB)
Gonzalez Giralda, C.
2005-07-01
The main objective of this thesis is to search for points of correspondence between the classic and quantum behavior of the dynamics of non-rigid molecular system HO2 (Hidroperoxil Radix), and too, the study of the manifestation mode as the regularity than the ergodicity from the point of view of the classical and quantum mechanics laws. (Author)
Energy Technology Data Exchange (ETDEWEB)
Kojima, H.; Yamada, A.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
2015-05-07
The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum–classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute–solvent interactions.
Quantum-classical hybrid dynamics - a summary
Elze, Hans-Thomas
2013-01-01
A summary of a recently proposed description of quantum-classical hybrids is presented, which concerns quantum and classical degrees of freedom of a composite object that interact directly with each other. This is based on notions of classical Hamiltonian mechanics suitably extended to quantum mechanics.
Amokrane, S.; Ayadim, A.; Levrel, L.
2015-11-01
We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Modeling the Hydrogen Bond within Molecular Dynamics
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Extending classical molecular theory with polarization.
Keyes, Tom; Napoleon, Raeanne L
2011-01-27
A classical, polarizable, electrostatic theory of short-ranged atom-atom interactions, incorporating the smeared nature of atomic partial charges, is presented. Detailed models are constructed for CO monomer and for CO interacting with an iron atom, as a first step toward heme proteins. A good representation is obtained of the bond-length-dependent dipole of CO monomer from fitting at the equilibrium distance only. Essential features of the binding of CO to myoglobin (Mb) and model heme compounds, including the binding energy, the position of the minimum in the Fe-C potential, the Fe-C frequency, the bending energy, the linear geometry of FeCO, and the increase of the Stark tuning rate and IR intensity, are obtained, suggesting that a substantial part of the Fe-CO interaction consists of a classical, noncovalent, "electrostatic bond ". The binding energy is primarily polarization energy, and the polarization energy of an OH pair in water is shown to be comparable to the experimental hydrogen bond energy.
Song, Hui; Dai, Dongxu; Wu, Guorong; Wang, Chia Chen; Harich, Steven A; Hayes, Michael Y; Wang, Xiuyan; Gerlich, Dieter; Yang, Xueming; Skodje, Rex T
2005-08-15
Recent molecular-beam experiments have probed the dynamics of the Rydberg-atom reaction, H(n)+D2-->HD+D(n) at low collision energies. It was discovered that the rotationally resolved product distribution was remarkably similar to a much more limited data set obtained at a single scattering angle for the ion-molecule reaction H++D2-->D++HD. The equivalence of these two problems would be consistent with the Fermi-independent-collider model (electron acting as a spectator) and would provide an important new avenue for the study of ion-molecule reactions. In this work, we employ a classical trajectory calculation on the ion-molecule reaction to facilitate a more extensive comparison between the two systems. The trajectory simulations tend to confirm the equivalence of the ion+molecule dynamics to that for the Rydberg-atom+molecule system. The theory reproduces the close relationship of the two experimental observations made previously. However, some differences between the Rydberg-atom experiments and the trajectory simulations are seen when comparisons are made to a broader data set. In particular, the angular distribution of the differential cross section exhibits more asymmetry in the experiment than in the theory. The potential breakdown of the classical model is discussed. The role of the "spectator" Rydberg electron is addressed and several crucial issues for future theoretical work are brought out.
[The molecular pathology of classical Hodgkin lymphoma].
Asano, Naoko
2015-10-01
In 1832, Dr. Thomas Hodgkin reported the first cases with this malignancy, which came to be named Hodgkin's disease. The cells that are a hallmark of this disease, Hodgkin and Reed-Sternberg (HRS) cells, account for only 1% of those in tumor tissues, with the majority of cells in Hodgkin lymphoma being of various inflammatory types. Advances in molecular techniques have contributed to molecular biological analysis of HRS cells. Intriguingly, HRS cells are derived from germinal center B-cells, but have lost their B-cell gene-expression and co-express non-B-cell genes. Multiple signaling pathways, including the NFκB and JAK/STAT pathways, show deregulated activity in HRS cells, suggesting an important role for these pathways in the pathogenesis of Hodgkin lymphoma. This article describes the molecular pathological characteristics of HRS cells: 1) the cellular origin of HRS cells, 2) deregulated gene expression in HRS cells, 3) genetic alterations and 4) epigenetic alterations in HRS cells, 5) the lost B-cell phenotype of HRS cells, 6) the role of EBV in Hodgkin lymphoma pathogenesis, and 7) micro-environmental interactions between HRS and reactive cells.
Classical and semiclassical aspects of chemical dynamics
Energy Technology Data Exchange (ETDEWEB)
Gray, S.K.
1982-08-01
Tunneling in the unimolecular reactions H/sub 2/C/sub 2/ ..-->.. HC/sub 2/H, HNC ..-->.. HCN, and H/sub 2/CO ..-->.. H/sub 2/ + CO is studied with a classical Hamiltonian that allows the reaction coordinate and transverse vibrational modes to be considered directly. A combination of classical perturbation theory and the semiclassical WKB method allows tunneling probabilities to be obtained, and a statistical theory (RRKM) is used to construct rate constants for these reactions in the tunneling regime. In this fashion, it is found that tunneling may be important, particularly for low excitation energies. Nonadiabatic charge transfer in the reaction Na + I ..-->.. Na /sup +/ + I/sup -/ is treated with classical trajectories based on a classical Hamiltonian that is the analogue of a quantum matrix representation. The charge transfer cross section obtained is found to agree reasonably well with the exact quantum results. An approximate semiclassical formula, valid at high energies, is also obtained. The interaction of radiation and matter is treated from a classical viewpoint. The excitation of an HF molecule in a strong laser is described with classical trajectories. Quantum mechanical results are also obtained and compared to the classical results. Although the detailed structure of the pulse time averaged energy absorption cannot be reproduced classically, classical mechanics does predict the correct magnitude of energy absorption, as well as certain other qualitative features. The classical behavior of a nonrotating diatomic molecule in a strong laser field is considered further, by generating a period advance map that allows the solution over many periods of oscillation of the laser to be obtained with relative ease. Classical states are found to form beautiful spirals in phase space as time progresses. A simple pendulum model is found to describe the major qualitative features. (WHM)
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Quasi-classical theory of electronic flux density in electronically adiabatic molecular processes.
Diestler, D J
2012-11-26
The standard Born-Oppenheimer (BO) description of electronically adiabatic molecular processes predicts a vanishing electronic flux density (EFD). A previously proposed "coupled-channels" theory permits the extraction of the EFD from the BO wave function for one-electron diatomic systems, but attempts at generalization to many-electron polyatomic systems are frustrated by technical barriers. An alternative "quasi-classical" approach, which eliminates the explicit quantum dynamics of the electrons within a classical framework, yet retains the quantum character of the nuclear motion, appears capable of yielding EFDs for arbitrarily complex systems. Quasi-classical formulas for the EFD in simple systems agree with corresponding coupled-channels formulas. Results of the application of the new quasi-classical formula for the EFD to a model triatomic system indicate the potential of the quasi-classical scheme to elucidate the dynamical role of electrons in electronically adiabatic processes in more complex multiparticle systems.
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....
Quantum dynamics in open quantum-classical systems.
Kapral, Raymond
2015-02-25
Often quantum systems are not isolated and interactions with their environments must be taken into account. In such open quantum systems these environmental interactions can lead to decoherence and dissipation, which have a marked influence on the properties of the quantum system. In many instances the environment is well-approximated by classical mechanics, so that one is led to consider the dynamics of open quantum-classical systems. Since a full quantum dynamical description of large many-body systems is not currently feasible, mixed quantum-classical methods can provide accurate and computationally tractable ways to follow the dynamics of both the system and its environment. This review focuses on quantum-classical Liouville dynamics, one of several quantum-classical descriptions, and discusses the problems that arise when one attempts to combine quantum and classical mechanics, coherence and decoherence in quantum-classical systems, nonadiabatic dynamics, surface-hopping and mean-field theories and their relation to quantum-classical Liouville dynamics, as well as methods for simulating the dynamics.
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.
Rovibrational dynamics of the RbCs molecule in static electric fields. Classical study
Energy Technology Data Exchange (ETDEWEB)
Arnaiz, Pedro F.; Iñarrea, Manuel [Área de Física, Universidad de la Rioja, E-26006 Logroño (Spain); Salas, J. Pablo, E-mail: josepablo.salas@unirioja.es [Área de Física, Universidad de la Rioja, E-26006 Logroño (Spain)
2012-04-02
We study the classical dynamics of the RbCs molecule in the presence of a static electric field. Under the Born–Oppenheimer approximation, we perform a rovibrational investigation which includes the interaction of the field with the molecular polarizability. The stability of the equilibrium points and the phase space structure of the system are explored in detail. We find that, for strong electric fields or for energies close to the dissociation threshold, the molecular polarizability causes relevant effects on the system dynamics. -- Highlights: ► We study the classical rovibrational dynamics of the alkali polar dimer RbCs. ► In the model we consider the interaction of the field with the molecular polarizability. ► The potential energy surface is studied depending on the electric field strength. ► Using surfaces of section we study the phase space structure. ► We find that the molecular polarizability causes relevant effects on the system dynamics.
Classical vs Quantum Games: Continuous-time Evolutionary Strategy Dynamics
Leung, Ming Lam
2011-01-01
This paper unifies the concepts of evolutionary games and quantum strategies. First, we state the formulation and properties of classical evolutionary strategies, with focus on the destinations of evolution in 2-player 2-strategy games. We then introduce a new formalism of quantum evolutionary dynamics, and give an example where an evolving quantum strategy gives reward if played against its classical counterpart.
Planar dynamical systems selected classical problems
Liu, Yirong; Huang, Wentao
2014-01-01
This book presents in an elementary way the recent significant developments in the qualitative theory of planar dynamical systems. The subjects are covered as follows: the studies of center and isochronous center problems, multiple Hopf bifurcations and local and global bifurcations of the equivariant planar vector fields which concern with Hilbert's 16th problem. This book is intended for graduate students, post-doctors and researchers in the area of theories and applications of dynamical systems. For all engineers who are interested the theory of dynamical systems, it is also a reasona
First-order partial differential equations in classical dynamics
Smith, B. R.
2009-12-01
Carathèodory's classic work on the calculus of variations explores in depth the connection between ordinary differential equations and first-order partial differential equations. The n second-order ordinary differential equations of a classical dynamical system reduce to a single first-order differential equation in 2n independent variables. The general solution of first-order partial differential equations touches on many concepts central to graduate-level courses in analytical dynamics including the Hamiltonian, Lagrange and Poisson brackets, and the Hamilton-Jacobi equation. For all but the simplest dynamical systems the solution requires one or more of these techniques. Three elementary dynamical problems (uniform acceleration, harmonic motion, and cyclotron motion) can be solved directly from the appropriate first-order partial differential equation without the use of advanced methods. The process offers an unusual perspective on classical dynamics, which is readily accessible to intermediate students who are not yet fully conversant with advanced approaches.
Identifying the Stern-Gerlach force of classical electron dynamics
Wen, Meng; Bauke, Heiko; Keitel, Christoph H.
2016-08-01
Different classical theories are commonly applied in various branches of physics to describe the relativistic dynamics of electrons by coupled equations for the orbital motion and spin precession. Exemplarily, we benchmark the Frenkel model and the classical Foldy-Wouthuysen model with spin-dependent forces (Stern-Gerlach forces) to the quantum dynamics as predicted by the Dirac equation. Both classical theories can lead to different or even contradicting predictions how the Stern-Gerlach forces modify the electron’s orbital motion, when the electron moves in strong electromagnetic field configurations of emerging high-intensity laser facilities. In this way, one may evaluate the validity and identify the limits of these classical theories via a comparison with possible experiments to provide a proper description of spin-induced dynamics. Our results indicate that the Foldy-Wouthuysen model is qualitatively in better agreement with the Dirac theory than the widely used Frenkel model.
Modeling hybrid perovskites by molecular dynamics.
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Modeling hybrid perovskites by molecular dynamics
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Quasi-classical dynamics of interacting Bose condensates
Salgueiro, A N; Sampaio, M D; De Toledo di Piza, A F R
1998-01-01
The dynamics of the composition of uniform Bose condensates involving two species capable of reciprocal interconversion is treated in terms of a collective quasi-spin model. This collective model quickly reduces to classical form towards the thermodynamic limit. Quantum solutions are easily obtained numerically short of this limit which give insight into the dynamically relevant correlation processes.
Quantum–classical correspondence and the role of the dipole function in molecular dissociation
Energy Technology Data Exchange (ETDEWEB)
Lima, E.F. de, E-mail: eflima@rc.unesp.br [Instituto de Geociências e Ciências Exatas, UNESP – Univ. Estadual Paulista, Rio Claro, São Paulo 13506-900 (Brazil); Rosado, E.C., E-mail: tcortez@rc.unesp.br [Departamento de Física, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905 (Brazil); Castelano, L.K., E-mail: lkcastelano@ufscar.br [Departamento de Física, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905 (Brazil); Egydio de Carvalho, R., E-mail: regydio@rc.unesp.br [Instituto de Geociências e Ciências Exatas, UNESP – Univ. Estadual Paulista, Rio Claro, São Paulo 13506-900 (Brazil)
2014-07-18
We consider the quantum and classical dissociation dynamics of heteronuclear diatomic molecules induced by infrared laser pulses. The field–molecule interaction is given by the product of the time-dependent electric field and the molecule permanent dipole. We investigate the influence of the dipole function in molecular dissociation. We show that the dissociation can be suppressed at certain external field frequencies for a nonlinear and finite-range dipole function. The correspondence between quantum and classical results is established by relating classical Fourier amplitudes to discrete–continuum quantum matrix elements. - Highlights: • A finite-range dipole can prevent laser-induced dissociation for particular external frequencies. • Quantum and classical calculations show good agreement when the system is initially in excited levels. • An approximation of discrete–continuum matrix elements by Fourier components is obtained.
Strong Analog Classical Simulation of Coherent Quantum Dynamics
Wang, Dong-Sheng
2017-02-01
A strong analog classical simulation of general quantum evolution is proposed, which serves as a novel scheme in quantum computation and simulation. The scheme employs the approach of geometric quantum mechanics and quantum informational technique of quantum tomography, which applies broadly to cases of mixed states, nonunitary evolution, and infinite dimensional systems. The simulation provides an intriguing classical picture to probe quantum phenomena, namely, a coherent quantum dynamics can be viewed as a globally constrained classical Hamiltonian dynamics of a collection of coupled particles or strings. Efficiency analysis reveals a fundamental difference between the locality in real space and locality in Hilbert space, the latter enables efficient strong analog classical simulations. Examples are also studied to highlight the differences and gaps among various simulation methods. Funding support from NSERC of Canada and a research fellowship at Department of Physics and Astronomy, University of British Columbia are acknowledged
Better, Cheaper, Faster Molecular Dynamics
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
Molecular dynamics for irradiation driven chemistry
DEFF Research Database (Denmark)
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-01-01
that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... 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...
Classical and quantum dynamics of the sphere
Lasukov, Vladimir; Moldovanova, Evgeniia; Abdrashitova, Maria; Malik, Hitendra; Gorbacheva, Ekaterina
2016-07-01
In Minkowski space, there has been developed the mathematic quantum model of the real particle located on the sphere evolving owing to the negative pressure inside the sphere. The developed model is analogous to the geometrodynamic model of the Lemaitre-Friedmann primordial atom in superspace-time, whose spatial coordinate is the scale factor functioning as a radial coordinate. There is a formulation of quantum geometrodynamics in which the spatial coordinate is an offset of the scale factor and wave function at the same time. With the help of the Dirac procedure for extracting the root from the Hamiltonian operator we have constructed a Dirac quantum dynamics of the sphere with fractional spin.
Interactive molecular dynamics
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Dynamics of classical and quantum fields an introduction
Setlur, Girish S
2014-01-01
Dynamics of Classical and Quantum Fields: An Introduction focuses on dynamical fields in non-relativistic physics. Written by a physicist for physicists, the book is designed to help readers develop analytical skills related to classical and quantum fields at the non-relativistic level, and think about the concepts and theory through numerous problems. In-depth yet accessible, the book presents new and conventional topics in a self-contained manner that beginners would find useful. A partial list of topics covered includes: Geometrical meaning of Legendre transformation in classical mechanics Dynamical symmetries in the context of Noether's theorem The derivation of the stress energy tensor of the electromagnetic field, the expression for strain energy in elastic bodies, and the Navier Stokes equation Concepts of right and left movers in case of a Fermi gas explained Functional integration is interpreted as a limit of a sequence of ordinary integrations Path integrals for one and two quantum particles and for...
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Phonon dynamics in a compressible classical Heisenberg chain
Fivez, Jan; Raedt, Hans De; Raedt, Bart De
1980-01-01
The dynamic properties of the compressible classical Heisenberg chain with bilinear coupling are investigated. The sound velocity is calculated exactly. The Fourier-transformed displacement-displacement correlation function is studied as a function of temperature, wave vector, and the model paramete
Liouville-von Neumann molecular dynamics
Jakowski, Jacek; Morokuma, Keiji
2009-06-01
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.
Operational dynamic modeling transcending quantum and classical mechanics.
Bondar, Denys I; Cabrera, Renan; Lompay, Robert R; Ivanov, Misha Yu; Rabitz, Herschel A
2012-11-09
We introduce a general and systematic theoretical framework for operational dynamic modeling (ODM) by combining a kinematic description of a model with the evolution of the dynamical average values. The kinematics includes the algebra of the observables and their defined averages. The evolution of the average values is drawn in the form of Ehrenfest-like theorems. We show that ODM is capable of encompassing wide-ranging dynamics from classical non-relativistic mechanics to quantum field theory. The generality of ODM should provide a basis for formulating novel theories.
Classical mechanics systems of particles and Hamiltonian dynamics
Greiner, Walter
2010-01-01
This textbook Classical Mechanics provides a complete survey on all aspects of classical mechanics in theoretical physics. An enormous number of worked examples and problems show students how to apply the abstract principles to realistic problems. The textbook covers Newtonian mechanics in rotating coordinate systems, mechanics of systems of point particles, vibrating systems and mechanics of rigid bodies. It thoroughly introduces and explains the Lagrange and Hamilton equations and the Hamilton-Jacobi theory. A large section on nonlinear dynamics and chaotic behavior of systems takes Classical Mechanics to newest development in physics. The new edition is completely revised and updated. New exercises and new sections in canonical transformation and Hamiltonian theory have been added.
Molecular Dynamics of Lipid Bilayers
1989-08-09
The aim of this work is to study, by molecular dynamics simulations, the properties of lipid bilayers. We have applied the vectorizable, order-N...fast angle-dependent force/potential algorithms to treat angle bending and torsion. Keywords: Molecular dynamics , Lipid bilayers.
Molecular machines operating on the nanoscale: from classical to quantum
Directory of Open Access Journals (Sweden)
Igor Goychuk
2016-03-01
Full Text Available The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed.
Scalar Field Dynamics Classical, Quantum and in Between
Salle, M; Vink, Jeroen C
2000-01-01
Using a Hartree ensemble approximation, we investigate the dynamics of the \\phi^4 model in 1+1 dimensions. We find that the fields initially thermalize with a Bose-Einstein distribution for the fields. Gradually, however, the distribution changes towards classical equipartition. Using suitable initial conditions quantum thermalization is achieved much faster than the onset of this undesirable equipartition. We also show how the numerical efficiency of our method can be significantly improved.
Sundararaman, Ravishankar
2014-01-01
Classical density-functional theory provides an efficient alternative to molecular dynamics simulations for understanding the equilibrium properties of inhomogeneous fluids. However, application of density-functional theory to multi-site molecular fluids has so far been limited by complications due to the implicit molecular geometry constraints on the site densities, whose resolution typically requires expensive Monte Carlo methods. Here, we present a general scheme of circumventing this so-called inversion problem: compressed representations of the orientation density. This approach allows us to combine the superior iterative convergence properties of multipole representations of the fluid configuration with the improved accuracy of site-density functionals. Next, from a computational perspective, we show how to extend the DFT++ algebraic formulation of electronic density-functional theory to the classical fluid case and present a basis-independent discretization of our formulation for molecular classical de...
Classical trajectory simulations of post-transition state dynamics
Lourderaj, Upakarasamy; Park, Kyoyeon; Hase, William L.
Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl- ··· CH3Br → ClCH3 + Br- and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl- ··· CH3Cl complexes mediating the Cl- + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH- + CH3F and F- + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.
Charge transport in high mobility molecular semiconductors: classical models and new theories.
Troisi, Alessandro
2011-05-01
The theories developed since the fifties to describe charge transport in molecular crystals proved to be inadequate for the most promising classes of high mobility molecular semiconductors identified in the recent years, including for example pentacene and rubrene. After reviewing at an elementary level the classical theories, which still provide the language for the understanding of charge transport in these systems, this tutorial review outlines the recent experimental and computational evidence that prompted the development of new theories of charge transport in molecular crystals. A critical discussion will illustrate how very rarely it is possible to assume a charge hopping mechanism for high mobility organic crystals at any temperature. Recent models based on the effect of non-local electron-phonon coupling, dynamic disorder, coexistence of localized and delocalized states are reviewed. Additionally, a few more recent avenues of theoretical investigation, including the study of defect states, are discussed.
The Computer Simulation of Liquids by Molecular Dynamics.
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
BOOK REVIEW: Quantum-Classical Correspondence: Dynamical Quantization and the Classical Limit
Turner, L.
2004-11-01
In only 150 pages, not counting appendices, references, or the index, this book is one author’s perspective of the massive theoretical and philosophical hurdles in the no-man’s-land separating the classical and quantum domains of physics. It ends with him emphasizing his own theoretical contribution to this area. In his own words, he has attempted to answer: 1. ‘How can we obtain the quantum dynamics of open systems initially described by the equations of motion of classical physics (quantization process)? 2. ‘How can we retrieve classical dynamics from the quantum mechanical equations of motion by means of a classical limiting process (dequantization process)?’ However, this monograph seems overly ambitious. Although the publisher’s description refers to this book as ‘an accessible entrée’, we find that this author scrambles too hastily over the peaks of information that are contained in his large collection of 272 references. Introductory motivating discussions are lacking. Profound ideas are glossed over superficially and shoddily. Equations morph. But no new convincing understanding of the physical world results. The author takes the viewpoint that physical systems are always in interaction with their environment and are thus not isolated and, therefore, not Hamiltonian. This impels him to produce a method of quantization of these stochastic systems without the need of a Hamiltonian. He also has interest in obtaining the classical limit of the quantized results. However, this reviewer does not understand why one needs to consider open systems to understand ‘quantum-classical correspondence’. The author demonstrates his method using various examples of the Smoluchowski form of the Fokker--Planck equation. He then renders these equations in a Wigner representation, uses what he terms ‘an infinitesimality condition’, and associates with a constant having the dimensions of an action. He thereby claims to develop master equations, such as
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Classically dynamical behaviour of a nucleon in heavy nuclei
Energy Technology Data Exchange (ETDEWEB)
Gu Jianzhong [CCAST World Lab., Beijing, BJ (China)]|[Institute of Theoretical Physics, Academia Sinica, P.O. Box 2735, Beijing, 100080 (China); Zhao Enguang; Zong Hongshi [Institute of Theoretical Physics, Academia Sinica, P.O. Box 2735, Beijing, 100080 (China); Zhuo Yizhong [Institute of Theoretical Physics, Academia Sinica, P.O. Box 2735, Beijing, 100080 (China)]|[China Institute of Atomic Energy, P.O. Box 275 18, Beijing, 102413 (China); Wu Xizhen [China Institute of Atomic Energy, P.O. Box 275 18, Beijing, 102413 (China)
1998-06-01
Within the framework of the two-center shell model the classically dynamical behaviour of a nucleon in heavy nuclei is investigated systematically with the change of nuclear shape parameters for the first time. It is found that as long as the nucleonic energy 0is appreciably higher than the height of the potential barrier there is a good quantum-classical correspondence of nucleonic regular (chaotic) motion. Thus, Bohigas, Giannoni and Schmit conjecture is confirmed once again. We find that the difference between the potential barrier for prolate nuclei and that for oblate ones is reponsible for the energy-dependence difference between the nucleonic chaotic dynamics for prolate nuclei and that for oblate ones. In addition, it is suggested that nuclear dissipation is shape-dependent, and strong nuclear dissipation can be expected for medium or large separations in the presence of a considerable neck deformation built on a pronounced octupole-like deformation, which provides us a dynamical understanding of nuclear shape dependence of nuclear dissipation. (orig.) With 5 figs., 22 refs.
The free rigid body dynamics: Generalized versus classic
Tudoran, Rǎzvan M.
2013-07-01
In this paper we analyze some normal forms of a general quadratic Hamiltonian system defined on the dual of the Lie algebra {o}(K) of real K-skew-symmetric matrices, where K is an arbitrary 3×3 real symmetric matrix. A consequence of the main results is that any first-order autonomous three-dimensional differential equation possessing two independent quadratic constants of motion, which admit a positive/negative definite linear combination, is affinely equivalent to the classical "relaxed" free rigid body dynamics with linear control parameters.
Molecular dynamics of silicon indentation
Energy Technology Data Exchange (ETDEWEB)
Kallman, J.S.; Hoover, W.G.; Hoover, C.G.; De Groot, A.J.; Lee, S.M.; Wooten, F. (Department of Applied Science Davis-Livermore, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States))
1993-04-01
We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.
Ryabinkin, Ilya G
2016-01-01
An accurate description of nonadiabatic dynamics of molecular species on metallic surfaces poses a serious computational challenge associated with a multitude of closely-spaced electronic states. We propose a mixed quantum-classical scheme that addresses this challenge by introducing collective electronic variables. These variables are defined through analytic block-diagonalization applied to the time-dependent Hamiltonian matrix governing the electronic dynamics. We compare our scheme with the Ehrenfest approach and with a full-memory electronic friction model on a one-dimensional "adatom + atomic chain" model. Our simulations demonstrate that collective-mode dynamics with only few (2-3) electronic variables is robust and can describe a variety of situations: from a chemisorbed atom on an insulator to an atom on a metallic surface. Our molecular model also reveals that the friction approach is prone to unpredictable and catastrophic failures.
Wrinkled Peas and White-Eyed Fruit Flies: The Molecular Basis of Two Classical Genetic Traits.
Guilfoile, Patrick
1997-01-01
Focuses on bridging the gap between classical and molecular genetics for two traits: wrinkled seeds in garden peas and white eye color in fruit flies. Discusses the molecular details of the underlying basis of these traits. Contains 15 references. (JRH)
Dynamic scaling at classical phase transitions approached through nonequilibrium quenching
Liu, Cheng-Wei; Polkovnikov, Anatoli; Sandvik, Anders W.
2014-02-01
We use Monte Carlo simulations to demonstrate generic scaling aspects of classical phase transitions approached through a quench (or annealing) protocol where the temperature changes as a function of time with velocity v. Using a generalized Kibble-Zurek ansatz, we demonstrate dynamic scaling for different types of stochastic dynamics (Metropolis, Swendsen-Wang, and Wolff) on Ising models in two and higher dimensions. We show that there are dual scaling functions governing the dynamic scaling, which together describe the scaling behavior in the entire velocity range v ∈[0,∞). These functions have asymptotics corresponding to the adiabatic and diabatic limits, and close to these limits they are perturbative in v and 1/v, respectively. Away from their perturbative domains, both functions cross over into the same universal power-law scaling form governed by the static and dynamic critical exponents (as well as an exponent characterizing the quench protocol). As a by-product of the scaling studies, we obtain high-precision estimates of the dynamic exponent z for the two-dimensional Ising model subject to the three variants of Monte Carlo dynamics: for single-spin Metropolis updates zM=2.1767(5), for Swendsen-Wang multicluster updates zSW=0.297(3), and for Wolff single-cluster updates zW=0.30(2). For Wolff dynamics, we find an interesting behavior with a nonanalytic breakdown of the quasiadiabatic and diabatic scalings, instead of the generic smooth crossover described by a power law. We interpret this disconnect between the two scaling regimes as a dynamic phase transition of the Wolff algorithm, caused by an effective sudden loss of ergodicity at high velocity.
Charge and Energy Transfer Dynamics in Molecular Systems
May, Volkhard
2004-01-01
This second edition is based on the successful concept of the first edition in presenting a unified perspective on molecular charge and energy transfer processes. The authors bridge the regimes of coherent and dissipative dynamics, thus establishing the connection between classic rate theories and modern treatments of ultrafast phenomena. The book serves as an introduction for graduate students and researchers. Among the new topics of this second edition are. - semiclassical and quantum-classical hybrid formulations of molecular dynamics. - the basics of femtosecond nonlinear spectroscopy. - e
Classical and quantum stability of higher-derivative dynamics
Kaparulin, D S; Sharapov, A A
2014-01-01
We observe that a wide class of higher-derivative systems admits a bounded integral of motion that ensures the classical stability of dynamics, while the canonical energy is unbounded. We use the concept of a Lagrange anchor to demonstrate that the bounded integral of motion is connected with the time-translation invariance. A procedure is suggested for switching on interactions in free higher-derivative systems without breaking their stability. We also demonstrate the quantization technique that keeps the higher-derivative dynamics stable at quantum level. The general construction is illustrated by the examples of the Pais-Uhlenbeck oscillator, higher-derivative scalar field model, and the Podolsky electrodynamics. For all these models, the positive integrals of motion are explicitly constructed and the interactions are included such that keep the system stable.
Feedback Control Of Dynamical Instabilities In Classical Lasers And Fels
Bielawski, S; Szwaj, C
2005-01-01
Dynamical instabilities lead to unwanted full-scale power oscillations in many classical lasers and FEL oscillators. For a long time, applications requiring stable operation were typically performed by working outside the problematic parameter regions. A breakthrough occurred in the nineties [1], when emphasis was made on the practical importance of unstable states (stationary or periodic) that coexist with unwanted oscillatory states. Indeed, although not observable in usual experiments, unstable states can be stabilized, using a feedback control involving arbitrarily small perturbations of a parameter. This observation stimulated a set of works leading to successful suppression of dynamical instabilities (initially chaos) in lasers, sometimes with surprisingly simple feedback devices [2]. We will review a set of key results, including in particular the recent works on the stabilization of mode-locked lasers, and of the super-ACO, ELETTRA and UVSOR FELs [3].
Information dynamics and open systems classical and quantum approach
Ingarden, R S; Ohya, M
1997-01-01
This book aims to present an information-theoretical approach to thermodynamics and its generalisations On the one hand, it generalises the concept of `information thermodynamics' to that of `information dynamics' in order to stress applications outside thermal phenomena On the other hand, it is a synthesis of the dynamics of state change and the theory of complexity, which provide a common framework to treat both physical and nonphysical systems together Both classical and quantum systems are discussed, and two appendices are included to explain principal definitions and some important aspects of the theory of Hilbert spaces and operator algebras The concept of higher-order temperatures is explained and applied to biological and linguistic systems The theory of open systems is presented in a new, much more general form Audience This volume is intended mainly for theoretical and mathematical physicists, but also for mathematicians, experimental physicists, physical chemists, theoretical biologists, communicat...
Isomorph invariance of the structure and dynamics of classical crystals
DEFF Research Database (Denmark)
Albrechtsen, Dan; Olsen, Andreas Elmerdahl; Pedersen, Ulf Rørbæk
2014-01-01
of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles......This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework......, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics...
Classical and quantum dynamics of driven elliptical billiards
Energy Technology Data Exchange (ETDEWEB)
Lenz, Florian
2009-12-09
Subject of this thesis is the investigation of the classical dynamics of the driven elliptical billiard and the development of a numerical method allowing the propagation of arbitrary initial states in the quantum version of the system. In the classical case, we demonstrate that there is Fermi acceleration in the driven billiard. The corresponding transport process in momentum space shows a surprising crossover from sub- to normal diffusion. This crossover is not parameter induced, but rather occurs dynamically in the evolution of the ensemble. The four-dimensional phase space is analyzed in depth, especially how its composition changes in different velocity regimes. We show that the stickiness properties, which eventually determine the diffusion, are intimately connected with this change of the composition of the phase space with respect to velocity. In the course of the evolution, the accelerating ensemble thus explores regions of varying stickiness, leading to the mentioned crossover in the diffusion. In the quantum case, a series of transformations tailored to the elliptical billiard is applied to circumvent the time-dependent Dirichlet boundary conditions. By means of an expansion ansatz, this eventually yields a large system of coupled ordinary differential equations, which can be solved by standard techniques. (orig.)
Jeanmairet, Guillaume; Levesque, Maximilien; Rotenberg, Benjamin; Borgis, Daniel
2014-01-01
We report here how the hydration of complex surfaces can be efficiently studied thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophylite clay. After presenting the most recent advances, we show that the strength of this implicit method is that (i) it is in quantitative or semi-quantitative agreement with reference all-atoms simulations (molecular dynamics here) for both the solvation structure and energetics, and that (ii) the computational cost is two to three orders of magnitude less than in explicit methods. The method remains imperfect, in that it locally overestimates the polarization of water close to hydrophylic sites of the clay. The high numerical efficiency of the method is illustrated and exploited to carry a systematic study of the electrostatic and van der Waals components of the surface-solvant interactions within the most popular force field for clays, CLAYFF. Hydration structure and energetics are found to weakly depend u...
Werbos, P J
2003-01-01
Quantum Field Theory (QFT) makes predictions by combining two sets of assumptions: (1) quantum dynamics, such as a Schrodinger or Liouville equation; (2) quantum measurement, such as stochastic collapse to an eigenfunction of a measurement operator. A previous paper defined a classical density matrix R encoding the statistical moments of an ensemble of states of classical second-order Hamiltonian field theory. It proved Tr(RQ)=E(Q), etc., for the usual field operators as defined by Weinberg, and it proved that those observables of the classical system obey the usual Heisenberg dynamic equation. However, R itself obeys dynamics different from the usual Liouville equation! This paper derives those dynamics, and calculates the discrepancy between CFT and normal form QFT in predicting general observables g(Q,P). There is some preliminary evidence for the conjecture that the discrepancies disappear in equilibrium states (bound states and scattering states) for finite bosonic field theories. Even if not, they appea...
Multiscale Reactive Molecular Dynamics
2012-08-15
as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP
Khrennikov, Andrei
2011-03-01
The idea that quantum randomness can be reduced to randomness of classical fields (fluctuating at time and space scales which are essentially finer than scales approachable in modern quantum experiments) is rather old. Various models have been proposed, e.g., stochastic electrodynamics or the semiclassical model. Recently a new model, so called prequantum classical statistical field theory (PCSFT), was developed. By this model a "quantum system" is just a label for (so to say "prequantum") classical random field. Quantum averages can be represented as classical field averages. Correlations between observables on subsystems of a composite system can be as well represented as classical correlations. In particular, it can be done for entangled systems. Creation of such classical field representation demystifies quantum entanglement. In this paper we show that quantum dynamics (given by Schrödinger's equation) of entangled systems can be represented as the stochastic dynamics of classical random fields. The "effect of entanglement" is produced by classical correlations which were present at the initial moment of time, cf. views of Albert Einstein.
Molecular dynamics simulation of pyridine
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
Rapid learning dynamics in individual honeybees during classical conditioning
Directory of Open Access Journals (Sweden)
Evren ePamir
2014-09-01
Full Text Available Associative learning in insects has been studied extensively by a multitude of classical conditioning protocols. However, so far little emphasis has been put on the dynamics of learning in individuals. The honeybee is a well-established animal model for learning and memory. We here studied associative learning as expressed in individual behavior based on a large collection of data on olfactory classical conditioning (25 datasets, 3,298 animals. We show that the group-averaged learning curve and memory retention score confound three attributes of individual learning: the ability or inability to learn a given task, the generally fast acquisition of a conditioned response in learners, and the high stability of the conditioned response during consecutive training and memory retention trials. We reassessed the prevailing view that more training results in better memory performance and found that 24h memory retention can be indistinguishable after single-trial and multiple-trial conditioning in individuals. We explain how inter-individual differences in learning can be accommodated within the Rescorla-Wagner theory of associative learning. In both data-analysis and modeling we demonstrate how the conflict between population-level and single-animal perspectives on learning and memory can be disentangled.
A course in mathematical physics 1 and 2 classical dynamical systems and classical field theory
Thirring, Walter
1992-01-01
The last decade has seen a considerable renaissance in the realm of classical dynamical systems, and many things that may have appeared mathematically overly sophisticated at the time of the first appearance of this textbook have since become the everyday tools of working physicists. This new edition is intended to take this development into account. I have also tried to make the book more readable and to eradicate errors. Since the first edition already contained plenty of material for a one semester course, new material was added only when some of the original could be dropped or simplified. Even so, it was necessary to expand the chap ter with the proof of the K-A-M Theorem to make allowances for the cur rent trend in physics. This involved not only the use of more refined mathe matical tools, but also a reevaluation of the word "fundamental. " What was earlier dismissed as a grubby calculation is now seen as the consequence of a deep principle. Even Kepler's laws, which determine the radii of the ...
Particle physics and dark energy. Beyond classical dynamics
Energy Technology Data Exchange (ETDEWEB)
Garny, Mathias
2008-10-24
In this work, quantum corrections to classical equations of motion are investigated for dynamical models of dark energy featuring a time-evolving quintessence scalar field. Employing effective quantum field theory, the robustness of tracker quintessence potentials against quantum corrections as well as their impact on cosmological observables are discussed. Furthermore, it is demonstrated that a rolling quintessence field can also play an important role for baryogenesis in the early universe. The macroscopic time-evolution of scalar quantum fields can be described from first principles within nonequilibrium quantum field theory based on Kadanoff-Baym equations derived from the 2PI effective action. A framework for the nonperturbative renormalization of Kadanoff-Baym equations is provided. Renormalized Kadanoff-Baym equations are proposed and their finiteness is shown for a special case. (orig.)
Classical and quantum particle dynamics in univariate background fields
Heinzl, Thomas; King, Ben
2016-01-01
We investigate deviations from the plane wave model in the interaction of charged particles with strong electromagnetic fields. A general result is that integrability of the dynamics is lost when going from lightlike to timelike or spacelike field dependence. For a special scenario in the classical regime we show how the radiation spectrum in the spacelike (undulator) case becomes well-approximated by the plane wave model in the high energy limit, despite the two systems being Lorentz inequivalent. In the quantum problem, there is no analogue of the WKB-exact Volkov solution. Nevertheless, WKB and uniform-WKB approaches give good approximations in all cases considered. Other approaches that reduce the underlying differential equations from second to first order are found to miss the correct physics for situations corresponding to barrier transmission and wide-angle scattering.
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Optical dynamics of molecular aggregates
de Boer, Steven
2006-01-01
The subject of this thesis is the spectroscopy and dynamics of molecular aggregates in amorphous matrices. Aggregates of three different molecules were studied. The molecules are depicted in Fig. (1.1). Supersaturated solutions of these molecules show aggregate formation. Aggregation is a process si
A classical reactive potential for molecular clusters of sulphuric acid and water
Stinson, Jake L; Ford, Ian J
2016-01-01
We present a two-state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent.
Classical and quantum analysis of a hetero-triatomic molecular Bose-Einstein condensate model
Energy Technology Data Exchange (ETDEWEB)
Tonel, A.P. [CCET da Universidade Federal do Pampa/Unipampa, Bag´e, RS (Brazil); Kuhn, C.C.N.; Foerster, A. [Instituto de F´ısica da UFRGS, Porto Alegre, RS (Brazil); Santos, G. [Departamento de Físi a - UFS, São Cristóvão, SE (Brazil); Roditi, I.; Santos, Z.V.T. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)
2014-11-15
We investigate an integrable Hamiltonian modelling a hetero-triatomic-molecular Bose-Einstein condensate. This model describes a mixture of two species of atoms in different proportions, which can combine to form a triatomic molecule. Beginning with a classical analysis, we determine the fixed points of the system. Bifurcations of these points separate the parameter space into different regions. Three distinct scenarios are found, varying with the atomic population imbalance. This result suggests the ground state properties of the quantum model exhibits a sensitivity on the atomic population imbalance, which is confirmed by a quantum analysis using different approaches, such as the ground-state expectation values, the behaviour of the quantum dynamics, the energy gap and the ground state fidelity. (author)
Surface hopping methodology in laser-driven molecular dynamics
Fiedlschuster, T; Gross, E K U; Schmidt, R
2016-01-01
A theoretical justification of the empirical surface hopping method for the laser-driven molecular dynamics is given utilizing the formalism of the exact factorization of the molecular wavefunction [Abedi et al., PRL $\\textbf{105}$, 123002 (2010)] in its quantum-classical limit. Employing an exactly solvable $\\textrm H_2^{\\;+}$-like model system, it is shown that the deterministic classical nuclear motion on a single time-dependent surface in this approach describes the same physics as stochastic (hopping-induced) motion on several surfaces, provided Floquet surfaces are applied. Both quantum-classical methods do describe reasonably well the exact nuclear wavepacket dynamics for extremely different dissociation scenarios. Hopping schemes using Born-Oppenheimer surfaces or instantaneous Born-Oppenheimer surfaces fail completely.
Grand canonical Molecular Dynamics Simulations
Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K
2011-01-01
For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.
Energy Technology Data Exchange (ETDEWEB)
Amokrane, S.; Ayadim, A.; Levrel, L. [Groupe “Physique des Liquides et Milieux Complexes,” Faculté des Sciences et Technologie, Université Paris-Est (Créteil), 61 av. du Général de Gaulle, 94010 Créteil Cedex (France)
2015-11-21
We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.
Mithen, James P; Gregori, G
2011-01-01
The complementarity of the liquid and plasma descriptions of the classical one-component plasma (OCP) is explored by studying wavevector and frequency dependent dynamical quantities: the dynamical structure factor (DSF), and the dynamic local field correction (LFC). Accurate Molecular Dynamics (MD) simulations are used to validate/test models of the DSF and LFC. Our simulations, which span the entire fluid regime ($\\Gamma = 0.1 - 175$), show that the DSF is very well represented by a simple and well known memory function model of generalized hydrodynamics. On the other hand, the LFC, which we have computed using MD for the first time, is not well described by existing models.
Molecular dynamics in high electric fields
Apostol, M.; Cune, L. C.
2016-06-01
Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called "dipolons"); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.
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)
Revisiting a Classic Study of the Molecular Clock.
Robinson, Lauren M; Boland, Joseph R; Braverman, John M
2016-03-01
A constant rate of molecular evolution among homologous proteins and across lineages is known as the molecular clock. This concept has been useful for estimating divergence times. Here, we revisit a study by Richard Dickerson (J Mol Evol 1:26-45, 1971), wherein he provided striking visual evidence for a constant rate of amino acid changes among various evolutionary branch points. Dickerson's study is commonly cited as support of the molecular clock and a figure from it is often reproduced in textbooks. Since its publication, however, there have been updates made to dates of common ancestors based on the fossil record that should be considered. Additionally, collecting the accession numbers and carefully outlining Dickerson's methods serves as a resource to students of the molecular clock hypothesis.
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
Available Instruments for Analyzing Molecular Dynamics Trajectories.
Likhachev, I V; Balabaev, N K; Galzitskaya, O V
2016-01-01
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed.
Mixed quantum-classical dynamics for charge transport in organics.
Wang, Linjun; Prezhdo, Oleg V; Beljonne, David
2015-05-21
Charge transport plays a crucial role in the working principle of most opto-electronic and energy devices. This is especially true for organic materials where the first theoretical models date back to the 1950s and have continuously evolved ever since. Most of these descriptions rely on perturbation theory to treat small interactions in the Hamiltonian. In particular, applying a perturbative treatment to the electron-phonon and electron-electron coupling results in the band and hopping models, respectively, the signature of which is conveyed by a characteristic temperature dependence of mobility. This perspective describes recent progress of studying charge transport in organics using mixed quantum-classical dynamics techniques, including mean field and surface hopping theories. The studies go beyond the perturbation treatments and represent the processes explicitly in the time-domain, as they occur in real life. The challenges, advantages, and disadvantages of both approaches are systematically discussed. Special focus is dedicated to the temperature dependence of mobility, the role of local and nonlocal electron-phonon couplings, as well as the interplay between electronic and electron-phonon interactions.
Dynamical Non-Equilibrium Molecular Dynamics
Directory of Open Access Journals (Sweden)
Giovanni Ciccotti
2013-12-01
Full Text Available In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD, which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from the problem of sampling the initial condition. D-NEMD provides the theoretical framework to compute time-dependent macroscopic dynamical behaviors by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions generated from a suitable (equilibrium or non-equilibrium distribution at time zero. We also discuss how to generate a large class of initial distributions. The same approach applies also to the calculation of the rate constants of activated processes. The range of problems treatable by this method is illustrated by discussing applications to a few key hydrodynamic processes (the “classical” flow under shear, the formation of convective cells and the relaxation of an interface between two immiscible liquids.
Generating shortcuts to adiabaticity in quantum and classical dynamics
Jarzynski, Christopher
2013-01-01
Transitionless quantum driving achieves adiabatic evolution in a hurry, using a counter-diabatic Hamiltonian to stifle non-adiabatic transitions. Here this strategy is cast in terms of a generator of adiabatic transport, leading to a classical analogue: dissipationless classical driving. For the single-particle piston, this approach yields simple and exact expressions for both the classical and quantal counter-diabatic terms. These results are further generalized to even-power-law potentials in one degree of freedom.
Molecular Dynamics for Dense Matter
Maruyama, Toshiki; Chiba, Satoshi
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...
DMS: A Package for Multiscale Molecular Dynamics
Somogyi, Endre; Ortoleva, Peter J
2013-01-01
Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables...
Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-01-01
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and
Rheology via nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.
Construction of exact complex dynamical invariant of a two-dimensional classical system
Indian Academy of Sciences (India)
Fakir Chand; S C Mishra
2006-12-01
We present the construction of exact complex dynamical invariant of a two-dimensional classical dynamical system on an extended complex space utilizing Lie algebraic approach. These invariants are expected to play a vital role in understanding the complex trajectories of both classical and quantum systems.
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.
Comparison of quantum and classical relaxation in spin dynamics.
Wieser, R
2013-04-01
The classical Landau-Lifshitz equation with a damping term has been derived from the time evolution of a quantum mechanical wave function under the assumption of a non-Hermitian Hamilton operator. Further, the trajectory of a classical spin (S) has been compared with the expectation value of the spin operator (Ŝ). A good agreement between classical and quantum mechanical trajectories can be found for Hamiltonians linear in Ŝ or S, respectively. Quadratic or higher order terms in the Hamiltonian result in a disagreement.
Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture
Directory of Open Access Journals (Sweden)
Wei Feng
2014-07-01
Full Text Available Mixed-quantum-classical molecular dynamics simulation implies an effective quantum measurement on the electronic states by the classical motion of atoms. Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.
DNA as a Model for Probing Polymer Entanglements: Circular Polymers and Non-Classical Dynamics
Directory of Open Access Journals (Sweden)
Kathryn Regan
2016-09-01
Full Text Available Double-stranded DNA offers a robust platform for investigating fundamental questions regarding the dynamics of entangled polymer solutions. The exceptional monodispersity and multiple naturally occurring topologies of DNA, as well as a wide range of tunable lengths and concentrations that encompass the entanglement regime, enable direct testing of molecular-level entanglement theories and corresponding scaling laws. DNA is also amenable to a wide range of techniques from passive to nonlinear measurements and from single-molecule to bulk macroscopic experiments. Over the past two decades, researchers have developed methods to directly visualize and manipulate single entangled DNA molecules in steady-state and stressed conditions using fluorescence microscopy, particle tracking and optical tweezers. Developments in microfluidics, microrheology and bulk rheology have also enabled characterization of the viscoelastic response of entangled DNA from molecular levels to macroscopic scales and over timescales that span from linear to nonlinear regimes. Experiments using DNA have uniquely elucidated the debated entanglement properties of circular polymers and blends of linear and circular polymers. Experiments have also revealed important lengthscale and timescale dependent entanglement dynamics not predicted by classical tube models, both validating and refuting new proposed extensions and alternatives to tube theory and motivating further theoretical work to describe the rich dynamics exhibited in entangled polymer systems.
Shaping mitotic chromosomes: From classical concepts to molecular mechanisms.
Kschonsak, Marc; Haering, Christian H
2015-07-01
How eukaryotic genomes are packaged into compact cylindrical chromosomes in preparation for cell divisions has remained one of the major unsolved questions of cell biology. Novel approaches to study the topology of DNA helices inside the nuclei of intact cells, paired with computational modeling and precise biomechanical measurements of isolated chromosomes, have advanced our understanding of mitotic chromosome architecture. In this Review Essay, we discuss - in light of these recent insights - the role of chromatin architecture and the functions and possible mechanisms of SMC protein complexes and other molecular machines in the formation of mitotic chromosomes. Based on the information available, we propose a stepwise model of mitotic chromosome condensation that envisions the sequential generation of intra-chromosomal linkages by condensin complexes in the context of cohesin-mediated inter-chromosomal linkages, assisted by topoisomerase II. The described scenario results in rod-shaped metaphase chromosomes ready for their segregation to the cell poles.
Hu, Zixuan; Ratner, Mark A; Seideman, Tamar
2014-12-14
We develop a numerical approach for simulating light-induced charge transport dynamics across a metal-molecule-metal conductance junction. The finite-difference time-domain method is used to simulate the plasmonic response of the metal structures. The Huygens subgridding technique, as adapted to Lorentz media, is used to bridge the vastly disparate length scales of the plasmonic metal electrodes and the molecular system, maintaining accuracy. The charge and current densities calculated with classical electrodynamics are transformed to an electronic wavefunction, which is then propagated through the molecular linker via the Heisenberg equations of motion. We focus mainly on development of the theory and exemplify our approach by a numerical illustration of a simple system consisting of two silver cylinders bridged by a three-site molecular linker. The electronic subsystem exhibits fascinating light driven dynamics, wherein the charge density oscillates at the driving optical frequency, exhibiting also the natural system timescales, and a resonance phenomenon leads to strong conductance enhancement.
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
A Formulation of the Ring Polymer Molecular Dynamics
Horikoshi, Atsushi
2014-01-01
The exact formulation of the path integral centroid dynamics is extended to include composites of the position and momentum operators. We present the generalized centroid dynamics (GCD), which provides a basis to calculate Kubo-transformed correlation functions by means of classical averages. We define various types of approximate GCD, one of which is equivalent to the ring polymer molecular dynamics (RPMD). The RPMD and another approximate GCD are tested in one-dimensional harmonic system, and it is shown that the RPMD works better in the short time region.
Spin Dynamics simulations of the dynamic properties of classical models for magnetic materials
Bunker, Alex; Landau, D. P.
1998-03-01
The Spin Dynamics simulation technique, which has had considerable success for the study of critical properties of classical Heisenberg antiferromagnets(A. Bunker, K. Chen, and D. P. Landau Phys. Rev. B) \\underline54, 9259 (1996), has been used to determine more general properties for a wider range of materials. A general spin dynamics program has been developed which can determine the dynamic structure factor, S(q,ω), in the [100], [110], and [111] directions for a wide range of classical magnetic models at any temperature desired. We have simulated the magnetic dynamics in the ordered phase of the isotropic Heisenberg model with both ferromagnetic and antiferromagnetic coupling on L×L×L BCC and SC lattices. Outside of the critical regime relatively small lattice sizes of L = 12, 24 could be used. From our simulation we have determined the stiffness coefficient and the spin relaxation rate which were compared to both experimental(J. Als-Nielsen in Phase Transitions and Critical Phenomena), ed. C. Domb, M. S. Green, Academic Press, (1976) and theoretical results. We have performed the same simulation with anisotropy appropriate for MnF2 and FeF_2. Research supported in part by the NSF
Boltzmann-conserving classical dynamics in quantum time-correlation functions: Matsubara dynamics
Hele, Timothy J H; Muolo, Andrea; Althorpe, Stuart C
2015-01-01
We show that a single change in the derivation of the linearized semiclassical-initial value representation (LSC-IVR or classical Wigner approximation) results in a classical dynamics which conserves the quantum Boltzmann distribution. We rederive the (standard) LSC-IVR approach by writing the (exact) quantum time-correlation function in terms of the normal modes of a free ring-polymer (i.e. a discrete imaginary-time Feynman path), taking the limit that the number of polymer beads $N \\to \\infty$, such that the lowest normal-mode frequencies take their Matsubara values. The change we propose is to truncate the quantum Liouvillian, not explicitly in powers of $\\hbar^2$ at $\\hbar^0$ (which gives back the standard LSC-IVR approximation), but in the normal-mode derivatives corresponding to the lowest Matsubara frequencies. The resulting Matsubara dynamics is inherently classical (since all terms $\\mathcal{O}\\left(\\hbar^{2}\\right)$ disappear from the Matsubara Liouvillian in the limit $N \\to \\infty$), and conserves...
Classical and quantum dynamics in an inverse square potential
Energy Technology Data Exchange (ETDEWEB)
Guillaumín-España, Elisa, E-mail: ege@correo.azc.uam.mx [Laboratorio de Sistemas Dinámicos, Departamento de Ciencias Básicas, Universidad Autónoma Metropolitana, Unidad Azcapotzalco, Azcapotzalco CP 02200 D. F. (Mexico); Núñez-Yépez, H. N., E-mail: nyhn@xanum.uam.mx [Departamento de Física, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Apartado Postal 55-534, Iztapalapa CP 09340 D. F. (Mexico); Salas-Brito, A. L., E-mail: asb@correo.azc.uam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México (ICN-UNAM), Apartado Postal 70-543, 04510 México D F (Mexico)
2014-10-15
The classical motion of a particle in a 3D inverse square potential with negative energy, E, is shown to be geodesic, i.e., equivalent to the particle's free motion on a non-compact phase space manifold irrespective of the sign of the coupling constant. We thus establish that all its classical orbits with E < 0 are unbounded. To analyse the corresponding quantum problem, the Schrödinger equation is solved in momentum space. No discrete energy levels exist in the unrenormalized case and the system shows a complete “fall-to-the-center” with an energy spectrum unbounded by below. Such behavior corresponds to the non-existence of bound classical orbits. The symmetry of the problem is SO(3) × SO(2, 1) corroborating previously obtained results.
Energy Technology Data Exchange (ETDEWEB)
Megow, Jörg, E-mail: megow@physik.hu-berlin.de; May, Volkhard, E-mail: may@physik.hu-berlin.de
2014-01-15
Highlights: • Enhancement of molecular absorption was shown for J-aggregate-like coupling between molecules and MNP. • A large number of molecules is required in order to observe the molecular absorption. • Pheos Qx-band coupling to the plasmon resonance is hardly observable in the spectrum. - Abstract: The application of a mixed quantum–classical methodology for an investigation of single pheophorbide-a molecules (Pheos) and respective supramolecular complexes is continued to effects caused by a nearby placed metal nanoparticle (MNP). Therefore, the classical simulation of the molecular nuclear degrees of freedom is combined with a uniform quantum description of the molecular electronic excitations coupled to those of the MNP. To account for the short MNP plasmon life time the quantum dynamics of the electronic degrees of freedom is formulated in the framework of a system-bath theory. Linear absorption spectra are calculated for a spherical 14 nm diameter Au–MNP decorated with isolated Pheos or with P{sub 16} complexes formed by 16 Pheos. The spectra are analyzed with respect to the molecular orientation at the MNP surface. While all studies on P{sub 16} only account for the Pheo Q{sub y}-transition we also present data on the MNP induced change of the single Pheo Q{sub x}-absorption.
Popa, Alexandru
2013-01-01
Applications of Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamical Systems is a reference on the new field of relativistic optics, examining topics related to relativistic interactions between very intense laser beams and particles. Based on 30 years of research, this unique book connects the properties of quantum equations to corresponding classical equations used to calculate the energetic values and the symmetry properties of atomic, molecular and electrodynamical systems. In addition, it examines applications for these methods, and for the calculation of
Spin dynamics of an ultra-small nanoscale molecular magnet
Directory of Open Access Journals (Sweden)
Ciftja Orion
2007-01-01
Full Text Available AbstractWe present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high Heisenberg spins. We derive exact analytic expressions (in integral form for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail.
Osmosis : a molecular dynamics computer simulation study
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Molecular Dynamics and Picosecond Vibrational Spectra.
1980-07-01
and Identify by block number) molecular dynamics picosecond infra-red spectra crmputer simulation vibrational spectra array processor linear rcsponse...that for molecular dynamics theoretical computation is now long enough, to significantly overlap. This overlap of theory and experiment can, at least...to discover these microscopic atomic trajectories, i.e. the molecular dynamics of solution processes, we must be able to both theoretically compute
Molecular Dynamics in the Vacuum Ultraviolet
1989-01-30
CLASSIFICATION OF THIS PAGE COMPLETED PROJECT SUMMARY TITLE: Molecular dynamics in the Vacuum Ultraviolet PRINCIPAL INVESTIGATOR: Paul L. Houston...DTIC TAB 0 Unannounced 0 By Distr ibution I Availability Codes Avail and I or Dist Special I Molecular Dynamics In the Vacuum Ultraviolet Final Technical...Further development of tunable vacuum ultraviolet sources has opened wide areas of molecular dynamics for study. Completed Research Photodissociation of
Brownian motion from molecular dynamics
Shin, Hyun Kyung; Talkner, Peter; Lee, Eok Kyun
2010-01-01
Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force which enter the generalized Langevin equation of the Brownian particle are determined and their dependence on mass and diameter are investigated for two different fluid densities. Deviations of the fluctuating force distribution from a Gaussian form are observed for small particle diameters. For heavy particles the deviations of the fluctuating force from the total force acting on the Brownian particle decrease linearly with the mass ratio m/M where m denotes the mass of a fluid particle.
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 Mole...
Programming an Interpreter Using Molecular Dynamics
Directory of Open Access Journals (Sweden)
C.A. Middelburg
2007-01-01
Full Text Available PGA (ProGram Algebra is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.
A classical reactive potential for molecular clusters of sulphuric acid and water
Energy Technology Data Exchange (ETDEWEB)
Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.
2015-10-12
We present a two state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent. SMK was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; JLS and IJF were supported by the IMPACT scheme at University College London (UCL). We acknowledge the UCL Legion High Performance Computing Facility, and associated support services together with the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy under Contract No. DE-AC02- 05CH11231. JLS thanks Dr. Gregory Schenter, Dr. Theo Kurtén and Prof. Hanna Vehkamäki for important guidance and discussions.
Dynamical analysis of highly excited molecular spectra
Energy Technology Data Exchange (ETDEWEB)
Kellman, M.E. [Univ. of Oregon, Eugene (United States)
1993-12-01
The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.
Institute of Scientific and Technical Information of China (English)
乔永芬; 张耀良; 韩广才
2002-01-01
In this paper, we present a general approach to the construction of conservation laws for generalized classical dynamical systems. Firstly, we give the definition of integrating factors and, secondly, we study in detail the necessary conditions for the existence of conserved quantities. Then we establish the conservation theorem and its inverse for the Hamilton's canonical equations of motion of holonomic nonconservative dynamical systems in generalized classical mechanics. Finally, we give an example to illustrate the application of the results.
Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ
DEFF Research Database (Denmark)
Euro, Liliya; Haapanen, Outi; Róg, Tomasz
2017-01-01
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...... 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...
Molecular dynamics simulations of bubble nucleation in dark matter detectors
Denzel, Philipp; Angélil, Raymond
2016-01-01
Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy di...
Exact Classical and Quantum Dynamics in Background Electromagnetic Fields
Heinzl, Tom; Ilderton, Anton
2017-03-01
Analytic results for (Q)ED processes in external fields are limited to a few special cases, such as plane waves. However, the strong focusing of intense laser fields implies a need to go beyond the plane wave model. By exploiting Poincaré symmetry and superintegrability we show how to construct, and solve without approximation, new models of laser-matter interactions. We illustrate the method with a model of a radially polarized (TM) laser beam, for which we exactly determine the classical orbits and quantum wave functions. Including in this way the effects of transverse field structure should improve predictions and analyses for experiments at intense laser facilities.
Quantum molecular dynamics simulations of dense matter
Energy Technology Data Exchange (ETDEWEB)
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Programming an interpreter using molecular dynamics
2008-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primari...
Programming an Interpreter Using Molecular Dynamics
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily...
Quantum and classical dynamics of reactive scattering of H2 from metal surfaces.
Kroes, Geert-Jan; Díaz, Cristina
2016-06-27
We review the state-of-the art in dynamics calculations on the reactive scattering of H2 from metal surfaces, which is an important model system of an elementary reaction that is relevant to heterogeneous catalysis. In many applications, quantum dynamics and classical trajectory calculations are performed within the Born-Oppenheimer static surface model. However, ab initio molecular dynamics (AIMD) is finding increased use in applications aimed at modeling the effect of surface phonons on the dynamics. Molecular dynamics with electronic friction has been used to model the effect of electron-hole pair excitation. Most applications are still based on potential energy surfaces (PESs) or forces computed with density functional theory (DFT), using a density functional within the generalized gradient approximation to the exchange-correlation energy. A new development is the use of a semi-empirical version of DFT (the specific reaction parameter (SRP) approach to DFT). We also discuss the accurate methods that have become available to represent electronic structure data for the molecule-surface interaction in global PESs. It has now become possible to describe highly activated H2 + metal surface reactions with chemical accuracy using the SRP-DFT approach, as has been shown for H2 + Cu(111) and Cu(100). However, chemical accuracy with SRP-DFT has yet to be demonstrated for weakly activated systems like H2 + Ru(0001) and non-activated systems like H2 + Pd(111), for which SRP DFs are not yet available. There is now considerable evidence that electron-hole pair (ehp) excitation does not need to be modeled to achieve the (chemically) accurate calculation of dissociative chemisorption and scattering probabilities. Dynamics calculations show that phonons can be safely neglected in the chemically accurate calculation of sticking probabilities on cold metal surfaces for activated systems, and in the calculation of a number of other observables. However, there is now sufficient
Classical black holes: the nonlinear dynamics of curved spacetime.
Thorne, Kip S
2012-08-03
Numerical simulations have revealed two types of physical structures, made from curved spacetime, that are attached to black holes: tendexes, which stretch or squeeze anything they encounter, and vortexes, which twist adjacent inertial frames relative to each other. When black holes collide, their tendexes and vortexes interact and oscillate (a form of nonlinear dynamics of curved spacetime). These oscillations generate gravitational waves, which can give kicks up to 4000 kilometers per second to the merged black hole. The gravitational waves encode details of the spacetime dynamics and will soon be observed and studied by the Laser Interferometer Gravitational Wave Observatory and its international partners.
Catalyst dynamics: consequences for classical kinetic descriptions of reactors
DEFF Research Database (Denmark)
Johannessen, Tue; Larsen, Jane Hvolbæk; Chorkendorff, Ib
2001-01-01
The modelling of catalytic reactions/reactors has undergone great improvements since the introduction of empirical power-law kinetics in chemical reaction engineering and micro-kinetic models based on insight into the nature of elementary steps have appeared for many reactions. However, recent...... of the dynamical behaviour of some catalytic systems and discuss the corresponding Limitations in existing models for catalytic reactions and reactors. Catalytic reactors operated in non-steady-state are becoming more frequent in industry. The additional efforts needed to accurately simulate these types...... of reactors are discussed. Finally, we discuss the role of computational fluid dynamics (CFD) as a tool for detailed simulation of catalytic reactors....
Quantum Trajectory Approach to Molecular Dynamics Simulation with Surface Hopping
Feng, Wei; Li, Xin-Qi; Fang, Weihai
2012-01-01
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic state. In this work we propose a quantum trajectory approach to the MD simulation with surface hopping, from an insight that an effective "observation" is actually implied in theMDsimulation through tracking the forces experienced, just like checking the meter's result in the quantum measurement process. This treatment can build the nonadiabatic surface hopping on a dynamical foundation, instead of the usual artificial and conceptually inconsistent hopping algorithms. The effects and advantages of the proposed scheme are preliminarily illustrated by a two-surface model system.
Hasegawa, Taisuke
2016-11-07
We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.
Hasegawa, Taisuke
2016-11-01
We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.
Combined molecular dynamics-spin dynamics simulations of bcc iron
Energy Technology Data Exchange (ETDEWEB)
Perera, Meewanage Dilina N [ORNL; Yin, Junqi [ORNL; Landau, David P [University of Georgia, Athens, GA; Nicholson, Don M [ORNL; Stocks, George Malcolm [ORNL; Eisenbach, Markus [ORNL; Brown, Greg [ORNL
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Chaotic Dynamics and Transport in Classical and Quantum Systems
Energy Technology Data Exchange (ETDEWEB)
NONE
2003-07-01
The aim of this summer school is to provide a set of extended and pedagogical lectures, on the major present-day topics in dynamical systems and statistical mechanics including applications. Some articles are dedicated to chaotic transport in plasma turbulence and to quantum chaos. This document gathers the summaries of some presentations.
Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture
Feng, Wei; Li, Xin-Qi; Fang, Weihai; Yan, YiJing
2013-01-01
Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.
Indian Academy of Sciences (India)
Aparna Saha; Bidhan Chandra Bag; Pranab Sarkar
2007-03-01
We present a numerical investigation of the tunneling dynamics of a particle moving in a bistable potential with fluctuating barrier which is coupled to a non-integrable classical system and study the interplay between classical chaos and barrier fluctuation in the tunneling dynamics. We found that the coupling of the quantum system with the classical subsystem decreases the tunneling rate irrespective of whether the classical subsystem is regular or chaotic and also irrespective of the fact that whether the barrier fluctuates or not. Presence of classical chaos always enhances the tunneling rate constant. The effect of barrier fluctuation on the tunneling rate in a mixed quantum-classical system is to suppress the tunneling rate. In contrast to the case of regular subsystem, the suppression arising due to barrier fluctuation is more visible when the subsystem is chaotic.
Wigner's dynamical transition state theory in phase space : classical and quantum
Waalkens, Holger; Schubert, Roman; Wiggins, Stephen
2008-01-01
We develop Wigner's approach to a dynamical transition state theory in phase space in both the classical and quantum mechanical settings. The key to our development is the construction of a normal form for describing the dynamics in the neighbourhood of a specific type of saddle point that governs t
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...
Quantum dynamics for classical systems with applications of the number operator
Bagarello, Fabio
2013-01-01
Mathematics is increasingly applied to classical problems in finance, biology, economics, and elsewhere. Quantum Dynamics for Classical Systems describes how quantum tools—the number operator in particular—can be used to create dynamical systems in which the variables are operator-valued functions and whose results explain the presented model. The book presents mathematical results and their applications to concrete systems and discusses the methods used, results obtained, and techniques developed for the proofs of the results. The central ideas of number operators are illuminated while avoiding excessive technicalities that are unnecessary for understanding and learning the various mathematical applications. The presented dynamical systems address a variety of contexts and offer clear analyses and explanations of concluded results. Additional features in Quantum Dynamics for Classical Systems include: Applications across diverse fields including stock markets and population migration as well as a uniqu...
Quantum-classical transition in the electron dynamics of thin metal films
Energy Technology Data Exchange (ETDEWEB)
Jasiak, R; Manfredi, G; Hervieux, P-A [Institut de Physique et Chimie des Materiaux, CNRS and Universite de Strasbourg, BP 43, F-67034 Strasbourg (France); Haefele, M [INRIA Nancy Grand-Est and Institut de Recherche en Mathematiques Avancees, 7 rue Rene Descartes, F-67084 Strasbourg (France)], E-mail: Giovanni.Manfredi@ipcms.u-strasbg.fr
2009-06-15
The quantum electrons dynamics in a thin metal film is studied numerically using the self-consistent Wigner-Poisson equations. The initial equilibrium is computed from the Kohn-Sham equations at finite temperature, and then mapped into the phase-space Wigner function. The time-dependent results are compared systematically with those obtained previously with a classical approach (Vlasov-Poisson equations). It is found that, for large excitations, the quantum and classical dynamics display the same low-frequency oscillations due to ballistic electrons bouncing back and forth on the film surfaces. However, below a certain excitation energy (roughly corresponding to one quantum of plasmon energy {Dirac_h}{omega}{sub p}), the quantum and classical results diverge, and the ballistic oscillations are no longer observed. These results provide an example of a quantum-classical transition that may be observed with current pump-probe experiments on thin metal films.
Langeveld, Jan P M; Jacobs, Jorg G; Erkens, Jo H F; Baron, Thierry; Andréoletti, Olivier; Yokoyama, Takahashi; van Keulen, Lucien J M; van Zijderveld, Fred G; Davidse, Aart; Hope, Jim; Tang, Yue; Bossers, Alex
2014-01-01
Efforts to differentiate bovine spongiform encephalopathy (BSE) from scrapie in prion infected sheep have resulted in effective methods to decide about the absence of BSE. In rare instances uncertainties remain due to assumptions that BSE, classical scrapie and CH1641-a rare scrapie variant-could occur as mixtures. In field samples including those from fallen stock, triplex Western blotting analyses of variations in the molecular properties of the proteinase K resistant part of the disease‑associated form of prion protein (PrP(res)) represents a powerful tool for quick discrimination purposes. In this study we examined 7 deviant ovine field cases of scrapie for some typical molecular aspects of PrP(res) found in CH1641‑scrapie, classical scrapie and BSE. One case was most close to scrapie with respect to molecular mass of its non-glycosylated fraction and N-terminally located 12B2‑epitope content. Two cases were unlike classical scrapie but too weak to differentiate between BSE or CH1641. The other 4 cases appeared intermediate between scrapie and CH1641 with a reduced molecular mass and 12B2‑epitope content, together with the characteristic presence of a second PrP(res) population. The existence of these 2 PrP(res) populations was further confirmed through deglycosylation by PNGaseF. The findings indicate that discriminatory diagnosis between classical scrapie, CH1641 and BSE can remain inconclusive with current biochemical methods. Whether such intermediate cases represent mixtures of TSE strains should be further investigated e.g. in bioassays with rodent lines that are varying in their susceptibility or other techniques suitable for strain typing.
Langeveld, Jan P. M.; Jacobs, Jorg G; Erkens, Jo H.F.; Baron, Thierry; Andreoletti, Olivier; Yokoyama, Takahashi; Van Keulen, Lucien J. M.; van Zijderveld, Fred G.; Davidse, Aart; Hope, Jim; Tang, Yue; Bossers, Alex
2014-01-01
Efforts to differentiate bovine spongiform encephalopathy (BSE) from scrapie in prion infected sheep have resulted in effective methods to decide about the absence of BSE. In rare instances uncertainties remain due to assumptions that BSE, classical scrapie and CH1641–a rare scrapie variant–could occur as mixtures. In field samples including those from fallen stock, triplex Western blotting analyses of variations in the molecular properties of the proteinase K resistant part of the disease‑as...
McCorvie, Thomas J; Kopec, Jolanta; Angel L Pey; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W.
2016-01-01
Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homod...
Quantum dynamics of bio-molecular systems in noisy environments
Plenio, M B
2012-01-01
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.
Popa, Alexandru
2013-01-01
Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamic Systems is intended for scientists and graduate students interested in the foundations of quantum mechanics and applied scientists interested in accurate atomic and molecular models. This is a reference to those working in the new field of relativistic optics, in topics related to relativistic interactions between very intense laser beams and particles, and is based on 30 years of research. The novelty of this work consists of accurate connections between the properties of quantum equations and correspon
On the classical dynamics of strongly driven anharmonic oscillators
Breuer, H. P.; Dietz, K.; Holthaus, M.
1990-12-01
We investigate the dynamics of periodically driven anharmonic oscillators. In particular, we consider values of the coupling strength which are orders of magnitude higher than those required for the overlap of primary resonances. We observe a division of phase space into a regular and a stochastic region. Both regions are separated by a sharp chaos border which sets an upper limit to the stochastic heating of particles; its dependence on the coupling strength is studied. We construct perpetual adiabatic invariants governing regular motion. A bifurcation mechanism leading to the annihilation of resonances is explained.
Quantum Dynamics in Classical Time Evolution of Correlation Functions
Wetterich, C
1997-01-01
The time-dependence of correlation functions under the influence of cla= ssical equations of motion is described by an exact evolution equation. For conservative systems thermodynamic equilibrium is a fixed point of these equations. We show that this fixed point is not universally stable, since infinitely many conserved correlation functions obstruct the approach to equilibrium. Equilibrium can therefore be reached at most for suitably av= eraged quantities or for subsystems, similar to quantum statistics. The classica= l time evolution of correlation functions shows many dynamical features of quant= um mechanics.
Entropic fluctuations in statistical mechanics: I. Classical dynamical systems
Jakšić, V.; Pillet, C.-A.; Rey-Bellet, L.
2011-03-01
Within the abstract framework of dynamical system theory we describe a general approach to the transient (or Evans-Searles) and steady state (or Gallavotti-Cohen) fluctuation theorems of non-equilibrium statistical mechanics. Our main objective is to display the minimal, model independent mathematical structure at work behind fluctuation theorems. In addition to its conceptual simplicity, another advantage of our approach is its natural extension to quantum statistical mechanics which will be presented in a companion paper. We shall discuss several examples including thermostated systems, open Hamiltonian systems, chaotic homeomorphisms of compact metric spaces and Anosov diffeomorphisms.
Entropic Fluctuations in Statistical Mechanics I. Classical Dynamical Systems
Jakšić, Vojkan; Rey-Bellet, Luc
2010-01-01
Within the abstract framework of dynamical system theory we describe a general approach to the Transient (or Evans-Searles) and Steady State (or Gallavotti-Cohen) Fluctuation Theorems of non-equilibrium statistical mechanics. Our main objective is to display the minimal, model independent mathematical structure at work behind fluctuation theorems. Besides its conceptual simplicity, another advantage of our approach is its natural extension to quantum statistical mechanics which will be presented in a companion paper. We shall discuss several examples including thermostated systems, open Hamiltonian systems, chaotic homeomorphisms of compact metric spaces and Anosov diffeomorphisms.
Note on classical string dynamics on AdS3
Bañados, Máximo; Ritz, Adam
1999-12-01
We consider bosonic strings propagating on Euclidean anti-de Sitter space (AdS3), and study in particular the realization of various worldsheet symmetries. We give a proper definition for the Brown-Henneaux asymptotic target space symmetry, when acting on the string action, and derive the Giveon-Kutasov-Seiberg worldsheet contour integral representation simply by using Noether's theorem. We show that making identifications in the target space is equivalent to the insertion of an (exponentiated) graviton vertex operator carrying the corresponding charge. Finally, we point out an interesting relation between 3D gravity and the dynamics of the worldsheet on AdS3. Both theories are described by an SL(2,C)/SU(2) Wess-Zumino-Witten (WZW) model, and we prove that the reduction conditions determined on one hand by worldsheet diffeomorphism invariance, and on the other by the Brown-Henneaux boundary conditions, are the same.
Hybrid simulation theory for a classical nonlinear dynamical system
Drazin, Paul L.; Govindjee, Sanjay
2017-03-01
Hybrid simulation is an experimental and computational technique which allows one to study the time evolution of a system by physically testing a subset of it while the remainder is represented by a numerical model that is attached to the physical portion via sensors and actuators. The technique allows one to study large or complicated mechanical systems while only requiring a subset of the complete system to be present in the laboratory. This results in vast cost savings as well as the ability to study systems that simply can not be tested due to scale. However, the errors that arise from splitting the system in two requires careful attention, if a valid simulation is to be guaranteed. To date, efforts to understand the theoretical limitations of hybrid simulation have been restricted to linear dynamical systems. In this work we consider the behavior of hybrid simulation when applied to nonlinear dynamical systems. As a model problem, we focus on the damped, harmonically-driven nonlinear pendulum. This system offers complex nonlinear characteristics, in particular periodic and chaotic motions. We are able to show that the application of hybrid simulation to nonlinear systems requires a careful understanding of what one expects from such an experiment. In particular, when system response is chaotic we advocate the need for the use of multiple metrics to characterize the difference between two chaotic systems via Lyapunov exponents and Lyapunov dimensions, as well as correlation exponents. When system response is periodic we advocate the use of L2 norms. Further, we are able to show that hybrid simulation can falsely predict chaotic or periodic response when the true system has the opposite characteristic. In certain cases, we are able to show that control system parameters can mitigate this issue.
Control of quantum localization and classical diffusion in laser-kicked molecular rotors
Bitter, M.; Milner, V.
2017-01-01
We experimentally study a system of quantum kicked rotors—an ensemble of diatomic molecules exposed to a periodic sequence of ultrashort laser pulses. In the regime where the underlying classical dynamics is chaotic, we investigate the quantum phenomenon of dynamical localization by means of state-resolved coherent Raman spectroscopy. We examine the dependence of the exponentially localized angular momentum distribution and of the total rotational energy on the time period between the pulses and their amplitude. The former parameter is shown to provide control over the localization center, whereas the latter one controls the localization length. Similar control of the center and width of a nonlocalized rotational distribution is demonstrated in the limit of classical diffusion, established by adding noise to the periodic pulse sequence.
Dynamical processes in atomic and molecular physics
Ogurtsov, Gennadi
2012-01-01
Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece
Surface hopping from the perspective of quantum-classical Liouville dynamics
Kapral, Raymond
2016-01-01
Fewest-switches surface hopping is studied in the context of quantum-classical Liouville dynamics. Both approaches are mixed quantum-classical theories that provide a way to describe and simulate the nonadiabatic quantum dynamics of many-body systems. Starting from a surface-hopping solution of the quantum-classical Liouville equation, it is shown how fewest-switches dynamics can be obtained by dropping terms that are responsible for decoherence and restricting the nuclear momentum changes that accompany electronic transitions to those events that occur between population states. The analysis provides information on some of the elements that are essential for the construction of accurate and computationally tractable algorithms for nonadiabatic processes.
Frank, Irmgard
2016-01-01
The notion from ab-initio molecular dynamics simulations that nuclear motion is best described by classical Newton dynamics instead of the time-dependent Schr{\\"o}dinger equation is substantiated. In principle a single experiment should bring clarity. Caution is however necessary, as temperature dependent effects must be eliminated when trying to determine the existence of a zero-point energy.
Triangleland. I. Classical dynamics with exchange of relative angular momentum
Anderson, Edward
2008-01-01
In Euclidean relational particle mechanics, only relative times, relative angles and relative separations are meaningful. Barbour-Bertotti (1982) theory is of this form and constitutes a recovery of a portion of Newtonian mechanics from relational premises. This is of interest in the absolute versus relative motion debate and also shares a number of features with the geometrodynamical formulation of general relativity, making it suitable for some modelling of the problem of time in quantum gravity. I also study similarity relational particle mechanics (`dynamics of pure shape'), in which only relative times, relative angles and ratios of relative separations are meaningful. This I consider firstly as it is simpler, particularly in 1 and 2 d, for which the configuration space geometry turns out to be well-known, e.g. S^2 for the `triangleland' (3-particle) case considered in detail. Secondly, the similarity model occurs as a submodel within the Euclidean model: that admits a shape-scale split. For harmonic osc...
Dynamical simulations of classical stochastic systems using matrix product states.
Johnson, T H; Clark, S R; Jaksch, D
2010-09-01
We adapt the time-evolving block decimation (TEBD) algorithm, originally devised to simulate the dynamics of one-dimensional quantum systems, to simulate the time evolution of nonequilibrium stochastic systems. We describe this method in detail; a system's probability distribution is represented by a matrix product state (MPS) of finite dimension and then its time evolution is efficiently simulated by repeatedly updating and approximately refactorizing this representation. We examine the use of MPS as an approximation method, looking at parallels between the interpretations of applying it to quantum state vectors and probability distributions. In the context of stochastic systems we consider two types of factorization for use in the TEBD algorithm: non-negative matrix factorization (NMF), which ensures that the approximate probability distribution is manifestly non-negative, and the singular value decomposition (SVD). Comparing these factorizations, we find the accuracy of the SVD to be substantially greater than current NMF algorithms. We then apply TEBD to simulate the totally asymmetric simple exclusion process (TASEP) for systems of up to hundreds of lattice sites in size. Using exact analytic results for the TASEP steady state, we find that TEBD reproduces this state such that the error in calculating expectation values can be made negligible even when severely compressing the description of the system by restricting the dimension of the MPS to be very small. Out of the steady state we show for specific observables that expectation values converge as the dimension of the MPS is increased to a moderate size.
Perspective: Quantum or classical coherence?
Miller, William H
2012-06-07
Some coherence effects in chemical dynamics are described correctly by classical mechanics, while others only appear in a quantum treatment--and when these are observed experimentally it is not always immediately obvious whether their origin is classical or quantum. Semiclassical theory provides a systematic way of adding quantum coherence to classical molecular dynamics and thus provides a useful way to distinguish between classical and quantum coherence. Several examples are discussed which illustrate both cases. Particularly interesting is the situation with electronically non-adiabatic processes, where sometimes whether the coherence effects are classical or quantum depends on what specific aspects of the process are observed.
Horsch, Martin T; Vrabec, Jadran; Glass, Colin W; Niethammer, Christoph; Bernreuther, Martin F; Müller, Erich A; Jackson, George
2011-01-01
Curved fluid interfaces are investigated on the nanometre length scale by molecular dynamics simulation. Thereby, droplets surrounded by a metastable vapour phase are stabilized in the canonical ensemble. Analogous simulations are conducted for cylindrical menisci separating vapour and liquid phases under confinement in planar nanopores. Regarding the emergence of nanodroplets during nucleation, a non-equilibrium phenomenon, both the non-steady dynamics of condensation processes and stationary quantities related to supersaturated vapours are considered. Results for the truncated and shifted Lennard-Jones fluid and for mixtures of quadrupolar fluids confirm the applicability of the capillarity approximation and the classical nucleation theory.
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programmi
A thread calculus with molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2010-01-01
We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact with services of which the states consist o
Molecular dynamics studies of entangled polymer chains
Bulacu, Monica Iulia
2008-01-01
The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a
Molecular Dynamics Studies of Matrix Metalloproteases.
Díaz, Natalia; Suárez, Dimas
2017-01-01
Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.
Markovian and non-Markovian dynamics in quantum and classical systems
Vacchini, Bassano; Laine, Elsi-Mari; Piilo, Jyrki; Breuer, Heinz-Peter
2011-01-01
We discuss the conceptually different definitions used for the non-Markovianity of classical and quantum processes. The well-established definition for non-Markovianity of a classical stochastic process represents a condition on the Kolmogorov hierarchy of the n-point joint probability distributions. Since this definition cannot be transferred to the quantum regime, quantum non-Markovianity has recently been defined and quantified in terms of the underlying quantum dynamical map, using either its divisibility properties or the behavior of the trace distance between pairs of initial states. Here, we investigate and compare these definitions and their relations to the classical notion of non-Markovianity by employing a large class of non-Markovian processes, known as semi-Markov processes, which admit a natural extension to the quantum case. A number of specific physical examples is constructed which allow to study the basic features of the classical and the quantum definitions and to evaluate explicitly the me...
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.
Molecular dynamics simulation: A tool for exploration and discovery
Rapaport, Dennis C.
2009-03-01
The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).
On classical and quantum dynamics of tachyon-like fields and their cosmological implications
Energy Technology Data Exchange (ETDEWEB)
Dimitrijević, Dragoljub D., E-mail: ddrag@pmf.ni.ac.rs; Djordjević, Goran S., E-mail: ddrag@pmf.ni.ac.rs; Milošević, Milan, E-mail: ddrag@pmf.ni.ac.rs [Department of Physics, Faculty of Science and Mathematics, University of Niš (Serbia); Vulcanov, Dumitru [Faculty of Physics, West University of Timisoara (Romania)
2014-11-24
We consider a class of tachyon-like potentials, motivated by string theory, D-brane dynamics and inflation theory in the context of classical and quantum mechanics. A formalism for describing dynamics of tachyon fields in spatially homogenous and one-dimensional - classical and quantum mechanical limit is proposed. A few models with concrete potentials are considered. Additionally, possibilities for p-adic and adelic generalization of these models are discussed. Classical actions and corresponding quantum propagators, in the Feynman path integral approach, are calculated in a form invariant on a change of the background number fields, i.e. on both archimedean and nonarchimedean spaces. Looking for a quantum origin of inflation, relevance of p-adic and adelic generalizations are briefly discussed.
Analytical Solution of Nonlinear Problems in Classical Dynamics by Means of Lagrange-Ham
DEFF Research Database (Denmark)
Kimiaeifar, Amin; Mahdavi, S. H; Rabbani, A.
2011-01-01
In this work, a powerful analytical method, called Homotopy Analysis Methods (HAM) is coupled with Lagrange method to obtain the exact solution for nonlinear problems in classic dynamics. In this work, the governing equations are obtained by using Lagrange method, and then the nonlinear governing...
Random Matrix Theory in molecular dynamics analysis.
Palese, Luigi Leonardo
2015-01-01
It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.
Energy Technology Data Exchange (ETDEWEB)
Draeger, E W; Bennion, B; Gygi, F; Lightstone, F
2006-02-10
The reaction mechanism of the human P450 CYP1A2 enzyme plays a fundamental role in understanding the effects of environmental carcinogens and mutagens on humans. Despite extensive experimental research on this enzyme system, key questions regarding its catalytic cycle and oxygen activation mechanism remain unanswered. In order to elucidate the reaction mechanism in human P450, new computational methods are needed to accurately represent this system. To enable us to perform computational simulations of unprecedented accuracy on these systems, we developed a dynamic quantum-classical (QM/MM) hybrid method, in which ab initio molecular dynamics are coupled with classical molecular mechanics. This will provide the accuracy needed to address such a complex, large biological system in a fully dynamic environment. We also present detailed calculations of the P450 active site, including the relative charge transfer between iron porphine and tetraphenyl porphyrin.
Exciton dynamics in molecular aggregates
Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A
2006-01-01
The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the characteri
Ishiyama, Tatsuya; Takahashi, Hideaki; Morita, Akihiro
2012-03-28
A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.
Quantum–classical correspondence in chaotic dynamics of laser-driven atoms
Prants, S. V.
2017-04-01
This paper is a review article on some aspects of quantum–classical correspondence in chaotic dynamics of cold atoms interacting with a standing-wave laser field forming an optical lattice. The problem is treated from both (semi)classical and quantum points of view. In both approaches, the interaction of an atomic electic dipole with the laser field is treated quantum mechanically. Translational motion is described, at first, classically (atoms are considered to be point-like objects) and then quantum mechanically as a propagation of matter waves. Semiclassical equations of motion are shown to be chaotic in the sense of classical dynamical chaos. Point-like atoms in an absolutely deterministic and rigid optical lattice can move in a random-like manner demonstrating a chaotic walking with typical features of classical chaos. This behavior is explained by random-like ‘jumps’ of one of the atomic internal variable when atoms cross nodes of the standing wave and occurs in a specific range of the atom-field detuning. When treating atoms as matter waves, we show that they can make nonadiabatic transitions when crossing the standing-wave nodes. The point is that atomic wave packets split at each node in the same range of the atom-field detuning where the classical chaos occurs. The key point is that the squared amplitude of those semiclassical ‘jumps’ equal to the quantum Landau–Zener parameter which defines the probability of nonadiabatic transitions at the nodes. Nonadiabatic atomic wave packets are much more complicated compared to adiabatic ones and may be called chaotic in this sense. A few possible experiments to observe some manifestations of classical and quantum chaos with cold atoms in horizontal and vertical optical lattices are proposed and discussed.
Advances in molecular vibrations and collision dynamics molecular clusters
Bacic, Zatko
1998-01-01
This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...
Effective model hierarchies for dynamic and static classical density functional theories
Energy Technology Data Exchange (ETDEWEB)
Majaniemi, S [Department of Applied Physics, Aalto University School of Science and Technology, PO Box 11100, FI-00076 Aalto (Finland); Provatas, N [Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S-4L7 (Canada); Nonomura, M, E-mail: maj@fyslab.hut.f [Department of Physics, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan)
2010-09-15
The origin and methodology of deriving effective model hierarchies are presented with applications to solidification of crystalline solids. In particular, it is discussed how the form of the equations of motion and the effective parameters on larger scales can be obtained from the more microscopic models. It will be shown that tying together the dynamic structure of the projection operator formalism with static classical density functional theories can lead to incomplete (mass) transport properties even though the linearized hydrodynamics on large scales is correctly reproduced. To facilitate a more natural way of binding together the dynamics of the macrovariables and classical density functional theory, a dynamic generalization of density functional theory based on the nonequilibrium generating functional is suggested.
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
Existence of globally bounded classical solution for nonisentropic gas dynamics system has long been studied, especially in the case of polytropic gas. In [4], Liu claimed that sufficient condition has been established. However, the authors find that the argument he used is not true in general. In this article, the authors give a counter example of his argument. Hence, his claim is not valid. The authors believe that it is difficult to impose general conditions on the initial data to obtain globally bounded classical solution.
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.
Theory and application of quantum molecular dynamics
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
Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers
2017-01-01
Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition
Molecular Scale Dynamics of Large Ring Polymers
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
Molecular dynamics model of dimethyl ether
Energy Technology Data Exchange (ETDEWEB)
Lin, B.; Halley, W.J. [Univ. of Minnesota, Minneapolis, MN (United States)
1995-11-02
We report a molecular dynamics model of the monomeric liquid dimethyl ether. The united atom approach is used to treat CH{sub 3} groups as point source centers. Partial charges are derived from the experimental dipole moment. Harmonic force constants are used for intramolecular interactions, and their values are so chosen that the model`s fundamental frequencies agree with experimental results. Because we are interested in solvation properties, the model contains flexible molecules, allowing molecular distortion and internal dynamical quantities. We report radial distribution functions and the static structure factors as well as some dynamical quantities such as the dynamical structure factor, infrared absorption, and Raman scattering spectra. Calculated results agree reasonably well with experimental and other simulation results. 25 refs., 8 figs., 1 tab.
Neutron Star Crust and Molecular Dynamics Simulation
Horowitz, C J; Schneider, A; Berry, D K
2011-01-01
In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.
De Martino, S; Illuminati, F; Martino, Salvatore De; Siena, Silvio De; Illuminati, Fabrizio
1999-01-01
The possibility is discussed of inferring or simulating some aspects of quantum dynamics by adding classical statistical fluctuations to classical mechanics. We introduce a general principle of mechanical stability and derive a necessary condition for classical chaotic fluctuations to affect confined dynamical systems, on any scale, ranging from microscopic to macroscopic domains. As a consequence we obtain, both for microscopic and macroscopic aggregates, dimensional relations defining the minimum unit of action of individual constituents, yielding in all cases Planck action constant.
Dynamics of cascade three-level system interacting with the classical and quantized ﬁeld
Indian Academy of Sciences (India)
Mihir Ranjan Nath; Surajit Sen; Gautam Gangopadhyay
2003-12-01
We study the exact solutions of the cascade three-level atom interacting with a single mode classical and quantized ﬁeld with different initial conditions ofthe atom. For the semiclassical model, it is found that if the atom is initially in the middle level, the time-dependent populations of the upper and lower levels are always equal. This dynamical symmetry exhibited by the classical ﬁeld is spoiled on quantization of the ﬁeld mode. To reveal this non-classical effect, a Euler matrix formalism is developed to solve the dressed states of the cascade Jaynes–Cummings model (JCM). Possible modiﬁcation of such an effect on the collapse and revival phenomenon is also discussed by taking the quantized ﬁeld in a coherent state.
Gauge fixing and classical dynamical r-matrices in (2+1)-gravity
Energy Technology Data Exchange (ETDEWEB)
Schoenfeld, Torsten
2012-11-20
We apply the Dirac gauge fixing procedure to the combinatorial description of the moduli space of flat ISO(2,1)-connections. This is motivated by two goals: one originates from physics while the other is of a mathematical nature. The first goal is to investigate the application of gauge fixing in Lorentzian (2+1)-gravity with vanishing cosmological constant, whose phase space is closely related to the moduli space of flat ISO(2,1)-connections. To this end, we first show that specifying gauge fixing conditions amounts to introducing an observer into the theory. Then we determine explicit expressions for the Dirac brackets of specific sets of gauge fixing conditions and give a physical interpretation of the results in terms of the geometry of spacetimes and their effective symmetries. To investigate the mathematical structures underlying the Dirac gauge fixing procedure we then consider general gauge fixing conditions. We first show that the resulting Dirac brackets are in one-to-one correspondence with solutions of the classical dynamical Yang-Baxter equation. We then analyze the relation between the Dirac brackets associated with two different sets of gauge fixing conditions. We find that this relation is given by the action of certain dynamical Poincare transformations which generalize the gauge transformations of classical dynamical r-matrices. Using these transformations, we give a classification of all resulting Dirac brackets and the associated solutions of the classical dynamical Yang-Baxter equation.
Quantum chaotic scattering in graphene systems in the absence of invariant classical dynamics.
Wang, Guang-Lei; Ying, Lei; Lai, Ying-Cheng; Grebogi, Celso
2013-05-01
Quantum chaotic scattering is referred to as the study of quantum behaviors of open Hamiltonian systems that exhibit transient chaos in the classical limit. Traditionally a central issue in this field is how the elements of the scattering matrix or their functions fluctuate as a system parameter, e.g., the electron Fermi energy, is changed. A tacit hypothesis underlying previous works was that the underlying classical phase-space structure remains invariant as the parameter varies, so semiclassical theory can be used to explain various phenomena in quantum chaotic scattering. There are, however, experimental situations where the corresponding classical chaotic dynamics can change characteristically with some physical parameter. Multiple-terminal quantum dots are one such example where, when a magnetic field is present, the classical chaotic-scattering dynamics can change between being nonhyperbolic and being hyperbolic as the Fermi energy is changed continuously. For such systems semiclassical theory is inadequate to account for the characteristics of conductance fluctuations with the Fermi energy. To develop a general framework for quantum chaotic scattering associated with variable classical dynamics, we use multi-terminal graphene quantum-dot systems as a prototypical model. We find that significant conductance fluctuations occur with the Fermi energy even for fixed magnetic field strength, and the characteristics of the fluctuation patterns depend on the energy. We propose and validate that the statistical behaviors of the conductance-fluctuation patterns can be understood by the complex eigenvalue spectrum of the generalized, complex Hamiltonian of the system which includes self-energies resulted from the interactions between the device and the semi-infinite leads. As the Fermi energy is increased, complex eigenvalues with extremely smaller imaginary parts emerge, leading to sharp resonances in the conductance.
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamics modeling of structural battery components
Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.
2015-01-01
A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo
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.
Molecular Exchange Dynamics in Block Copolymer Micelles
Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy
2012-02-01
Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.
Refinement of homology-based protein structures by molecular dynamics simulation techniques
Fan, H; Mark, AE
2004-01-01
The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to asses
Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations
DEFF Research Database (Denmark)
Xiang, Ye; Du, Jincheng; Smedskjær, Morten Mattrup;
2013-01-01
the recent Corning® Gorilla® Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al/Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role...
Riniker, Sereina
2014-09-01
The research in the group for computational chemistry at the ETH Zurich focuses on the development of methods and software for classical molecular dynamics simulations and cheminformatics, and their application to biological and chemical questions. Here, important advances and challenges in these subfields of computational chemistry are reviewed and potential opportunities for cross-fertilization are outlined.
Multiscale coupling of molecular dynamics and peridynamics
Tong, Qi; Li, Shaofan
2016-10-01
We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.
Long-Term Dynamics and the Orbital Inclinations of the Classical Kuiper Belt Objects
Kuchner, M J; Holman, M; Kuchner, Marc J.; Brown, Michael E.; Holman, Matthew
2002-01-01
We numerically integrated the orbits of 1458 particles in the region of the classical Kuiper Belt (41 AU < a < 47 AU) to explore the role of dynamical instabilities in sculpting the inclination distribution of the classical Kuiper Belt Objects (KBOs). We find that the selective removal of low-inclination objects by overlapping secular resonances (nu_17 and nu_18) acts to raise the mean inclination of the surviving population of particles over 4 billion years of interactions with Jupiter, Saturn, Uranus and Neptune, though these long-term dynamical effects do not themselves appear to explain the discovery of KBOs with inclinations near 30 degrees. Our integrations also imply that after 3 billion years of interaction with the massive planets, high inclination KBOs more efficiently supply Neptune-encountering objects, the likely progenitors of short-period comets, Centaurs, and scattered KBOs. The secular resonances at low inclinations may indirectly cause this effect by weeding out objects unprotected by ...
Directory of Open Access Journals (Sweden)
Wayne Cheng-Wei Huang
2013-01-01
Full Text Available Stochastic electrodynamics (SED predicts a Gaussian probability distribution for a classical harmonic oscillator in the vacuum field. This probability distribution is identical to that of the ground state quantum harmonic oscillator. Thus, the Heisenberg minimum uncertainty relation is recovered in SED. To understand the dynamics that give rise to the uncertainty relation and the Gaussian probability distribution, we perform a numerical simulation and follow the motion of the oscillator. The dynamical information obtained through the simulation provides insight to the connection between the classic double-peak probability distribution and the Gaussian probability distribution. A main objective for SED research is to establish to what extent the results of quantum mechanics can be obtained. The present simulation method can be applied to other physical systems, and it may assist in evaluating the validity range of SED.
Socio-Cultural Dynamics of Education in the Context of the Post-Non-Classical Science
Directory of Open Access Journals (Sweden)
V. A. Ignatova
2012-01-01
Full Text Available The paper deals with the interrelations between society, education and culture. Using the comparative analysis of classical approaches to defining the above spheres, the author comes to conclusion that the nature of socio-cultural processes can be explored and described most consistently by applying comprehensive models of the post-non-classical science and considering civilization, education and culture in the context of the unified dynamic flow of socio-cultural genesis. The research investigates the dialectics of socio-cultural processes in the light of systematic synergetic approach, the advancing role of education in socio-cultural dynamics being revealed and substantiated. The author emphasizes its inevitably rising priority due to sustained development of civilization bringing about the new environmentally-oriented meta-culture.The obtained results can be used in pedagogic research methodology, designing and modeling the educational process, its content, technology and organization.
Socio-Cultural Dynamics of Education in the Context of the Post-Non-Classical Science
Directory of Open Access Journals (Sweden)
V. A. Ignatova
2015-02-01
Full Text Available The paper deals with the interrelations between society, education and culture. Using the comparative analysis of classical approaches to defining the above spheres, the author comes to conclusion that the nature of socio-cultural processes can be explored and described most consistently by applying comprehensive models of the post-non-classical science and considering civilization, education and culture in the context of the unified dynamic flow of socio-cultural genesis. The research investigates the dialectics of socio-cultural processes in the light of systematic synergetic approach, the advancing role of education in socio-cultural dynamics being revealed and substantiated. The author emphasizes its inevitably rising priority due to sustained development of civilization bringing about the new environmentally-oriented meta-culture.The obtained results can be used in pedagogic research methodology, designing and modeling the educational process, its content, technology and organization.
MDMovie: a molecular dynamics viewing tool.
Greenberg, J P
1996-10-01
The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.
Insights from molecular dynamics simulations for computational protein design.
Childers, Matthew Carter; Daggett, Valerie
2017-02-01
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
Quasi-classical modeling of molecular quantum-dot cellular automata multidriver gates
Rahimi, Ehsan; Nejad, Shahram Mohammad
2012-05-01
Molecular quantum-dot cellular automata (mQCA) has received considerable attention in nanoscience. Unlike the current-based molecular switches, where the digital data is represented by the on/off states of the switches, in mQCA devices, binary information is encoded in charge configuration within molecular redox centers. The mQCA paradigm allows high device density and ultra-low power consumption. Digital mQCA gates are the building blocks of circuits in this paradigm. Design and analysis of these gates require quantum chemical calculations, which are demanding in computer time and memory. Therefore, developing simple models to probe mQCA gates is of paramount importance. We derive a semi-classical model to study the steady-state output polarization of mQCA multidriver gates, directly from the two-state approximation in electron transfer theory. The accuracy and validity of this model are analyzed using full quantum chemistry calculations. A complete set of logic gates, including inverters and minority voters, are implemented to provide an appropriate test bench in the two-dot mQCA regime. We also briefly discuss how the QCADesigner tool could find its application in simulation of mQCA devices.
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.
Geometric approach to chaos in the classical dynamics of abelian lattice gauge theory
Casetti, L; Pettini, M; Casetti, Lapo; Gatto, Raoul; Pettini, Marco
1998-01-01
A Riemannian geometrization of dynamics is used to study chaoticity in the classical Hamiltonian dynamics of a U(1) lattice gauge theory. This approach allows one to obtain analytical estimates of the largest Lyapunov exponent in terms of time averages of geometric quantities. These estimates are compared with the results of numerical simulations, and turn out to be very close to the values extrapolated for very large lattice sizes even when the geometric quantities are computed using small lattices. The scaling of the Lyapunov exponent with the energy density is found to be well described by a quadratic power law.
Geometric approach to chaos in the classical dynamics of Abelian lattice gauge theory
Energy Technology Data Exchange (ETDEWEB)
Casetti, Lapo [Istituto Nazionale per la Fisica della Materia (INFM), Unita di Ricerca del Politecnico di Torino, Dipartimento di Fisica, Politecnico di Torino, Turin (Italy); Gatto, Raoul [Departement de Physique Theorique, Universite de Geneve, Geneva (Switzerland); Pettini, Marco [Osservatorio Astrofisico di Arcetri, Largo Enrico Fermi 5, Florence (Italy)
1999-04-23
A Riemannian geometrization of dynamics is used to study chaoticity in the classical Hamiltonian dynamics of a U(1) lattice gauge theory. This approach allows one to obtain analytical estimates of the largest Lyapunov exponent in terms of time averages of geometric quantities. These estimates are compared with the results of numerical simulations, and turn out to be very close to the values extrapolated for very large lattice sizes even when the geometric quantities are computed using small lattices. The scaling of the Lyapunov exponent {lambda} with the energy density {epsilon} is found to be well described by the law {lambda}{proportional_to}{epsilon}{sup 2}. (author)
Green, D. G.; Harvey, C. N.
2015-07-01
We present the Fortran program SIMLA, which is designed for the study of charged particle dynamics in laser and other background fields. The dynamics can be determined classically via the Lorentz force and Landau-Lifshitz equations or, alternatively, via the simulation of photon emission events determined by strong-field quantum-electrodynamics amplitudes and implemented using Monte-Carlo routines. Multiple background fields can be included in the simulation and, where applicable, the propagation direction, field type (plane wave, focussed paraxial, constant crossed, or constant magnetic), and time envelope of each can be independently specified.
Wolfe, Michael; Kestner, Jason
Electrons confined in lateral quantum dots are promising candidates for scalable quantum bits. Particularly, singlet-triplet qubits can entangle electrostatically and offer long coherence times due to their weak interactions with the environment. However, fast two-qubit operations are challenging. We examine the dynamics of singlet triplet qubits capacitively coupled to a classical transmission line resonator driven near resonance. We numerically simulate the dynamics of the von Neumann entanglement entropy and investigate parameters of the coupling element that optimizes the operation time for the qubit.
Luban, Marshall; Modler, Robert; Axenovich, Maria; Canfield, Paul; Bud'Ko, Sergey; Schröder, Christian; Schnack, Jürgen; Müller, Achim; Kögerler, Paul; Harrison, Neil
2001-03-01
The Keplerate species Mo_72Fe_30 containing 30 high-spin Fe^3+ ions, is by far the largest paramagnetic molecule synthesized to date, and it serves as an effective building block and prototype for a new class of diverse molybdenum-oxygen based compounds. These substances are of importance for identifying the most pertinent criteria for the passage from microscopic to macroscopic magnetism, and for their potential as molecular-based electronic and magnetic devices. We report excellent agreement, from room temperature down to 0.1 K, and for magnetic fields up to 60 Tesla between our theoretical results based on the classical Heisenberg model and our measurements of its magnetic properties.
A new dynamics of electroweak symmetry breaking with classically scale invariance
Haba, Naoyuki; Kitazawa, Noriaki; Yamaguchi, Yuya
2015-01-01
We propose a new dynamics of the electroweak symmetry breaking in a classically scale invariant version of the standard model. The scale invariance is broken by the condensations of additional fermions under a strong coupling dynamics. The electroweak symmetry breaking is triggered by negative mass squared of the elementary Higgs doublet, which is dynamically generated through the bosonic seesaw mechanism. We introduce a real pseudo-scalar singlet field interacting with additional fermions and Higgs doublet in order to avoid massless Nambu-Goldstone bosons from the chiral symmetry breaking in a strong coupling sector. We investigate the mass spectra and decay rates of these pseudo-Nambu-Goldstone bosons, and show they can decay fast enough without cosmological problems. We further evaluate the energy dependences of the couplings between elementary fields perturbatively, and find that our model is the first one which realizes the flatland scenario with the dimensional transmutation by the strong coupling dynam...
Energy Technology Data Exchange (ETDEWEB)
Kinugawa, Kenichi [Nara Women`s Univ., Nara (Japan). Dept. of Chemistry
1998-10-01
It has been unsuccessful to solve a set of time-dependent Schroedinger equations numerically for many-body quantum systems which involve, e.g., a number of hydrogen molecules, protons, and excess electrons at a low temperature, where quantum effect evidently appears. This undesirable situation is fatal for the investigation of real low-temperature chemical systems because they are essentially composed of many quantum degrees of freedom. However, if we use a new technique called `path integral centroid molecular dynamics (CMD) simulation` proposed by Cao and Voth in 1994, the real-time semi-classical dynamics of many degrees of freedom can be computed by utilizing the techniques already developed in the traditional classical molecular dynamics (MD) simulations. Therefore, the CMD simulation is expected to be very powerful tool for the quantum dynamics studies or real substances. (J.P.N.)
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...... of the important trade-off between power output and efficiency. Steric motor-motor interactions are shown to play an important thermodynamic role by enhancing the EMP as compared to the noninteracting case. Remarkably, the enhancement occurs at biologically relevant parameters. Finally, a generic model of motor...
Li, B; Li, Baowen; Robnik, Marko
1995-01-01
In this work we study the geometrical properties of the high-lying eigenfunctions (200,000 and above) which are deep in the semiclassical regime. The system we are analyzing is the billiard system inside the region defined by the quadratic (complex) conformal map w = z + \\lambda z^{2} of the unit disk |z| \\le 1 as introduced by Robnik (1983), with the shape parameter value \\lambda = 0.15, so that the billiard is still convex and has KAM-type classical dynamics, where regular and irregular regions of classical motion coexist in the classical phase space. By inspecting 100 and by showing 36 consecutive numerically calculated eigenfunctions we reach the following conclusions: (1) Percival's (1973) conjectured classification in regular and irregular states works well: the mixed type states "living" on regular {\\em and} irregular regions disappear in the semiclassical limit. (2) The irregular (chaotic) states can be strongly localized due to the slow classical diffusion, but become fully extended in the semiclassi...
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.
Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F
2008-02-01
We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.
Molecular Dynamics Simulations of Network Glasses
Drabold, David A.
The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References
Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems
Energy Technology Data Exchange (ETDEWEB)
Miller, William H.
2006-04-27
The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.
Characterization of Rare Events in Molecular Dynamics
Directory of Open Access Journals (Sweden)
Carsten Hartmann
2013-12-01
Full Text Available A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Energy Technology Data Exchange (ETDEWEB)
Arbelo-Gonzalez, W., E-mail: wilmer@instec.cu [Institut des Sciences Moleculaires, Universite Bordeaux 1, 351 Cours de la Liberation, 33405 Talence Cedex (France); Departamento de Fisica General, Instituto Superior de Tecnologias y Ciencias Aplicadas, Habana 10600 (Cuba); Bonnet, L., E-mail: l.bonnet@ism.u-bordeaux1.fr [Institut des Sciences Moleculaires, Universite Bordeaux 1, 351 Cours de la Liberation, 33405 Talence Cedex (France); Larregaray, P.; Rayez, J.-C. [Institut des Sciences Moleculaires, Universite Bordeaux 1, 351 Cours de la Liberation, 33405 Talence Cedex (France); Rubayo-Soneira, J. [Departamento de Fisica General, Instituto Superior de Tecnologias y Ciencias Aplicadas, Habana 10600 (Cuba)
2012-05-03
Graphical abstract: A recent classical description of photodissociation dynamics in a quantum spirit is applied for the first time to a realistic process, the fragmentation of NeBr{sub 2}. Highlights: Black-Right-Pointing-Pointer The photo-dissociation of NeBr{sub 2} is studied by means of two approaches. Black-Right-Pointing-Pointer The first is the standard classical one with Gaussian binning. Black-Right-Pointing-Pointer The second is a new method applied for the first time to a realistic system. Black-Right-Pointing-Pointer The new method leads to exactly the same results as the standard one. Black-Right-Pointing-Pointer However, it requires about 10 times less trajectories in the present case. - Abstract: The recent classical dynamical approach of photodissociations with Bohr quantization [L. Bonnet, J. Chem. Phys. 133 (2010) 174108] is applied for the first time to a realistic process, the photofragmentation of the van der Waals cluster NeBr{sub 2}. We illustrate the fact that this approach, formally equivalent to the standard one, may be numerically much more efficient.
McCorvie, Thomas J.; Kopec, Jolanta; Pey, Angel L.; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W.
2016-01-01
Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homodimer arrangement that contains a covalent uridylylated intermediate and glucose-1-phosphate in the active site, as well as a structural zinc-binding site, per monomer. hGALT reveals significant structural differences from bacterial GALT homologues in metal ligation and dimer interactions, and therefore is a zbetter model for understanding the molecular consequences of disease mutations. Both uridylylation and zinc binding influence the stability and aggregation tendency of hGALT. This has implications for disease-associated variants where p.Gln188Arg, the most commonly detected, increases the rate of aggregation in the absence of zinc likely due to its reduced ability to form the uridylylated intermediate. As such our structure serves as a template in the future design of pharmacological chaperone therapies and opens new concepts about the roles of metal binding and activity in protein misfolding by disease-associated mutants. PMID:27005423
McCorvie, Thomas J; Kopec, Jolanta; Pey, Angel L; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W
2016-06-01
Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homodimer arrangement that contains a covalent uridylylated intermediate and glucose-1-phosphate in the active site, as well as a structural zinc-binding site, per monomer. hGALT reveals significant structural differences from bacterial GALT homologues in metal ligation and dimer interactions, and therefore is a zbetter model for understanding the molecular consequences of disease mutations. Both uridylylation and zinc binding influence the stability and aggregation tendency of hGALT. This has implications for disease-associated variants where p.Gln188Arg, the most commonly detected, increases the rate of aggregation in the absence of zinc likely due to its reduced ability to form the uridylylated intermediate. As such our structure serves as a template in the future design of pharmacological chaperone therapies and opens new concepts about the roles of metal binding and activity in protein misfolding by disease-associated mutants.
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Directory of Open Access Journals (Sweden)
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
Thermal vibration of a single-walled carbon nanotube predicted by semiquantum molecular dynamics.
Liu, Rumeng; Wang, Lifeng
2015-02-21
Quantum effects should be considered in the thermal vibrations of carbon nanotubes (CNTs). To this end, molecular dynamics based on modified Langevin dynamics, which accounts for quantum statistics by introducing a quantum heat bath, is used to simulate the thermal vibration of a cantilevered single-walled CNT (SWCNT). A nonlocal elastic Timoshenko beam model with quantum effects (TBQN), which can take the effect of microstructure into consideration, has been established to explain the resulting power spectral density of the SWCNT. The root of mean squared (RMS) amplitude of the thermal vibration of the SWCNT obtained from semiquantum molecular dynamics (SQMD) is lower than that obtained from classical molecular dynamics, especially at very low temperature and high-order modes. The natural frequencies of the SWCNT obtained from the Timoshenko beam model are closer to those obtained from molecular dynamics if the nonlocal effect is taken into consideration. However, the nonlocal Timoshenko beam model with the law of energy equipartition (TBCN) can only predict the RMS amplitude of the SWCNT obtained from classical molecular dynamics without considering quantum effects. The RMS amplitude of the SWCNT obtained from SQMD and that obtained from TBQN coincide very well. These results indicate that quantum effects are important for the thermal vibration of the SWCNT in the case of high-order modes, short length and low temperature.
Molecular dynamics simulations of bubble nucleation in dark matter detectors.
Denzel, Philipp; Diemand, Jürg; Angélil, Raymond
2016-01-01
Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.
Molecular dynamics modelling of solidification in metals
Energy Technology Data Exchange (ETDEWEB)
Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)
1997-12-31
Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.
Study of Nanowires Using Molecular Dynamics Simulations
Monk, Joshua D
2007-01-01
In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...
Molecular crowding and protein enzymatic dynamics.
Echeverria, Carlos; Kapral, Raymond
2012-05-21
The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding.
Nonequilibrium molecular dynamics theory, algorithms and applications
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...
Monoamine transporters: insights from molecular dynamics simulations
Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit
2015-01-01
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185
Monoamine transporters: Insights from molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Julie eGrouleff
2015-10-01
Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.
Bead-Fourier path integral molecular dynamics
Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto
2003-06-01
Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.
Dynamic Maintenance and Visualization of Molecular Surfaces
Energy Technology Data Exchange (ETDEWEB)
Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N
2004-12-16
Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.
McMillan, Ryan J; Grüning, Myrta
2016-01-01
We introduce a hybrid method for dielectric-metal composites that describes the dynamics of the metallic system classically whilst retaining a quantum description of the dielectric. The time-dependent dipole moment of the classical system is mimicked by the introduction of projected equations of motion (PEOM) and the coupling between the two systems is achieved through an effective dipole-dipole interaction. To benchmark this method, we model a test system (semiconducting quantum dot-metal nanoparticle hybrid). We begin by examining the energy absorption rate, showing agreement between the PEOM method and the analytical rotating wave approximation (RWA) solution. We then investigate population inversion and show that the PEOM method provides an accurate model for the interaction under ultrashort pulse excitation where the traditional RWA breaks down.
Pankovic, V; Predojevic, M; Krmar, M; Pankovic, Vladan; Hubsch, Tristan; Predojevic, Milan; Krmar, Miodrag
2004-01-01
Developing an earlier proposal (Ne'eman, Damnjanovic, etc), we show herein that there is a Landau continuous phase transition from the exact quantum dynamics to the effectively classical one, occurring via spontaneous superposition breaking (effective hiding), as a special case of the corresponding general formalism (Bernstein). Critical values of the order parameters for this transition are determined by Heisenberg's indeterminacy relations, change continuously, and are in excellent agreement with the recent and remarkable experiments with Bose condensation. It is also shown that such a phase transition can sucessfully model self-collapse (self-decoherence), as an effective classical phenomenon, on the measurement device. This then induces a relative collapse (relative decoherence) as an effective quantum phenomenon on the measured quantum object by measurement. We demonstrate this (including the case of Bose-Einstein condensation) in the well-known cases of the Stern-Gerlach spin measurement, Bell's inequal...
A new dynamics of electroweak symmetry breaking with classically scale invariance
Directory of Open Access Journals (Sweden)
Naoyuki Haba
2016-04-01
Full Text Available We propose a new dynamics of the electroweak symmetry breaking in a classically scale invariant version of the standard model. The scale invariance is broken by the condensations of additional fermions under a strong coupling dynamics. The electroweak symmetry breaking is triggered by negative mass squared of the elementary Higgs doublet, which is dynamically generated through the bosonic seesaw mechanism. We introduce a real pseudo-scalar singlet field interacting with additional fermions and Higgs doublet in order to avoid massless Nambu–Goldstone bosons from the chiral symmetry breaking in a strong coupling sector. We investigate the mass spectra and decay rates of these pseudo-Nambu–Goldstone bosons, and show they can decay fast enough without cosmological problems. We further show that our model can make the electroweak vacuum stable.
Thermal conductivity of penta-graphene from molecular dynamics study.
Xu, Wen; Zhang, Gang; Li, Baowen
2015-10-21
Using classical equilibrium molecular dynamics simulations and applying the original Tersoff interatomic potential, we study the thermal transport property of the latest two dimensional carbon allotrope, penta-graphene. It is predicted that its room-temperature thermal conductivity is about 167 W/mK, which is much lower than that of graphene. With normal mode decomposition, the accumulated thermal conductivity with respect to phonon frequency and mean free path is analyzed. It is found that the acoustic phonons make a contribution of about 90% to the thermal conductivity, and phonons with mean free paths larger than 100 nm make a contribution over 50%. We demonstrate that the remarkably lower thermal conductivity of penta-graphene compared with graphene results from the lower phonon group velocities and fewer collective phonon excitations. Our study highlights the importance of structure-property relationship and provides better understanding of thermal transport property and valuable insight into thermal management of penta-graphene.
Pasta Elasticity: Molecular dynamics simulations of nuclear pasta deformations
Caplan, M. E.; Horowitz, C. J.; Berry, D. K.
2015-04-01
Nuclear pasta is expected in the inner crust of neutron stars at densities near the nuclear saturation density. In this work, the elastic properties of pasta are calculated from large scale molecular dynamics simulations by deforming the simulation volume. Our model uses a semi-classical two-nucleon potential that reproduces nuclear saturation. We report the shear modulus and breaking strain of a variety of pasta phases for different temperatures, densities, and proton fractions. The presence of pasta in neutron stars could have significant effects on crustal oscillations and could be inferred from observations of soft-gamma repeaters. Additionally, these elastic parameters will enable us to improve estimates of the maximum size and lifetime of ``mountains'' on the crust, which could efficiently radiate gravitational waves.
Molecular dynamics simulations of magnetized dusty plasmas
Piel, Alexander; Reichstein, Torben; Wilms, Jochen
2012-10-01
The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)
Application of optimal prediction to molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Barber, IV, John Letherman [Univ. of California, Berkeley, CA (United States)
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is δ-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
Combining Molecular Dynamics and Density Functional Theory
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Roy, S.
2015-06-27
Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and important roles for microbiocidal activity, regulation of inflammation and tissue homeostasis. Despite this, their transcriptional regulatory dynamics are poorly understood. Using promoter-level expression profiling by non-biased deepCAGE we have studied the transcriptional dynamics of classically and alternatively activated macrophages. Transcription factor (TF) binding motif activity analysis revealed four motifs, NFKB1_REL_RELA, IRF1,2, IRF7 and TBP that are commonly activated but have distinct activity dynamics in M1 and M2 activation. We observe matching changes in the expression profiles of the corresponding TFs and show that only a restricted set of TFs change expression. There is an overall drastic and transient up-regulation in M1 and a weaker and more sustainable up-regulation in M2. Novel TFs, such as Thap6, Maff, (M1) and Hivep1, Nfil3, Prdm1, (M2) among others, were suggested to be involved in the activation processes. Additionally, 52 (M1) and 67 (M2) novel differentially expressed genes and, for the first time, several differentially expressed long non-coding RNA (lncRNA) transcriptome markers were identified. In conclusion, the finding of novel motifs, TFs and protein-coding and lncRNA genes is an important step forward to fully understand the transcriptional machinery of macrophage activation.
Quantum and quasi-classical collisional dynamics of O2-Ar at high temperatures
Ulusoy, Inga S.; Andrienko, Daniil A.; Boyd, Iain D.; Hernandez, Rigoberto
2016-06-01
A hypersonic vehicle traveling at a high speed disrupts the distribution of internal states in the ambient flow and introduces a nonequilibrium distribution in the post-shock conditions. We investigate the vibrational relaxation in diatom-atom collisions in the range of temperatures between 1000 and 10 000 K by comparing results of extensive fully quantum-mechanical and quasi-classical simulations with available experimental data. The present paper simulates the interaction of molecular oxygen with argon as the first step in developing the aerothermodynamics models based on first principles. We devise a routine to standardize such calculations also for other scattering systems. Our results demonstrate very good agreement of vibrational relaxation time, derived from quantum-mechanical calculations with the experimental measurements conducted in shock tube facilities. At the same time, the quasi-classical simulations fail to accurately predict rates of vibrationally inelastic transitions at temperatures lower than 3000 K. This observation and the computational cost of adopted methods suggest that the next generation of high fidelity thermochemical models should be a combination of quantum and quasi-classical approaches.
Wavepacket dynamics in energy space, RMT and Quantum-Classical correspondence
Cohen, D; Kottos, T; Cohen, Doron; Izrailev, Felix M.; Kottos, Tsampikos
1999-01-01
We apply random-matrix-theory (RMT) to the analysis of evolution of wavepackets in energy space. We study the crossover from ballistic behavior to saturation, the possibility of having an intermediate diffusive behavior, and the feasibility of strong localization effect. Both theoretical considerations and numerical results are presented. Using quantal-classical correspondence (QCC) considerations we question the validity of the emerging dynamical picture. In particular we claim that the appearance of the intermediate diffusive behavior is possibly an artifact of the RMT strategy.
Wave packet dynamics in energy space, random matrix theory, and the quantum-classical correspondence
Cohen; Izrailev; Kottos
2000-03-06
We apply random-matrix-theory (RMT) to the analysis of evolution of wave packets in energy space. We study the crossover from ballistic behavior to saturation, the possibility of having an intermediate diffusive behavior, and the feasibility of strong localization effect. Both theoretical considerations and numerical results are presented. Using quantal-classical correspondence considerations we question the validity of the emerging dynamical picture. In particular, we claim that the appearance of the intermediate diffusive behavior is possibly an artifact of the RMT strategy.
Classical Order Parameter Dynamics and the Decay of a Metastable Vacuum State
Szép, Z
2000-01-01
Transition of the ground state of a classical $\\Phi^4$ theory in 2+1 dimensions is studied from a metastable state into the stable equilibrium. The transition occurs in the broken $Z_2$ symmetry phase and is triggered by a vanishingly small amplitude homogeneous external field $h$. A phenomenological theory is proposed in form of an effective equation of the quantitatively accounts for the decay of the false vacuum. The large amplitude transition of the order parameter between the two minima displays characteristics reflecting dynamical aspects of the Maxwell construction.
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
WANG; Hui(
2001-01-01
［1］Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.［2］Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.［3］Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.［4］Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.［5］Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.［6］Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.［7］Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.［8］Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.［9］Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.［10］Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.［11］Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.［12］Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.［13］Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.
Classical and quantum dynamics of a perfect fluid scalar-energy dependent metric cosmology
Khodadi, M.; Nozari, K.; Vakili, B.
2016-05-01
Inspired from the idea of minimally coupling of a real scalar field to geometry, we investigate the classical and quantum models of a flat energy-dependent FRW cosmology coupled to a perfect fluid in the framework of the scalar-rainbow metric gravity. We use the standard Schutz' representation for the perfect fluid and show that under a particular energy-dependent gauge fixing, it may lead to the identification of a time parameter for the corresponding dynamical system. It is shown that, under some circumstances on the minisuperspace prob energy, the classical evolution of the of the universe represents a late time expansion coming from a bounce instead of the big-bang singularity. Then we go forward by showing that this formalism gives rise to a Schrödinger-Wheeler-DeWitt equation for the quantum-mechanical description of the model under consideration, the eigenfunctions of which can be used to construct the wave function of the universe. We use the resulting wave function in order to investigate the possibility of the avoidance of classical singularities due to quantum effects by means of the many-worlds and Bohmian interpretation of quantum cosmology.
Byeon, Sun-Ju; Cho, Hwa Jin; Baek, Hae Woon; Park, Chul-Kee; Choi, Seung-Hong; Kim, Se-Hoon; Kim, Hee Kyung; Park, Sung-Hye
2014-03-01
The clinicopathologic and molecular genetic features of 5 cases of rhabdoid glioblastoma, an extremely rare variant of glioblastoma that tends to affect patients at a young age, were investigated by immunohistochemical analysis and focused molecular genetic studies including array-based comparative genomic hybridization. All 5 cases had supratentorial tumors that immunohistochemical analysis revealed to be robustly positive for epithelial membrane antigen, vimentin, p53, and PDGFRα (platelet-derived growth factor receptor, alpha polypeptide) but only focally positive for glial fibrillary acidic protein. Although complete retention of SMARCB1 (INI1) was observed in all 5 cases, epidermal growth factor receptor (EGFR) amplification, PTEN (phosphatase and tensin homolog) loss, homozygous deletion of cyclin-dependent kinase inhibitor 2A, 1p/19q codeletion, and isocitrate dehydrogenase 1 R132/IDH2 R172 mutation were not observed in any case, although a high level of EGFR polysomy was detected in 1 recurrent tumor. Although c-MET (MET protein) expression was focal but robustly positive in 3 cases, met proto-oncogene (MET) fluorescence in situ hybridization revealed low polysomy but not MET amplification. MGMT (O-6-methylguanine-DNA methyl-40 transferase) methylation-specific polymerase chain reaction revealed MGMT methylation in only 1 case. Furthermore, array-based comparative genomic hybridization revealed gain of chromosome 7 and loss of 1p, 6, 8p, 11, 13q, and 18q but no deletion of chromosome 22. In contrast to the classical subtype of primary glioblastoma, the cases studied here were characterized by the absence of EGFR amplification, PTEN loss, and 9p homozygous deletion and overexpression of p53, PDGFRα, and c-MET, suggesting that they can be classified as the proneural or mesenchymal subtype of glioblastoma and benefit from intensive therapy that includes temozolomide.
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.
Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
2016-01-01
Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.
Gutiérrez, R; Caetano, R A; Woiczikowski, B P; Kubar, T; Elstner, M; Cuniberti, G
2009-05-22
We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.
Computational Studies on the Anharmonic Dynamics of Molecular Clusters
Mancini, John S.
Molecular nanoclusters present ideal systems to probe the physical forces and dynamics that drive the behavior of larger bulk systems. At the nanocluster limit the first instances of several phenomena can be observed including the breaking of hydrogen and molecular bonds. Advancements in experimental and theoretical techniques have made it possible to explore these phenomena in great detail. The most fruitful of these studies have involved the use of both experimental and theoretical techniques to leverage to strengths of the two approaches. This dissertation seeks to explore several important phenomena of molecular clusters using new and existing theoretical methodologies. Three specific systems are considered, hydrogen chloride clusters, mixed water and hydrogen chloride clusters and the first cluster where hydrogen chloride autoionization occurs. The focus of these studies remain as close as possible to experimentally observable phenomena with the intention of validating, simulating and expanding on experimental work. Specifically, the properties of interested are those related to the vibrational ground and excited state dynamics of these systems. Studies are performed using full and reduced dimensional potential energy surface alongside advanced quantum mechanical methods including diffusion Monte Carlo, vibrational configuration interaction theory and quasi-classical molecular dynamics. The insight gained from these studies are great and varied. A new on-they-fly ab initio method for studying molecular clusters is validated for (HCl)1--6. A landmark study of the dissociation energy and predissociation mechanism of (HCl)3 is reported. The ground states of mixed (HCl)n(H2O)m are found to be highly delocalized across multiple stationary point configurations. Furthermore, it is identified that the consideration of this delocalization is required in vibrational excited state calculations to achieve agreement with experimental measurements. Finally, the theoretical
Müser, Martin H.
2001-04-01
Classical and path integral molecular dynamics (PIMD) simulations are used to study α and β quartz in a large range of temperatures at zero external stress. PIMD account for quantum fluctuations of atomic vibrations, which can modify material properties at temperatures below the Debye temperature. The difference between classical and quantum mechanical results for bond lengths, bond angles, elastic moduli, and some dynamical properties is calculated and comparison to experimental data is done. Only quantum mechanical simulations are able to reproduce the correct thermomechanical properties below room temperature. It is discussed in how far classical and PIMD simulations can be helpful in constructing improved potential energy surfaces for silica.
Visceral Leishmaniasis: Advancements in vaccine development via classical and molecular approaches
Directory of Open Access Journals (Sweden)
Sumit eJoshi
2014-08-01
Full Text Available Visceral Leishmaniasis (VL or kala-azar, a vector-borne protozoan disease, shows endemicity in larger areas of the tropical, subtropical and the Mediterranean countries. WHO report suggested that nearly 500,000 new cases of VL occur annually, including 100,000 cases from India itself. Treatment with available anti-leishmanial drugs are not cost effective, with varied efficacies and higher relapse rate, which poses a major challenge to current kala-azar control program in Indian subcontinent. Therefore, a vaccine against VL is imperative and knowing the fact that recovered individuals developed lifelong immunity against re-infection, it is feasible. Vaccine development program, though time taking, has recently gained momentum with the emergence of omic era i.e. from genomics to immunomics. Classical as well as molecular methodologies has been overtaken with alternative strategies wherein proteomics based knowledge combined with computational techniques (immunoinformatics speed up the identification and detailed characterization of new antigens for potential vaccine candidates. This may eventually help in the designing of polyvalent synthetic and recombinant chimeric vaccines as an effective intervention measures to control the disease in endemic areas. This review focuses on such newer approaches being utilized for vaccine development against VL.
CLASSICAL AND MOLECULAR CYTOGENETIC STUDIES FOR BREEDING AND SELECTION OF TULIPS
Directory of Open Access Journals (Sweden)
Aurel Popescu
2012-12-01
Full Text Available Due to their extreme popularity as fresh cut flowers and garden plants, and being used extensively for landscaping, tulips undergone a continuous process of selective breeding. For almost nine decades, classical cytogenetic studies, mainly the chromosome counts, have been an important part in the breeding programme for polyploid tulips. The efficiency of breeding is greatly aided by a thorough knowledge of the occurrence of polyploidy in the plant material. While the traditional cytogenetic approaches are still highly useful in selecting polyploids and aneuploids arising from crosses involving (most often parents of different ploidy or from the material subjected to ploidy manipulation, the new strategies for inducing polyploidy in tulips, either in vivo or in vitro, and advances in molecular cytogenetics are expected to allow a significant increase in breeding efficiency. Together with the shortening of breeding cycle, major genetic improvements could be made for specific traits. In this we review the development of cytogenetic studies in tulips, and the most relevant achievements so far, providing an overview of what we consider to be valuable tools for the processes of selective breeding .
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
Based on the cascade two-photon laser dynamic equation derived with the technique of quantum Langevin operators with the considerations of coherently prepared three-level atoms and the classical field injected into the cavity, we numerically study the effects of atomic coherence and classical field on the chaotic dynamics of a two-photon laser. Lyapunov exponent and bifurcation diagram calculations show that the Lorenz chaos and hyperchaos can be induced or inhibited by the atomic coherence and the classical field via crisis or Hopf bifurcations.
Pérez, Alejandro; Tuckerman, Mark E.
2011-08-01
Higher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the Takahashi-Imada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the end-to-end distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems.
Energy Technology Data Exchange (ETDEWEB)
Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R. [A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova Str. 28, 119991 Moscow (Russian Federation)
2014-04-07
An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.
Attosecond VUV Coherent Control of Molecular Dynamics
Ranitovic, P; Riviere, P; Palacios, A; Tong, X M; Toshima, N; Gonzalez-Castrillo, A; Martin, L; Martin, F; Murnane, M M; Kapteyn, H C
2014-01-01
High harmonic light sources make it possible to access attosecond time-scales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized. This is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep ultraviolet, which have not yet been synthesized. Here, we present a novel approach using attosecond vacuum ultraviolet pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly-ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipula...
Molecular Dynamics Studies of Nanofluidic Devices
DEFF Research Database (Denmark)
Zambrano Rodriguez, Harvey Alexander
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...... in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays, silica nanochannels...... 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...
Geometry of dynamics and phase transitions in classical lattice $\\phi^{4}$ theories
Caiani, L; Clementi, C; Pettini, G; Pettini, M; Gatto, R; Caiani, Lando; Casetti, Lapo; Clementi, Cecilia; Pettini, Giulio; Pettini, Marco; Gatto, Raoul
1998-01-01
We perform a microcanonical study of classical lattice phi^4 field models in 3 dimensions with O(n) symmetries. The Hamiltonian flows associated to these systems that undergo a second order phase transition in the thermodynamic limit are here investigated. The microscopic Hamiltonian dynamics neatly reveals the presence of a phase transition through the time averages of conventional thermodynamical observables. Moreover, peculiar behaviors of the largest Lyapunov exponents at the transition point are observed. A Riemannian geometrization of Hamiltonian dynamics is then used to introduce other relevant observables, that are measured as functions of both energy density and temperature. On the basis of a simple and abstract geometric model, we suggest that the apparently singular behaviour of these geometric observables might probe a major topological change of the manifolds whose geodesics are the natural motions.
Interplay of classical and quantum dynamics in a thermal ensemble of atoms
Laskar, Arif Warsi; Mukherjee, Arunabh; Ghosh, Saikat
2016-01-01
In a thermal ensemble of atoms driven by coherent fields, how does evolution of quantum superposition compete with classical dynamics of optical pumping and atomic diffusion? Is it optical pumping that first prepares a thermal ensemble, with coherent superposition developing subsequently or is it the other way round: coherently superposed atoms driven to steady state via optical pumping? Using a stroboscopic probing technique, here we experimentally explore these questions. A 100 ns pulse is used to probe an experimentally simulated, closed three-level, lambda-like configuration in rubidium atoms, driven by strong coherent control and incoherent fields. Temporal evolution of probe transmission shows an initial overshoot with turn-on of control, resulting in a scenario akin to lasing without inversion (LWI). The corresponding rise time is dictated by coherent dynamics, with a distinct experimental signature of half-cycle Rabi flop in a thermal ensemble of atoms. Our results indicate that, in fact, optical pump...
Molecular Dynamics: New Frontier in Personalized Medicine.
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.
Molecular Dynamics Simulations of Interface Failure
Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.
2007-03-01
The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
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...
Implementing peridynamics within a molecular dynamics code.
Energy Technology Data Exchange (ETDEWEB)
Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James; Parks, Michael L.
2007-12-01
Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite distance may exert force upon each other. A meshless method results when PD is discretized with material behavior approximated as a collection of interacting particles. This paper describes how PD can be implemented within a molecular dynamics (MD) framework, and provides details of an efficient implementation. This adds a computational mechanics capability to an MD code, enabling simulations at mesoscopic or even macroscopic length and time scales.
Extension of Isospin Dependent Quantum Molecular Dynamics
Institute of Scientific and Technical Information of China (English)
FengZhaoqing; ZhangFengshou; LiWenfei; JinGenming
2003-01-01
Isospin dependent molecular dynamics (IQMD) has been used with success for studying isospin effects in heavy ion collisions at intermediate energies[1,2]. However, this model meets difficulty to study heavy ion collisions at low energies near Coulomb barrier since unsuitable dealing with the deformation, such as surface term induced by deformation during approaching projectile and target, which is not important at high energies, and it results in the calculated cross sections with IQMD which are much smaller than the experimental data at low energies. In this report, we propose a new method in which the surface term in the mean field is included in a proper way, the switch function method.
Exchange frequency in replica exchange molecular dynamics
Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.
2008-01-01
The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.
Kenfack, Lionel Tenemeza; Tchoffo, Martin; Fai, Lukong Cornelius
2017-02-01
We address the dynamics of quantum correlations, including entanglement and quantum discord of a three-qubit system interacting with a classical pure dephasing random telegraph noise (RTN) in three different physical environmental situations (independent, mixed and common environments). Two initial entangled states of the system are examined, namely the Greenberger-Horne-Zeilinger (GHZ)- and Werner (W)-type states. The classical noise is introduced as a stochastic process affecting the energy splitting of the qubits. With the help of suitable measures of tripartite entanglement (entanglement witnesses and lower bound of concurrence) and quantum discord (global quantum discord and quantum dissension), we show that the evolution of quantum correlations is not only affected by the type of the system-environment interaction but also by the input configuration of the qubits and the memory properties of the environmental noise. Indeed, depending on the memory properties of the environmental noise and the initial state considered, we find that independent, common and mixed environments can play opposite roles in preserving quantum correlations, and that the sudden death and revival phenomena or the survival of quantum correlations may occur. On the other hand, we also show that the W-type state has strong dynamics under this noise than the GHZ-type ones.
An Approach to Some Non-Classical Eigenvalue Problems of Structural Dynamics
Directory of Open Access Journals (Sweden)
Sandi Horea
2015-12-01
Full Text Available Two main shortcomings of common formulations, encountered in the literature concerning the linear problems of structural dynamics are revealed: the implicit, not discussed, postulation, of the use of Kelvin – Voigt constitutive laws (which is often infirmed by experience and the calculation difficulties involved by the attempts to use other constitutive laws. In order to overcome these two categories of shortcomings, the use of the bilateral Laplace – Carson transformation is adopted. Instead of the dependence on time, t, of a certain function f (t, the dependence of its image f# (p on the complex parameter p = χ + iω (ω: circular frequency will occur. This leads to the formulation of associated non-classical eigenvalue problems. The basic relations satisfied by the eigenvalues λr#(p and the eigenvectors vr#(p of dynamic systems are examined (among other, the property of orthogonality of eigenvectors is replaced by the property of pseudo-orthogonality. The case of points p = p’, where multiple eigenvalues occur and where, as a rule, chains of principal vectors are to be considered, is discussed. An illustrative case, concerning a non-classical eigenvalue problem, is presented. Plots of variation along the ω axis, for the real and imaginary components of eigenvalues and eigenvectors, are presented. A brief final discussion closes the paper.
Dynamics of classical particles in oval or elliptic billiards with a dispersing mechanism
Energy Technology Data Exchange (ETDEWEB)
Costa, Diogo Ricardo da [Instituto de Física da USP, Rua do Matão, Travessa R, 187, Cidade Universitária, CEP 05314-970 São Paulo, SP (Brazil); School of Mathematics, University of Bristol, Bristol (United Kingdom); Departamento de Física, UNESP-Univ Estadual Paulista, Av. 24A, 1515, 13506-900 Rio Claro, SP (Brazil); Dettmann, Carl P. [School of Mathematics, University of Bristol, Bristol (United Kingdom); Oliveira, Juliano A. de [UNESP-Univ Estadual Paulista, Câmpus de São João da Boa Vista, São João da Boa Vista, SP (Brazil); Leonel, Edson D. [Departamento de Física, UNESP-Univ Estadual Paulista, Av. 24A, 1515, 13506-900 Rio Claro, SP (Brazil)
2015-03-15
Some dynamical properties for an oval billiard with a scatterer in its interior are studied. The dynamics consists of a classical particle colliding between an inner circle and an external boundary given by an oval, elliptical, or circle shapes, exploring for the first time some natural generalizations. The billiard is indeed a generalization of the annular billiard, which is of strong interest for understanding marginally unstable periodic orbits and their role in the boundary between regular and chaotic regions in both classical and quantum (including experimental) systems. For the oval billiard, which has a mixed phase space, the presence of an obstacle is an interesting addition. We demonstrate, with details, how to obtain the equations of the mapping, and the changes in the phase space are discussed. We study the linear stability of some fixed points and show both analytically and numerically the occurrence of direct and inverse parabolic bifurcations. Lyapunov exponents and generalized bifurcation diagrams are obtained. Moreover, histograms of the number of successive iterations for orbits that stay in a cusp are studied. These histograms are shown to be scaling invariant when changing the radius of the scatterer, and they have a power law slope around −3. The results here can be generalized to other kinds of external boundaries.
Sammalkorpi, Maria; Panagiotopoulos, Athanassios Z; Haataja, Mikko
2008-03-13
We have examined the structure and dynamics of sodium dodecyl sulfate (SDS) and dodecane (C12) molecular aggregates at varying surface coverages on the basal plane of graphite via classical molecular dynamics simulations. Our results suggest that graphite-hydrocarbon chain interactions favor specific molecular orientations at the single-molecule level via alignment of the tail along the crystallographic directions. This orientational bias is reduced greatly upon increasing the surface coverage for both molecules due to intermolecular interactions, leading to very weak bias at intermediate surface coverages. Interestingly, for complete monolayers, we find a re-emergent orientational bias. Furthermore, by comparing the SDS behavior with C12, we demonstrate that the charged head group plays a key role in the aggregate structures: SDS molecules display a tendency to form linear file-like aggregates while C12 forms tightly bound planar ones. The observed orientational bias for SDS molecules is in agreement with experimental observations of hemimicelle orientation and provides support for the belief that an initial oriented layer governs the orientation of hemimicellar aggregates.
Hybrid molecular dynamics simulation for plasma induced damage analysis
Matsukuma, Masaaki
2016-09-01
In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam
Belyaev, Andrey K.; Domcke, Wolfgang; Lasser, Caroline; Trigila, Giulio
2015-03-01
The Landau-Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected for the nuclear dynamics: Ultrafast Jahn-Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow
Archereau, Aurelien Y M; Willmott, Geoff R
2016-01-01
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.
Coarse-grained protein molecular dynamics simulations
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation
Hung, Shih-Wei; Shiomi, Junichiro
2015-11-01
Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.
Directory of Open Access Journals (Sweden)
Trullàs J.
2011-05-01
Full Text Available Molecular dynamics simulations of molten NaI at 995 K have been carried out using polarizable ion models based on rigid ion pair potentials to which the anion induced dipole polarization is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and deformation short-range damping interactions that oppose the electrically induced dipole moments. The structure and self-diffusion results are compared with those obtained by Galamba and Costa Cabral using first principles Hellmann-Feynman molecular dynamics simulations and using classical molecular dynamics of a shell model which allows only the iodide polarization
Directory of Open Access Journals (Sweden)
Deborah J Evans
Full Text Available The current model of planarian anterior regeneration evokes the establishment of low levels of Wnt signalling at anterior wounds, promoting anterior polarity and subsequent elaboration of anterior fate through the action of the TALE class homeodomain PREP. The classical observation that decapitations positioned anteriorly will regenerate heads more rapidly than posteriorly positioned decapitations was among the first to lead to the proposal of gradients along an anteroposterior (AP axis in a developmental context. An explicit understanding of this phenomenon is not included in the current model of anterior regeneration. This raises the question what the underlying molecular and cellular basis of this temporal gradient is, whether it can be explained by current models and whether understanding the gradient will shed light on regenerative events. Differences in anterior regeneration rate are established very early after amputation and this gradient is dependent on the activity of Hedgehog (Hh signalling. Animals induced to produce two tails by either Smed-APC-1(RNAi or Smed-ptc(RNAi lose anterior fate but form previously described ectopic anterior brain structures. Later these animals form peri-pharyngeal brain structures, which in Smed-ptc(RNAi grow out of the body establishing a new A/P axis. Combining double amputation and hydroxyurea treatment with RNAi experiments indicates that early ectopic brain structures are formed by uncommitted stem cells that have progressed through S-phase of the cell cycle at the time of amputation. Our results elaborate on the current simplistic model of both AP axis and brain regeneration. We find evidence of a gradient of hedgehog signalling that promotes posterior fate and temporarily inhibits anterior regeneration. Our data supports a model for anterior brain regeneration with distinct early and later phases of regeneration. Together these insights start to delineate the interplay between discrete existing, new
Evans, Deborah J; Owlarn, Suthira; Tejada Romero, Belen; Chen, Chen; Aboobaker, A Aziz
2011-01-01
The current model of planarian anterior regeneration evokes the establishment of low levels of Wnt signalling at anterior wounds, promoting anterior polarity and subsequent elaboration of anterior fate through the action of the TALE class homeodomain PREP. The classical observation that decapitations positioned anteriorly will regenerate heads more rapidly than posteriorly positioned decapitations was among the first to lead to the proposal of gradients along an anteroposterior (AP) axis in a developmental context. An explicit understanding of this phenomenon is not included in the current model of anterior regeneration. This raises the question what the underlying molecular and cellular basis of this temporal gradient is, whether it can be explained by current models and whether understanding the gradient will shed light on regenerative events. Differences in anterior regeneration rate are established very early after amputation and this gradient is dependent on the activity of Hedgehog (Hh) signalling. Animals induced to produce two tails by either Smed-APC-1(RNAi) or Smed-ptc(RNAi) lose anterior fate but form previously described ectopic anterior brain structures. Later these animals form peri-pharyngeal brain structures, which in Smed-ptc(RNAi) grow out of the body establishing a new A/P axis. Combining double amputation and hydroxyurea treatment with RNAi experiments indicates that early ectopic brain structures are formed by uncommitted stem cells that have progressed through S-phase of the cell cycle at the time of amputation. Our results elaborate on the current simplistic model of both AP axis and brain regeneration. We find evidence of a gradient of hedgehog signalling that promotes posterior fate and temporarily inhibits anterior regeneration. Our data supports a model for anterior brain regeneration with distinct early and later phases of regeneration. Together these insights start to delineate the interplay between discrete existing, new, and then
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
On the dynamics of a polaron in a classical chain with finite temperature
Energy Technology Data Exchange (ETDEWEB)
Lakhno, V. D., E-mail: lak@impb.psn.ru; Fialko, N. S., E-mail: fialka@impb.psn.ru [Russian Academy of Sciences, Institute of Mathematical Problems of Biology (Russian Federation)
2015-01-15
In today’s literature, polaron states in classical molecular chains are mostly calculated at zero temperature. It is assumed that the properties of these states change little if the temperature is different from zero but is much less than the characteristic energy equal to the depth of the polaron level. By numerical experiments, we demonstrate that the temperature decay of a polaron depends on the chain length. The longer the chain, the lower the critical temperature above which the charge is in a delocalized state, and, conversely, the shorter the chain, the higher the decay temperature of a polaron. The results of numerical experiments lead to a conclusion that, in an indefinitely long chain, polaron states decay at temperatures differing arbitrarily little from zero.
Molecular structures and intramolecular dynamics of pentahalides
Ischenko, A. A.
2017-03-01
This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.
Molecular dynamics for irradiation driven chemistry: application to the FEBID process*
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.
Li, Jing; D'Avino, Gabriele; Duchemin, Ivan; Beljonne, David; Blase, Xavier
2016-07-21
We present an original hybrid QM/MM scheme merging the many-body Green's function GW formalism with classical discrete polarizable models and its application to the paradigmatic case of a pentacene crystal. Our calculated transport gap is found to be in excellent agreement with reference periodic bulk GW calculations, together with properly parametrized classical microelectrostatic calculations, and with photoionization measurements at crystal surfaces. More importantly, we prove that the gap is insensitive to the partitioning of pentacene molecules in QM and MM subsystems, as a result of the mutual compensation of quantum and classical polarizabilities, clarifying the relation between polarization energy and delocalization. The proposed hybrid method offers a computationally attractive strategy to compute the full spectrum of charged excitations in complex molecular environments, accounting for both QM and MM contributions to the polarization energy, a crucial requirement in the limit of large QM subsystems.
Classical and quantum dynamics of a perfect fluid scalar-energy dependent metric cosmology
Khodadi, M; Vakili, B
2016-01-01
Inspired from the idea of minimally coupling of a real scalar field to geometry, we investigate the classical and quantum models of a flat energy-dependent FRW cosmology coupled to a perfect fluid in the framework of the scalar-rainbow metric gravity. We use the standard Schutz' representation for the perfect fluid and show that under a particular energy-dependent gauge fixing, it may lead to the identification of a time parameter for the corresponding dynamical system. It is shown that, under some circumstances on the minisuperspace prob energy, the classical evolution of the of the universe represents a late time expansion coming from a bounce instead of the big-bang singularity. Then we go forward by showing that this formalism gives rise to a Schr\\"{o}dinger-Wheeler-DeWitt (SWD) equation for the quantum-mechanical description of the model under consideration, the eigenfunctions of which can be used to construct the wave function of the universe. We use the resulting wave function in order to investigate t...
Energy Technology Data Exchange (ETDEWEB)
Fosco, Cesar D. [Comision Nacional de Energia Atomica, Centro Atomico Bariloche, Instituto Balseiro, Bariloche (Argentina); Lombardo, Fernando C. [Ciudad Universitaria, Departamento de Fisica Juan Jose Giambiagi, FCEyN UBA y IFIBA CONICET-UBA, Facultad de Ciencias Exactas y Naturales, Buenos Aires (Argentina)
2015-12-15
We study the properties of the classical electromagnetic radiation produced by two physically different yet closely related systems, which may be regarded as classical analogues of the dynamical Casimir effect. They correspond to two flat, infinite, parallel planes, one of them static and imposing perfect-conductor boundary conditions, while the other performs a rigid oscillatory motion. The systems differ just in the electrical properties of the oscillating plane: one of them is just a planar dipole layer (representing, for instance, a small-width electret). The other, instead, has a dipole layer on the side which faces the static plane, but behaves as a conductor on the other side: this can be used as a representation of a conductor endowed with patch potentials (on the side which faces the conducting plane). We evaluate, in both cases, the dissipative flux of energy between the system and its environment, showing that, at least for small mechanical oscillation amplitudes, it can be written in terms of the dipole layer autocorrelation function. We show that there are resonances as a function of the frequency of the mechanical oscillation. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Fosco, César D. [Centro Atómico Bariloche, Instituto Balseiro, Comisión Nacional de Energía Atómica, R8402AGP, Bariloche (Argentina); Lombardo, Fernando C., E-mail: lombardo@df.uba.ar [Departamento de Física Juan José Giambiagi, FCEyN UBA and IFIBA CONICET-UBA, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Pabellón I, 1428, Buenos Aires (Argentina)
2015-12-17
We study the properties of the classical electromagnetic radiation produced by two physically different yet closely related systems, which may be regarded as classical analogues of the dynamical Casimir effect. They correspond to two flat, infinite, parallel planes, one of them static and imposing perfect-conductor boundary conditions, while the other performs a rigid oscillatory motion. The systems differ just in the electrical properties of the oscillating plane: one of them is just a planar dipole layer (representing, for instance, a small-width electret). The other, instead, has a dipole layer on the side which faces the static plane, but behaves as a conductor on the other side: this can be used as a representation of a conductor endowed with patch potentials (on the side which faces the conducting plane). We evaluate, in both cases, the dissipative flux of energy between the system and its environment, showing that, at least for small mechanical oscillation amplitudes, it can be written in terms of the dipole layer autocorrelation function. We show that there are resonances as a function of the frequency of the mechanical oscillation.
Some fundamental problems for an energy conserving adaptive resolution molecular dynamics scheme
Site, L. Delle
2007-01-01
Adaptive resolution molecular dynamics (MD) schemes allow for changing the number of degrees of freedom on the fly and preserve the free exchange of particles between regions of different resolution. There are two main alternatives on how to design the algorithm to switch resolution using auxiliary ''switching'' functions; force based and potential energy based approach. In this work we show that, in the framework of classical MD, the latter presents fundamental conceptual problems which make...
Ma, Y.G.
2000-01-01
The emission of clusters in the nuclear disassembly is investigated within the framework of isospin dependent lattice gas model and classical molecular dynamics model. As observed in the recent experimental data, it is found that the emission of individual cluster is poissonian and thermal scaling is observed in the linear Arrhenius plots made from the average multiplicity of each cluster. The mass, isotope and charge dependent "emission barriers" are extracted from the slopes of the Arrheniu...
分子高激发振动态的经典非线性性质%The classical nonlinear properties of molecular highly excited vibration
Institute of Scientific and Technical Information of China (English)
吴国祯
2011-01-01
The concepts of classical nonlinear dynamics are employed to interpret the spectroscopic properties of the molecular highly excited vibration. These concepts include the Morse oscillator, the pendulum dynamics, chaos and the overlapping of resonances leading to chaos. The relations of resonance, constant of motion and the basic dynamical unit to the pendulum dynamics are stressed. An algebraic Hamiltonian in the coset space is employed for the dynamical analysis from which the dynamical potential can be easily obtained. The dynamical potential is closely related to the classical fixed points in which the quantized levels are embedded in various quantal environments.Localized modes are easily identified in various systems which share similar dynamical potentials. The dissociation of DCO radical is finally interpreted by these concepts from the classical nonlinear dynamics.%该文阐述如何运用经典非线性力学的概念,来理解分子高激发振动态的谱学性质.内容包括:莫尔斯振子,单摆的动力学和共振的关系,力学体系的构成单元是单摆,一个共振对应于一个守恒量,混沌,共振的重叠导致混沌的产生等.我们的出发点是运用二次量子化算子构成的代数哈密顿量,经由海森伯对应而得到的陪集空间上的动力学体系.从此哈密顿量,可以得到动力学势.而动力学势和经典的不动点关系密切,并且量子态就处在由动力学势所包围,分成的几个量子环境中.从动力学势,可以依据它的对称性,方便推得局域模式的存在,最后我们利用这些非线性力学的概念,来分析DCO分子高激发振动态的解离问题.
Belyaev, Andrey K; Lasser, Caroline; Trigila, Giulio
2014-01-01
The Landau--Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs the recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Four different time scales are detected for the nuclear dynamics: Ultrafast Jahn--Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs; and nearly constant ...
Molecular dynamics study of the mechanical loss in amorphous pure and doped silica
Energy Technology Data Exchange (ETDEWEB)
Hamdan, Rashid; Trinastic, Jonathan P.; Cheng, H. P., E-mail: cheng@qtp.ufl.edu [Department of Physics and Quantum Theory Project, University of Florida, Gainesville, Florida 32611 (United States)
2014-08-07
Gravitational wave detectors and other precision measurement devices are limited by the thermal noise in the oxide coatings on the mirrors of such devices. We have investigated the mechanical loss in amorphous oxides by calculating the internal friction using classical, atomistic molecular dynamics simulations. We have implemented the trajectory bisection method and the non-local ridge method in the DL-POLY molecular dynamics simulation software to carry out those calculations. These methods have been used to locate the local potential energy minima that a system visits during a molecular dynamics trajectory and the transition state between any two consecutive minima. Using the numerically calculated barrier height distributions, barrier asymmetry distributions, relaxation times, and deformation potentials, we have calculated the internal friction of pure amorphous silica and silica mixed with other oxides. The results for silica compare well with experiment. Finally, we use the numerical calculations to comment on the validity of previously used theoretical assumptions.
Calvo, F.; Parneix, P.; Van-Oanh, N.-T.
2010-03-01
The vibrational spectra of the naphthalene, pyrene, and coronene molecules have been computed in the 0-3500 cm-1 infrared range using classical and quantum molecular dynamics simulations based on a dedicated tight-binding potential energy surface. The ring-polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (CMD) methods have been employed to account for quantum nuclear effects. The contributions of quantum delocalization to the line shift and broadening are significant in the entire spectral range and of comparable magnitude as pure thermal effects. While the two methods generally produce similar results, the CMD method may converge slower at low temperature with increasing Trotter discretization number. However, and contrary to the CMD method, the RPMD approach suffers from serious resonance problems at high frequencies and low temperatures.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
Ceriotti, Michele; Manolopoulos, David E
2014-01-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high pressure water.
Size effects in molecular dynamics thermal conductivity predictions
Sellan, D. P.; Landry, E. S.; Turney, J. E.; McGaughey, A. J. H.; Amon, C. H.
2010-06-01
We predict the bulk thermal conductivity of Lennard-Jones argon and Stillinger-Weber silicon using the Green-Kubo (GK) and direct methods in classical molecular dynamics simulations. While system-size-independent thermal conductivities can be obtained with less than 1000 atoms for both materials using the GK method, the linear extrapolation procedure [Schelling , Phys. Rev. B 65, 144306 (2002)] must be applied to direct method results for multiple system sizes. We find that applying the linear extrapolation procedure in a manner consistent with previous researchers can lead to an underprediction of the GK thermal conductivity (e.g., by a factor of 2.5 for Stillinger-Weber silicon at a temperature of 500 K). To understand this discrepancy, we perform lattice dynamics calculations to predict phonon properties and from these, length-dependent thermal conductivities. From these results, we find that the linear extrapolation procedure is only accurate when the minimum system size used in the direct method simulations is comparable to the largest mean-free paths of the phonons that dominate the thermal transport. This condition has not typically been satisfied in previous works. To aid in future studies, we present a simple metric for determining if the system sizes used in direct method simulations are sufficiently large so that the linear extrapolation procedure can accurately predict the bulk thermal conductivity.
Molecular dynamics, spin dynamics study of phonon-magnon interactions in BCC iron
Perera, Dilina; Landau, David P.; Stocks, G. Malcolm; Nicholson, Don; Eisenbach, Markus; Yin, Junqi
2013-03-01
By combining an atomistic many-body potential (Finnis-Sinclair) with a classical Heisenberg-like spin Hamiltonian, we perform combined molecular and spin dynamics simulations to investigate phonon-magnon interactions in BCC iron. The coupling between atomic and spin degrees of freedom is established via a distance dependent exchange interaction derived from first principles electronic structure calculations. Coupled equations of motion are integrated using a second order Suzuki-Trotter decomposition of the exponential time evolution operator. To investigate the effect of lattice vibrations on spin wave spectrum, we calculate spin-spin and density-density dynamic structure factors S(q, ω), and compare that to the results obtained from pure spin dynamics simulations performed on a rigid lattice. In the presence of lattice vibrations, we observe an additional peak in the longitudinal spin-spin dynamic structure factor which coincides with the peak position in density-density dynanmic structure factor. Research sponsored by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, ''Center for Defect Physics,'' an Energy Frontier Research Center
Molecular Dynamics Simulations and XAFS (MD-XAFS)
Energy Technology Data Exchange (ETDEWEB)
Schenter, Gregory K.; Fulton, John L.
2017-01-20
MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.
A general solution for classical sequential growth dynamics of Causal Sets
Varadarajan, M; Rideout, David; Varadarajan, Madhavan
2006-01-01
A classical precursor to a full quantum dynamics for causal sets has been forumlated in terms of a stochastic sequential growth process in which the elements of the causal set arise in a sort of accretion process. The transition probabilities of the Markov growth process satisfy certain physical requirements of causality and general covariance, and the generic solution with all transition probabilities non-zero has been found. Here we remove the assumption of non-zero probabilities, define a reasonable extension of the physical requirements to cover the case of vanishing probabilities, and find the completely general solution to these physical conditions. The resulting family of growth processes has an interesting structure reminiscent of an ``infinite tower of turtles'' cosmology.
Regular and chaotic classical dynamics in the U(5)-SU(3) quantum phase transition of the IBM
Macek, M
2012-01-01
We study the classical dynamics in a generic first-order quantum phase transition between the U(5) and SU(3) limits of the interacting boson model. The dynamics is chaotic, of H\\'enon-Heiles type, in the spherical phase and is regular, yet sensitive to local degeneracies, in the deformed phase. Both types of dynamics persist in the coexistence region resulting in a divided phase space.
Ammari, Zied; Falconi, Marco
2014-10-01
We consider the classical limit of the Nelson model, a system of stable nucleons interacting with a meson field. We prove convergence of the quantum dynamics towards the evolution of the coupled Klein-Gordon-Schrödinger equation. Also, we show that the ground state energy level of nucleons, when is large and the meson field approaches its classical value, is given by the infimum of the classical energy functional at a fixed density of particles. Our study relies on a recently elaborated approach for mean field theory and uses Wigner measures.
Molecular Dynamics Simulations of Hypervelocity Impacts
Owens, Eli T.; Bachlechner, Martina E.
2007-03-01
Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.
Molecular dynamics simulation of laser shock phenomena
Energy Technology Data Exchange (ETDEWEB)
Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).
2001-10-01
Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)
Molecular dynamics study of ice structural evolution
Institute of Scientific and Technical Information of China (English)
Wang Yan; Dong Shun-Le
2008-01-01
Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of～1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.
Molecular Dynamics Simulations for Predicting Surface Wetting
Directory of Open Access Journals (Sweden)
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Nanodrop contact angles from molecular dynamics simulations
Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim
2016-11-01
The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
A molecular dynamics approach to barrodiffusion
Cooley, James; Marciante, Mathieu; Murillo, Michael
2016-10-01
Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin
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.
Molecular-dynamic study of liquid ethylenediamine
Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.
2016-10-01
Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.
Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.
Energy Technology Data Exchange (ETDEWEB)
Ogata, S.
1998-01-27
Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.
Molecular Dynamics Simulations of Polyelectrolyte Solutions
Dobrynin, Andrey
2014-03-01
Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) β . The exponent β = -1/2 for chain persistence length lp , β = 1/4 for solution correlation length, β = -1/5 and β = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings
Mixtures of protic ionic liquids and molecular cosolvents: a molecular dynamics simulation.
Docampo-Álvarez, Borja; Gómez-González, Víctor; Méndez-Morales, Trinidad; Carrete, Jesús; Rodríguez, Julio R; Cabeza, Óscar; Gallego, Luis J; Varela, Luis M
2014-06-07
In this work, the effect of molecular cosolvents (water, ethanol, and methanol) on the structure of mixtures of these compounds with a protic ionic liquid (ethylammonium nitrate) is analyzed by means of classical molecular dynamics simulations. Included are as-yet-unreported measurements of the densities of these mixtures, used to test our parameterized potential. The evolution of the structure of the mixtures throughout the concentration range is reported by means of the calculation of coordination numbers and the fraction of hydrogen bonds in the system, together with radial and spatial distribution functions for the various molecular species and molecular ions in the mixture. The overall picture indicates a homogeneous mixing process of added cosolvent molecules, which progressively accommodate themselves in the network of hydrogen bonds of the protic ionic liquid, contrarily to what has been reported for their aprotic counterparts. Moreover, no water clustering similar to that in aprotic mixtures is detected in protic aqueous mixtures, but a somehow abrupt replacing of [NO3](-) anions in the first hydration shell of the polar heads of the ionic liquid cations is registered around 60% water molar concentration. The spatial distribution functions of water and alcohols differ in the coordination type, since water coordinates with [NO3](-) in a bidentate fashion in the equatorial plane of the anion, while alcohols do it in a monodentate fashion, competing for the oxygen atoms of the anion. Finally, the collision times of the different cosolvent molecules are also reported by calculating their velocity autocorrelation functions, and a caging effect is observed for water molecules but not in alcohol mixtures.
Duran-Olivencia, Miguel A.; Yatsyshin, Peter; Lutsko, James F.; Kalliadasis, Serafim
2016-11-01
Classical density functional theory (DFT) for fluids and its dynamic extension (DDFT) provide an appealing mean-field framework for describing equilibrium and dynamics of complex soft matter systems. For a long time, homogeneous nucleation was considered to be outside the limits of applicability of DDFT. However, our recently developed mesoscopic nucleation theory (MeNT) based on fluctuating hydrodynamics, reconciles the inherent randomness of the nucleation process with the deterministic nature of DDFT. It turns out that in the weak-noise limit, the most likely path (MLP) for nucleation to occur is determined by the DDFT equations. We present computations of MLPs for homogeneous and heterogeneous nucleation in colloidal suspensions. For homogeneous nucleation, the MLP obtained is in excellent agreement with the reduced order-parameter description of MeNT, which predicts a multistage nucleation pathway. For heterogeneous nucleation, the presence of impurities in the fluid affects the MLP, but remarkably, the overall qualitative picture of homogeneous nucleation persists. Finally, we highlight the use of DDFT as a simulation tool, which is especially appealing as there are no known applications of MeNT to heterogeneous nucleation. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031 and from EPSRC via Grants No. EP/L020564 and EP/L025159.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)
2015-06-28
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-06-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Force, Thomas; Woulfe, Kathleen; Koch, Walter J; Kerkelä, Risto
2007-07-31
Signaling downstream of classical seven-transmembrane domain receptors (7TMRs) had generally been thought to recruit factors that are in large part separate from those recruited by atypical 7TMRs, such as Frizzleds (Fzs), receptors for the Wnt family of glycoproteins. Classical 7TMRs are also known as G protein-coupled receptors (GPCRs) and are mediated by signaling factors such as heterotrimeric guanine nucleotide-binding proteins (G proteins), GPCR kinases (GRKs), and beta-arrestins. Over the past few years, it has become increasingly apparent that classical and atypical 7TMRs share these factors, which are often associated with mediating classical 7TMR signaling, as well as the scaffolding proteins that were initially thought to be involved in transmitting atypical 7TMR signals. This sharing of signaling components by agonists that bind classical 7TMRs and those binding to atypical 7TMRs establishes the possibility of extensive crosstalk between these receptor classes. We discuss the evidence for, and against, crosstalk, and examine mechanisms by which this can occur.
Wolthers, M.; Di Tommaso, D.; Du, Zhimei; de Leeuw, Nora H.
2013-01-01
It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two orde
Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure
2014-08-30
properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to
Galapon, E A
2001-01-01
We raise the problem of constructing quantum observables that have classical counterparts without quantization. Specifically we seek to define and motivate a solution to the quantum-classical correspondence problem independent from quantization and discuss the general insufficiency of prescriptive quantization, particularly the Weyl quantization. We demonstrate our points by constructing time of arrival operators without quantization and from these recover their classical counterparts.
Indian Academy of Sciences (India)
Bhabani S Mallik; Amalendu Chandra
2012-01-01
We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.
Energy Technology Data Exchange (ETDEWEB)
Horner, Daniel A.; Miyabe, Shungo; Rescigno, Thomas N; McCurdy, C. William; Morales, Felipe; Martin, Fernando
2008-07-06
Recent experiments on double photoionization of H$_2$ with photon energies between 160 and 240 eV have revealed body-frame angular distributions that suggest classical two-slit interference effects may be present when one electron carries most of the available energy and the second electron is not observed. We report precise quantum mechanical calculations that reproduce the experimental findings. They reveal that the interpretation in terms of classical diffraction is only appropriate atsubstantially higher photon energies. At the energies considered in the experiment we offer an alternative explanation based on the mixing of two non-diffractive contributions by circularly polarized light.
How Dynamic Visualization Technology Can Support Molecular Reasoning
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
Molecular Dynamics Studies of Energy Transfer Processes in Crystal Systems.
1984-11-30
Computer molecular dynamics studies have been carried out on the problem of attaining a fundamental understanding of shock-induced initiation of...intramolecular energy exchange in shock-loaded systems are presented. Originator-supplied keywords include: Molecular dynamics , Energy transfer, Shock front, Shock wave, Explosives, Shock structure.
Nanoscale deicing by molecular dynamics simulation
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-07-01
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice
Molecular dynamics study on a frequency-changeable nanotube cantilever resonator
Energy Technology Data Exchange (ETDEWEB)
Kang, Jeong Won; Choi, Young Gyu; Kim, Ki Sub [Chungju National University, Chungju (Korea, Republic of); Lee, Jun Ha [Sangmyung University, Chonan (Korea, Republic of); Song, Young Jin [Konyang University, Nonsan (Korea, Republic of); Hwang, Ho Jung [Chung-Ang National University, Seoul (Korea, Republic of)
2010-05-15
In this paper, the dynamics of a tunable resonator, which is based on the application of a telescoped multi-walled carbon nanotube that can be used repeatedly, is investigated via classical molecular dynamics simulations based on a double-walled carbon nanotube as the most simple multi-walled carbon nanotube. The fixed short outer nanotube rigidly confines the longer core nanotube, which can be freely telescoped. Such a system can tune its resonance frequency by controlling the length of the oscillating carbon nanotube.
Phonon-magnon interactions in body centered cubic iron: A combined molecular and spin dynamics study
Energy Technology Data Exchange (ETDEWEB)
Perera, Dilina, E-mail: dilinanp@physast.uga.edu; Landau, David P. [Center for Simulational Physics, The University of Georgia, Georgia 30602 (United States); Nicholson, Don M.; Malcolm Stocks, G.; Eisenbach, Markus; Yin, Junqi [Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Brown, Gregory [Florida State University, Tallahassee, Florida 32306 (United States)
2014-05-07
Combining an atomistic many-body potential with a classical spin Hamiltonian parameterized by first principles calculations, molecular-spin dynamics computer simulations were performed to investigate phonon-magnon interactions in body centered cubic iron. Results obtained for spin-spin and density-density dynamic structure factors show that noticeable softening and damping of magnon modes occur due to the presence of lattice vibrations. Furthermore, as a result of the phonon-magnon coupling, additional longitudinal spin wave excitations are observed, with the same frequencies as the longitudinal phonon modes.
Phonon-magnon interactions in BCC iron: A combined molecular and spin dynamics study
Energy Technology Data Exchange (ETDEWEB)
Perera, Meewanage Dilina N [ORNL; Landau, David P [University of Georgia, Athens, GA; Nicholson, Don M [ORNL; Stocks, George Malcolm [ORNL; Eisenbach, Markus [ORNL; Yin, Junqi [ORNL; Brown, Greg [ORNL
2014-01-01
Combining an atomistic many-body potential with a classical spin Hamiltonian pa- rameterized by first principles calculations, molecular-spin dynamics computer sim- ulations were performed to investigate phonon-magnon interactions in BCC iron. Results obtained for spin-spin and density-density dynamic structure factors show that noticeable softening and damping of magnon modes occur due to the presence of lattice vibrations. Furthermore, as a result of the phonon-magnon coupling, addi- tional longitudinal spin wave excitations are observed, with the same frequencies as the longitudinal phonon modes.
Langeveld, J.P.M.; Jacobs, J.G.; Erkens, J.H.F.; Baron, T.; Andreoletti, O.; Yokoyama, T.; Keulen, van L.J.M.; Zijderveld, van F.G.; Davidse, A.; Hope, J.; Tang, Y.; Bossers, A.
2014-01-01
Efforts to differentiate bovine spongiform encephalopathy (BSE) from scrapie in prion infected sheep have resulted
in effective methods to decide about the absence of BSE. In rare instances uncertainties remain due to assumptions
that BSE, classical scrapie and CH1641–a rare scrapie variant–
Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach.
Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano
2017-03-10
Peptides have gained increased interest as therapeutic agents during recent years. The high specificity and relatively low toxicity of peptide drugs derive from their extremely tight binding to their targets. Indeed, understanding the molecular mechanism of protein-peptide recognition has important implications in the fields of biology, medicine, and pharmaceutical sciences. Even if crystallography and nuclear magnetic resonance are offering valuable atomic insights into the assembling of the protein-peptide complexes, the mechanism of their recognition and binding events remains largely unclear. In this work we report, for the first time, the use of a supervised molecular dynamics approach to explore the possible protein-peptide binding pathways within a timescale reduced up to three orders of magnitude compared with classical molecular dynamics. The better and faster understating of the protein-peptide recognition pathways could be very beneficial in enlarging the applicability of peptide-based drug design approaches in several biotechnological and pharmaceutical fields.
The MOLDY short-range molecular dynamics package
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
Direct anharmonic correction method by molecular dynamics
Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang
2017-04-01
The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.
Efficient compression of molecular dynamics trajectory files.
Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James
2012-10-15
We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases.
Molecular Dynamics Study of Helicobacter pylori Urease.
Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M
2014-05-13
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.
Molecular dynamics simulation of flow in pores
Blömer, Jan
2001-08-01
The gaseous flow in nano-scale pores is of wide interest for many today's industrial applications, e.g., in microelectronics, nano-mechanical devices (Knudsen compressor) and reaction and adsorption at porous surfaces. This can be seen from a variety of papers of recent RGD Symposia. Furthermore it is possible to separate gases by porous membranes. Although the fundamental problem of all these applications is same, namely the important role of the gas-surface interaction in such small structures, we will primarily concentrate on the separation of different gas species by porous membranes. These membranes are typically very robust (temperature, chemical resistance) because they are made from ceramics which offers new application fields. Porous flow can roughly be divided in several flow regimes by the Knudsen number: From viscous flow to Knudsen diffusion to surface diffusion and up to capillary condensation. A Molecular Dynamics (MD) model for the gas as well as the surface is formulated to investigate the interaction of gas atoms or molecules with internal degrees of freedom and the pore. The MD method seems to be well suited to study these phenomena because it can deal with the high density and the many-body-interactions, which occur during the multilayer adsorption and condensation at the surface, although it is clear that it is limited to a small physical space because of its high computational consumption.
Molecular dynamics simulations of vibrated granular gases.
Barrat, Alain; Trizac, Emmanuel
2002-11-01
We present molecular dynamics simulations of monodisperse or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met experimentally, density and temperature fields display heterogeneous profiles in the direction perpendicular to the walls. A general equation of state for an arbitrary mixture of fluidized inelastic hard spheres is derived and successfully tested against numerical data. Single-particle velocity distribution functions with non-Gaussian features are also obtained, and the influence of various parameters (inelasticity coefficients, density, etc.) are analyzed. The validity of a recently proposed random restitution coefficient model is assessed through the study of projected collisions onto the direction perpendicular to that of energy injection. For the binary mixture, the nonequipartition of translational kinetic energy is studied and compared both to experimental data and to the case of homogeneous energy injection ("stochastic thermostat"). The rescaled velocity distribution functions are found to be very similar for both species.
Nanoscale deicing by molecular dynamics simulation.
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-08-14
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.
MOLECULAR DYNAMIC SIMULATION OF PEPTIDE POLYELECTROLYTES
Directory of Open Access Journals (Sweden)
I. M. Neelov
2014-07-01
Full Text Available The paper deals with investigation of the conformational properties of some charged homopolypeptides in dilute aqueous solutions by computer simulation. A method of molecular dynamics for the full-atomic models of polyaspartic acid and polylysine with explicit account of water and counter-ions is used for this purpose. For systems containing these polypeptides we calculated time trajectories and the size, shape, distribution functions and time correlation functions of inertia radius and the distances between the ends of peptide chains. We have also calculated the solvatation characteristics of considered polyelectrolytes. We have found out that polyaspartic acid in dilute aqueous solution has more compact structure and more spherical shape than polylysine. We have shown that these differences are due to different interaction between the polypeptides and water molecules (in particular, the quality and quantity of hydrogen bonds formed by these peptides with water, and the difference in an amount of ion pairs formed by the charged groups of the peptides and counter-ions. The obtained results should be taken into account for elaboration of new products based on the investigated peptides and their usage in various industrial and biomedical applications.
Transport properties of liquid para-hydrogen: The path integral centroid molecular dynamics approach
Yonetani, Yoshiteru; Kinugawa, Kenichi
2003-11-01
Several fundamental transport properties of a quantum liquid para-hydrogen (p-H2) at 17 K have been numerically evaluated by means of the quantum dynamics simulation called the path integral centroid molecular dynamics (CMD). For comparison, classical molecular dynamics (MD) simulations have also been performed under the same condition. In accordance with the previous path integral simulations, the calculated static properties of the liquid agree well with the experimental results. For the diffusion coefficient, thermal conductivity, and shear viscosity, the CMD predicts the values closer to the experimental ones though the classical MD results are far from the reality. The agreement of the CMD result with the experimental one is especially good for the shear viscosity with the difference less than 5%. The calculated diffusion coefficient and the thermal conductivity agree with the experimental values at least in the same order. We predict that the ratio of bulk viscosity to shear viscosity for liquid p-H2 is much larger than classical van der Waals simple liquids such as rare gas liquids.
Molecular dynamics simulations of non-Fourier heat conduction
Institute of Scientific and Technical Information of China (English)
2008-01-01
Unsteady heat conduction is known to deviate significantly from Fourier's law when the system time and length scales are within certain temporal and spatial windows of relaxation. Classical molecular dynamics simulations were used to investigate unsteady heat conduction in argon thin films with a sudden temperature increase or heat flux at one surface to study the non-Fourier heat conduction effects in argon thin films. The studies were conducted with both pure argon films and films with vacancy defects. The temperature pro- files in the argon films showed the existence of mechanical waves when the thin film was suddenly heated and the wave nature of the heat propagation. The flux phase relaxation time, τq, and the temperature phase relaxation time, τq were calculated from the temporal vari- ations of the energy flux and temperature distribution in the film. Comparisons of the MD temperature profiles with temperature profiles predicted by Fourier's law show that Fourier's law is not able to predict the temperature variations with time. Different film thicknesses were also studied to illustrate the variation of the time needed for the films to reach steady-state temperature profiles after a sudden tem- perature rise at one surface and to illustrate the finite speed of the energy waves.
Can molecular dynamics help in understanding dielectric phenomena?
Olmi, Roberto; Bittelli, Marco
2017-01-01
Molecular dynamics (MD) is a modeling technique widely used in material science as well as in chemical physics, biochemistry and biophysics. MD is based on ‘first principles’, allowing one to compute the physical characteristics of a material, such as density, heat capacity, isothermal compressibility and also the dielectric constant and relaxation, mixing a classical physics approach and statistical mechanics. Although a number of papers exist in the literature concerning the study of the dielectric properties of liquid and solid materials, the MD approach appears to be almost ignored in the electromagnetic aquametry community. We use a rather simple example, a mixture of ethanol and water at various concentrations, to introduce MD as a theoretical tool for investigating the dielectric behavior of more complex moist substances. We show that MD simulations suggest a time-domain model for alcohol-water solutions, consisting in a mixture of a KWW stretched-exponential and a simple exponential, whose validity could be subjected to an experimental verification.
Wave packet molecular dynamics simulations of warm dense hydrogen
Knaup, M; Toepffer, C; Zwicknagel, G
2003-01-01
Recent shock-wave experiments with deuterium in a regime where a plasma phase-transition has been predicted and their theoretical interpretation are the matter of a controversial discussion. In this paper, we apply 'wave packet molecular dynamics' (WPMD) simulations to investigate warm dense hydrogen. The WPMD method was originally used by Heller for a description of the scattering of composite particles such as simple atoms and molecules; later it was applied to Coulomb systems by Klakow et al. In the present version of our model the protons are treated as classical point-particles, whereas the electrons are represented by a completely anti-symmetrized Slater sum of periodic Gaussian wave packets. We present recent results for the equation of state of hydrogen at constant temperature T = 300 K and of deuterium at constant Hugoniot E - E sub 0 + 1/2(1/n - 1/n sub 0)(p + p sub 0) = 0, and compare them with the experiments and several theoretical approaches.
Pasta Nucleosynthesis: Molecular dynamics simulations of nuclear statistical equilibrium
Caplan, M E; Horowitz, C J; Berry, D K
2014-01-01
Background: Exotic non-spherical nuclear pasta shapes are expected in nuclear matter at just below saturation density because of competition between short range nuclear attraction and long range Coulomb repulsion. Purpose: We explore the impact of nuclear pasta on nucleosynthesis, during neutron star mergers, as cold dense nuclear matter is ejected and decompressed. Methods: We perform classical molecular dynamics simulations with 51200 and 409600 nucleons, that are run on GPUs. We expand our simulation region to decompress systems from an initial density of 0.080 fm^{-3} down to 0.00125 fm^{-3}. We study proton fractions of Y_P=0.05, 0.10, 0.20, 0.30, and 0.40 at T =0.5, 0.75, and 1.0 MeV. We calculate the composition of the resulting systems using a cluster algorithm. Results: We find final compositions that are in good agreement with nuclear statistical equilibrium models for temperatures of 0.75 and 1 MeV. However, for proton fractions greater than Y_P=0.2 at a temperature of T = 0.5 MeV, the MD simulatio...
Indian Academy of Sciences (India)
A NASSOUR
2016-09-01
In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the ‘force matching’ method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various temperatures. Classical molecular dynamics simulations are performed to examine structural, coordination numbers, structure factors and dynamic properties of Au$_{81}$Si$_{19}$ alloy, with the interaction described via EAM model. The results are in good agreement with AIMD simulations and experimental data.
Guillemin, Ernst A
2013-01-01
An eminent electrical engineer and authority on linear system theory presents this advanced treatise, which approaches the subject from the viewpoint of classical dynamics and covers Fourier methods. This volume will assist upper-level undergraduates and graduate students in moving from introductory courses toward an understanding of advanced network synthesis. 1963 edition.
Molecular dynamics simulation study of water adsorption on hydroxylated graphite surfaces.
Picaud, Sylvain; Collignon, B; Hoang, Paul N M; Rayez, J C
2006-04-27
In this paper, we present results from molecular dynamic simulations devoted to the characterization of the interaction between water molecules and hydroxylated graphite surfaces considered as models for surfaces of soot emitted by aircraft. The hydroxylated graphite surfaces are modeled by anchoring several OH groups on an infinite graphite plane. The molecular dynamics simulations are based on a classical potential issued from quantum chemical calculations. They are performed at three temperatures (100, 200, and 250 K) to provide a view of the structure and dynamics of water clusters on the model soot surface. These simulations show that the water-OH sites interaction is quite weak compared to the water-water interaction. This leads to the clustering of the water molecules above the surface, and the corresponding water aggregate can only be trapped by the OH sites when the temperature is sufficiently low, or when the density of OH sites is sufficiently high.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Energy Technology Data Exchange (ETDEWEB)
Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy)
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Environment and initial state engineered dynamics of quantum and classical correlations
Wang, Cheng-Zhi; Li, Chun-Xian; Guo, Yu; Lu, Geng-Biao; Ding, Kai-He
2016-11-01
Based on an open exactly solvable system coupled to an environment with nontrivial spectral density, we connect the features of quantum and classical correlations with some features of the environment, initial states of the system, and the presence of initial system-environment correlations. Some interesting features not revealed before are observed by changing the structure of environment, the initial states of system, and the presence of initial system-environment correlations. The main results are as follows. (1) Quantum correlations exhibit temporary freezing and permanent freezing even at high temperature of the environment, for which the necessary and sufficient conditions are given by three propositions. (2) Quantum correlations display a transition from temporary freezing to permanent freezing by changing the structure of environment. (3) Quantum correlations can be enhanced all the time, for which the condition is put forward. (4) The one-to-one dependency relationship between all kinds of dynamic behaviors of quantum correlations and the initial states of the system as well as environment structure is established. (5) In the presence of initial system-environment correlations, quantum correlations under local environment exhibit temporary multi-freezing phenomenon. While under global environment they oscillate, revive, and damp, an explanation for which is given.
Qin, Yue
Scope and method of study. The tunneling effects in isomerization of HONO and HSiOH have been studied by using classical trajectories with semiclassical tunneling corrections. The potential energy surfaces were constructed by using the available ab initio, spectroscopic and thermodynamic data. A constrained classical trajectory method was employed to study the roles of the various vibrational modes and molecular rotation in intramolecular energy transfer in cis trans HONO. Findings and conclusions. The results show that the rate constants for cisto trans are generally larger than transto cis for HONO isomerizations. Excitations of the OH and N=O stretches yield the smallest rate constants while the N -O stretch excitation gives the largest rate for both cis to trans and transto cis. The rate of energy transfer from bath modes to the torsional mode is found to be a dominant factor for determining the tunneling rate. Similar behaviors are found in the isomerization of HSiOH. The Si-O stretch excitation gives the largest rate constants and the OH stretch excitation yields the smallest rate constants for both cisto trans and transto cis isomerizations. The ratio of the decay rate with tunneling correction to that without tunneling increases with decreasing total energy of the system. Furthermore, the rate difference between the cisto trans and trans to cis decreases with increasing the excitation energy. The values of the effective mass along the tunneling coordinate can facilitate or hinder the tunneling probability. We find that tunneling effects plays an important role in the isomerization of HSiOH. Our results also elucidate that the ONO bending and torsional modes are important for the relaxation of the excited OH stretch. Removing the torsional motion eliminates the influence of rotation on the intramolecular vibrational energy relaxation. The effects of constraining the ONO bending plays a much smaller role than does constraining the HON bending for decreasing
Hsu, Po Jen; Lai, S K; Rapallo, Arnaldo
2014-03-14
solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations.
Canning, A.; Galli, G.; Mauri, F.; De Vita, A.; Car, R.
1996-04-01
The implementation of an O( N) tight-binding molecular dynamics code on the Cray T3D parallel computer is discussed. The O( N) energy functional depends on non-orthogonal, localised orbitals and a chemical potential parameter which determines the number of electrons in the system. The localisation introduces a sparse nature to the orbital data and Hamiltonian matrix, greatly changing the coding on parallel machines compared to non-localised systems. The data distribution, communication routines and dynamic load-balancing scheme of the program are presented in detail together with the speed and scaling of the code on various homogeneous and inhomogeneous physical systems. Performance results will be presented for systems of 2048 to 32768 atoms on 32 to 512 processors. We discuss the relevance to quantum molecular dynamics simulations with localised orbitals, of techniques used for programming short-range classical molecular dynamics simulations on parallel machines. The absence of global communications and the localised nature of the orbitals makes these algorithms extremely scalable in terms of memory and speed on parallel systems with fast communications. The main aim of this article is to present in detail all the new concepts and programming techniques that localisation of the orbitals introduces which scientists, coming from a background in non-localised quantum molecular dynamics simulations, may be unfamiliar with.
Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure
Garcia-Garibay, Miguel A.
2005-01-01
Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the...
Jambrina, P G; Aoiz, F J; Bulut, N; Smith, Sean C; Balint-Kurti, G G; Hankel, M
2010-02-01
A detailed study of the proton exchange reaction H(+) + D(2)(v = 0, j = 0) --> HD + D(+) on its ground 1(1)A' potential energy surface has been carried out using 'exact' close-coupled quantum mechanical wavepacket (WP-EQM), quasi-classical trajectory (QCT), and statistical quasi-classical trajectory (SQCT) calculations for a range of collision energies starting from the reaction threshold to 1.3 eV. The WP-EQM calculations include all total angular momenta up to J(max) = 50, and therefore the various dynamical observables are converged up to 0.6 eV. It has been found that it is necessary to include all Coriolis couplings to obtain reliable converged results. Reaction probabilities obtained using the different methods are thoroughly compared as a function of the total energy for a series of J values. Comparisons are also made of total reaction cross sections as function of the collision energy, and rate constants. In addition, opacity functions, integral cross sections (ICS) and differential cross sections (DCS) are presented at 102 meV, 201.3 meV and 524.6 meV collision energy. The agreement between the three sets of results is only qualitative. The QCT calculations fail to describe the overall reactivity and most of the dynamical observables correctly. At low collision energies, the QCT method is plagued by the lack of conservation of zero point energy, whilst at higher collision energies and/or total angular momenta, the appearance of an effective repulsive potential associated with the centrifugal motion "over" the well causes a substantial decrease of the reactivity. In turn, the statistical models overestimate the reactivity over the whole range of collision energies as compared with the WP-EQM method. Specifically, at sufficiently high collision energies the reaction cannot be deemed to be statistical and important dynamical effects seem to be present. In general the WP-EQM results lie in between those obtained using the QCT and SQCT methods. One of the main
Molecular Dynamics of Materials Possessing High Energy Content.
1988-01-26
I -RI90 634 MOLECULAR DYNAMICS OF MATERIALS POSSESSING HIGH ENERGY 1/1 r CONTENTCU) COLUMBIA UNIV MENd YORK N J TURRO 26 JAN GO I RFOSR-TR-88-0168...Bolling Air Force Base, D.C. 2 61102F_ 2303 I B2 11 T,TL.E (Inciuoe Security Classification) Molecular Dynamics of Materials Possessing High Energy...York 10027 (212) 280-2175 TITLE: MOLECULAR DYNAMICS OF MATERIALS POSSESSING HIGH ENERGY CONTENT .. 0 0 88 2 ... "" ’% ,i u , . .. .. ....... ŝ" ;! ,i
Visualization and orchestration of the dynamic molecular society in cells
Institute of Scientific and Technical Information of China (English)
Xuebiao Yao; Guowei Fang
2009-01-01
@@ Visualization of specific molecules and their interactions in real space and time is essential to delineate how cellular plasticity and dynamics are achieved and orchestrated as perturbation of cellular plasticity and dynamics is detrimental to health. Elucidation of cellular dynamics requires molecular imaging at nanometer scale at millisecond resolution. The 1st International Conference on Cellular Dynamics and Chemical Biology held in Hefei, China (from 12 September to 15 September,2008) launched the quest by bringing synergism among photonics, chemistry and biology.
Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics
Vila Verde, A.; Beltramo, Peter J.; Maranas, Janna K.
2011-01-01
We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala 10 , Ser 10 , Thr 10 , Arg 10 , Lys 10 , and Gln 10 ], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movemen...
Zimmermann, Tomas
2011-01-01
We propose to measure nonadiabaticity of molecular quantum dynamics rigorously with the quantum fidelity between the Born-Oppenheimer and fully nonadiabatic dynamics. It is shown that this measure of nonadiabaticity applies in situations where other criteria, such as the energy gap criterion or the extent of population transfer, fail. We further propose to estimate this quantum fidelity efficiently with a generalization of the dephasing representation to multiple surfaces. Two variants of the multiple-surface dephasing representation (MSDR) are introduced, in which the nuclei are propagated either with the fewest-switches surface hopping (FSSH) or with the locally mean field dynamics (LMFD). The LMFD can be interpreted as the Ehrenfest dynamics of an ensemble of nuclear trajectories, and has been used previously in the nonadiabatic semiclassical initial value representation. In addition to propagating an ensemble of classical trajectories, the MSDR requires evaluating nonadiabatic couplings and solving the Sc...
Molecular dynamics using quasielastic neutron scattering
Mitra, S
2003-01-01
Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)
Capillary dynamics driven by molecular self-layering.
Wu, Pingkeng; Nikolov, Alex; Wasan, Darsh
2017-02-10
Capillary dynamics is a ubiquitous everyday phenomenon. It has practical applications in diverse fields, including ink-jet printing, lab-on-a-chip, biotechnology, and coating. Understanding capillary dynamics requires essential knowledge on the molecular level of how fluid molecules interact with a solid substrate (the wall). Recent studies conducted with the surface force apparatus (SFA), atomic force microscope (AFM), and statistical mechanics simulation revealed that molecules/nanoparticles confined into the film/wall surfaces tend to self-layer into 2D layer/s and even 2D in-layer with increased confinement and fluid volume fraction. Here, the capillary rise dynamics of simple molecular fluids in cylindrical capillary is explained by the molecular self-layering model. The proposed model considers the role of the molecular shape on self-layering and its effect on the molecularly thin film viscosity in regards to the advancing (dynamic) contact angle. The model was tested to explain the capillary rise dynamics of fluids of spherical, cylindrical, and disk shape molecules in borosilicate glass capillaries. The good agreement between the capillary rise data and SFA data from the literature for simple fluid self-layering shows the validity of the present model. The present model provides new insights into the design of many applications where dynamic wetting is important because it reveals the significant impact of molecular self-layering close to the wall on dynamic wetting.
Maheux, Andrée F; Huppé, Vicky; Bissonnette, Luc; Boissinot, Maurice; Rodrigue, Lynda; Bérubé, Ève; Bergeron, Michel G
2012-11-01
The microbiological quality of 165 1 litre well water samples collected in the Québec City region was assessed by culture-based methods (mFC agar, Chromocult coliform agar, Colilert(®), MI agar, Chromocult enterococci, Enterolert™, and mEI agar) and by a molecular microbiology strategy, dubbed CRENAME-rtPCR, developed for the detection of Escherichia coli, Enterococcus spp., Enterococcus faecalis/faecium, and Bacillus atrophaeus subsp. globigii. In these drinking water samples, approved culture-based methods detected E. coli at rates varying from 1.8 to 3.6% and Enterococcus spp. at rates varying from 3.0 to 11.5%, while the molecular microbiology approach for E. coli was found to be as efficient, detecting contamination in 3.0% of samples. In contrast, CRENAME-rtPCR detected Enterococcus spp. in 27.9% of samples while the E. faecalis/faecium molecular assay did not uncover a single contaminated sample, thereby revealing a discrepancy in the coverage of waterborne enterococcal species detected by classical and molecular microbiology methods. The validation of the CRENAME-E. coli rtPCR test as a new tool to assess the quality of drinking water will require larger scale studies elaborated to demonstrate its equivalence to approved methods.
Onisko, Agnieszka; Druzdzel, Marek J.; Austin, R. Marshall
2016-01-01
Background: Classical statistics is a well-established approach in the analysis of medical data. While the medical community seems to be familiar with the concept of a statistical analysis and its interpretation, the Bayesian approach, argued by many of its proponents to be superior to the classical frequentist approach, is still not well-recognized in the analysis of medical data. Aim: The goal of this study is to encourage data analysts to use the Bayesian approach, such as modeling with graphical probabilistic networks, as an insightful alternative to classical statistical analysis of medical data. Materials and Methods: This paper offers a comparison of two approaches to analysis of medical time series data: (1) classical statistical approach, such as the Kaplan–Meier estimator and the Cox proportional hazards regression model, and (2) dynamic Bayesian network modeling. Our comparison is based on time series cervical cancer screening data collected at Magee-Womens Hospital, University of Pittsburgh Medical Center over 10 years. Results: The main outcomes of our comparison are cervical cancer risk assessments produced by the three approaches. However, our analysis discusses also several aspects of the comparison, such as modeling assumptions, model building, dealing with incomplete data, individualized risk assessment, results interpretation, and model validation. Conclusion: Our study shows that the Bayesian approach is (1) much more flexible in terms of modeling effort, and (2) it offers an individualized risk assessment, which is more cumbersome for classical statistical approaches. PMID:28163973
Dynamical Systems and Control Theory Inspired by Molecular Biology
2014-10-02
in both bacterial and eukaryotic signaling pathways. A common theme in the systems biology literature is that certain systems whose output variables...AFRL-OSR-VA-TR-2014-0282 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY Eduardo Sontag RUTGERS THE STATE UNIVERSITY OF NEW JERSEY...Standard Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY AFOSR FA9550-11-1-0247
Classical against molecular-genetic methods for susceptibility testing of antituberculotics.
Porvaznik, I; Mokry, J; Solovic, I
2015-01-01
Tuberculosis currently belongs to rare respiratory diseases in Slovakia. However, the emergence and spread of multi-drug resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) are major challenges for global tuberculosis control, since the treatment of resistant forms creates both medical and financial problems. Cultivation methods of diagnosis are time-consuming, many times exceeding the time of the initial phase of tuberculosis treatment. Therefore, in the presented study we compared the standard procedures, based on the cultivation of mycobacteria and subsequent drug susceptibility testing to antituberculotics, with molecular-genetic methods using PCR diagnostic kits. The molecular-genetic testing enables to obtain direct and fast evidence of Mycobacterium tuberculosis, with genomic verification of resistance to the most important anti-tuberculosis drugs - isoniazid and rifampicin in MDR-TB, and ethambutol, aminoglycosides, and fluoroquinolones in XDR-TB. In 2012-2013, we confirmed 19 cases of drug-resistant tuberculosis in Slovakia. The resistance to rifampicin was confirmed in all strains with both methods. In two cases, the molecular-genetic testing did not show resistance to isoniazid, as confirmed by conventional cultivation. Furthermore, two strains demonstrating susceptibility in conventional microbiological testing to ethambutol and five strains to fluoroquinolones were verified as actually being resistant using a PCR method. Rapid diagnosis and identification of MDR-TB or XDR-TB strains using molecular-genetic testing is an essential tool for the timely and appropriate drug treatment and prevention of spread of drug resistant strains.
Stanyon, Roscoe; Wienberg, Johannes; Romagno, D.; Bigoni, F.; Jauch, Anna; Cremer, Thomas
1992-01-01
The existence of an apomorphic reciprocal chromosomal translocation in the gorilla lineage has been asserted or denied by various cytogeneticists. We employed a new molecular cytogenetic strategy (chromosomal in situ suppression hybridization) combined with high-resolution banding, replication sequence analysis, and fluorochrome staining to demonstrate that a reciprocal translocation between ancestral chromosomes homologous to human chromosome 5 and 17 has indeed occurred.
Brown, Sandra E
2014-01-01
Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been augmented with a rotational correction for improved accuracy when working with clusters. Comparison of the SCP results with the RS results suggests a fairly broad temperature range over which the SCP approximation can be expected to give accurate results for systems of water clusters, and complements a previously reported assessment of SCP. Discrepancies between the SCP and RS results presented here, and recently published replica exchange molecular dynamics (REMD) results bring into question the convergence of the REMD and accompanying replica exchange path integral molecular dynamics results. In addition to the ever-present specter of unconverged results, several possible sources for the discrepancy are explored based on inherent characteristics of the methods used.
Shojaei, S H Reza; Morini, Filippo; Deleuze, Michael S
2013-03-07
The results of experimental studies of the valence electronic structure of tetrahydrofuran employing He I photoelectron spectroscopy as well as Electron Momentum Spectroscopy (EMS) have been reinterpreted on the basis of Molecular Dynamical simulations employing the classical MM3 force field and large-scale quantum mechanical simulations employing Born-Oppenheimer Molecular Dynamics in conjunction with the dispersion corrected ωB97XD exchange-correlation functional. Analysis of the produced atomic trajectories demonstrates the importance of thermal deviations from the lowest energy path for pseudorotation, in the form of considerable variations of the ring-puckering amplitude. These deviations are found to have a significant influence on several outer-valence electron momentum distributions, as well as on the He I photoelectron spectrum.
First principles molecular dynamics without self-consistent field optimization
Souvatzis, Petros
2013-01-01
We present a first principles molecular dynamics approach that is based on time-reversible ex- tended Lagrangian Born-Oppenheimer molecular dynamics [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) costruction are required in each integration time step. The proposed dy- namics 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 an ideal starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents ...
Elucidation of molecular dynamics of invasive species of rice
Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...
What is a Multiscale Problem in Molecular Dynamics?
Directory of Open Access Journals (Sweden)
Luigi Delle Site
2013-12-01
Full Text Available In this work, we make an attempt to answer the question of what a multiscale problem is in Molecular Dynamics (MD, or, more in general, in Molecular Simulation (MS. By introducing the criterion of separability of scales, we identify three major (reference categories of multiscale problems and discuss their corresponding computational strategies by making explicit examples of applications.
Unified rotational dynamics of molecular crystals with orientational phase transition
Michel, K.H.; Raedt, H. De
1976-01-01
A unified theory for the rotational dynamics of molecular crystals with orientational phase transitions is given. As basic secular variables one takes symmetry adapted functions, which describe the molecular orientations, and the angular momenta of the molecules. Using Mori’s projection operator tec
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
Volkovich, Roie
2010-01-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor molecular junction model yields currents which transfer charge (electron and holes) unevenly to the two leads in the absence of a bias potential. The utility of this mechanism for charge pumping in steady state conditions is proposed.
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.
Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G
2016-04-12
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features.
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
2010-01-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor ...
Quantum molecular dynamics of methyl rotors in peptide links
Del Mar, J
2002-01-01
A particles wavefunction extends beyond the classically accessible regions of the potential energy surface. Quantum mechanical tunnelling is the result of this partial delocalisation, which enables the surpassing of classically inaccessible potential barriers. A particles mass is an important aspect, reflecting the tunnelling probability; a consequence of this is that a proton is ideally suited to this behaviour. Symmetrical molecular rotors such as Ch sub 3 provide a clear example of quantum mechanical tunnelling, seen in their motional spectrum. The advantage of the methyl rotor is that it's found in a wide range of organic compounds, giving a wide range in hindering potentials. It is effectively a proton rotor, and is easily observed using techniques such as Nuclear Magnetic Resonance (NMR), and Inelastic Neutron Scattering (INS). Both NMR and INS techniques are sensitive to molecular motion, and as they measure the tunnel frequencies in different energy windows, are complementary. Of central importance to...
Molecular dynamics simulation of ion transport in a nanochannel
Institute of Scientific and Technical Information of China (English)
CHEN Min; CHEN YunFei; ZHONG Wu; YANG JueKuan
2008-01-01
A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented,and the process of ion transport in the nanochannel was simulated in this paper.The model consists of two water sinks at the two ends and a pump in the middle,which is different from a single pump model in previous MD simulations.Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the en-richment of counterions in the nanochannel.A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel,and the current in the pump region is mainly induced by the motion of counterions.In addition,the ion number in the pump region rapidly decreases as the external electric field is applied.In the equilibrated system,the electrically neutral character in the pump region is destroyed and this region displays a certain electrical char-acter,which depends on the surface charge.The ion distribution is greatly different from the results predicted by the continuum theory,e.g.a smaller peak value of Na+ concentration appears near the wall.The transport efficiency of counterions (co-ions) can be effectively increased (decreased) by increasing the surface charge density.The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel cannot be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model.The mechanism of some special ex-perimental phenomena in a nanochannel and the effect of the surface charge den-sity on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps.
Molecular dynamics simulation of ion transport in a nanochannel
Institute of Scientific and Technical Information of China (English)
2008-01-01
A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented, and the process of ion transport in the nanochannel was simulated in this paper. The model consists of two water sinks at the two ends and a pump in the middle, which is different from a single pump model in previous MD simulations. Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the enrichment of counterions in the nanochannel. A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel, and the current in the pump region is mainly induced by the motion of counterions. In addition, the ion number in the pump region rapidly decreases as the external electric field is applied. In the equilibrated system, the electrically neutral character in the pump region is destroyed and this region displays a certain electrical character, which depends on the surface charge. The ion distribution is greatly different from the results predicted by the continuum theory, e.g. a smaller peak value of Na+ concentration appears near the wall. The transport efficiency of counterions (co-ions) can be effectively increased (decreased) by increasing the surface charge density. The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel cannot be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model. The mechanism of some special experimental phenomena in a nanochannel and the effect of the surface charge density on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps.
Theoretical aspects of gas-phase molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Muckerman, J.T. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
Research in this program is focused on the development and application of time-dependent quantum mechanical and semiclassical methods for treating inelastic and reactive molecular collisions, and the photochemistry and photophysics of atoms and molecules in laser fields. Particular emphasis is placed on the development and application of grid methods based on discrete variable representations, on time-propagation methods, and, in systems with more that a few degrees of freedom, on the combined use of quantal wavepackets and classical trajectories.
Collet, P; Métens, S; Neishtadt, A; Zaslavsky, G; Chaotic Dynamics and Transport in Classical and Quantum Systems
2005-01-01
This book offers a modern updated review on the most important activities in today dynamical systems and statistical mechanics by some of the best experts in the domain. It gives a contemporary and pedagogical view on theories of classical and quantum chaos and complexity in hamiltonian and ergodic systems and their applications to anomalous transport in fluids, plasmas, oceans and atom-optic devices and to control of chaotic transport. The book is issued from lecture notes of the International Summer School on "Chaotic Dynamics and Transport in Classical and Quantum Systems" held in Cargèse (Corsica) 18th to the 30th August 2003. It reflects the spirit of the School to provide lectures at the post-doctoral level on basic concepts and tools. The first part concerns ergodicity and mixing, complexity and entropy functions, SRB measures, fractal dimensions and bifurcations in hamiltonian systems. Then, models of dynamical evolutions of transport processes in classical and quantum systems have been largely expla...
Interfacial Properties of an Ionic Liquid by Molecular Dynamics
Heggen, B.; Zhao, W.; Leroy, F.; Dammers, A.T.; Müller-Plathe, F.
2010-01-01
We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) by molecular dynamics simulations. In the interfacial region, reorientation of
Molecular dynamics simulation of a polysorbate 80 micelle in water
Amani, Amir; York, Peter; de Waard, Hans; Anwar, Jamshed
2011-01-01
The structure and dynamics of a single molecule of the nonionic surfactant polysorbate 80 (POE (20) sorbitan monooleate; Tween 80 (R)) as well as a micelle comprising sixty molecules of polysorbate 80 in water have been investigated by molecular dynamics simulation. In its free state in water the po
Zimmermann, Tomas
2010-01-01
We propose an approximate method for evaluating the importance of non-Born-Oppenheimer effects on the quantum dynamics of nuclei. The method uses a generalization of the dephasing representation (DR) of quantum fidelity to several diabatic potential energy surfaces and its computational cost is the cost of dynamics of a classical phase space distribution. It can be implemented easily into any molecular dynamics program and also can utilize on-the-fly ab initio electronic structure information. We test the methodology on three model problems introduced by Tully and on the photodissociation of NaI. The results show that for dynamics close to the diabatic regime the decay of fidelity due to nondiabatic effects is described accurately by the DR. In the nearly diabatic regime, unlike the mixed quantum-classical methods such as surface hopping or Ehrenfest dynamics, the DR can capture more subtle quantum effects than the population transfer between potential energy surfaces. Hence we propose using the DR to estimat...
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
Energy Technology Data Exchange (ETDEWEB)
Lau, E Y; Krishnan, V V
2007-07-18
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
Molecular dynamics simulations of microscopic structure of ultra strong shock waves in dense helium
Liu, Hao; Kang, Wei; Zhang, Qi; Zhang, Yin; Duan, Huilin; He, X. T.
2016-12-01
Hydrodynamic properties and structure of strong shock waves in classical dense helium are simulated using non-equilibrium molecular dynamics methods. The shock speed in the simulation reaches 100 km/s and the Mach number is over 250, which are close to the parameters of shock waves in the implosion process of inertial confinement fusion. The simulations show that the high-Mach-number shock waves in dense media have notable differences from weak shock waves or those in dilute gases. These results will provide useful information on the implosion process, especially the structure of strong shock wave front, which remains an open question in hydrodynamic simulations.
Crystallization in nano-confinement seeded by a nanocrystal—A molecular dynamics study
Pan, Heng
2014-03-14
Seeded crystallization and solidification in nanoscale confinement volumes have become an important and complex topic. Due to the complexity and limitations in observing nanoscale crystallization, computer simulation can provide valuable details for supporting and interpreting experimental observations. In this article, seeded crystallization from nano-confined liquid, as represented by the crystallization of a suspended gold nano-droplet seeded by a pre-existing gold nanocrystal seed, was investigated using molecular dynamics simulations in canonical (NVT) ensemble. We found that the crystallization temperature depends on nano-confinement volume, crystal orientation, and seed size as explained by classical two-sphere model and Gibbs-Thomson effect. © 2014 AIP Publishing LLC.
Analysis of C60 insertion into single wall carbon nanotube by molecular dynamics simulation
Ishii, Takafumi; Esfarjani, Keivan; Hashi, Yuichi; Kawazoe, Yoshiyuki; Iijima, Sumio
2001-10-01
Classical molecular dynamics is used to simulate the insertion of C60 into a (10, 10) single wall nano tube (SWNT). We propose that the insertion process occurs through the open end of the tube. After insertion, the energy exchange between the C60 and the nanotube causes the kinetic energy of the former to decrease as it moves inside the tube. This kinetic energy loss is due to a "friction force" which we calculated for several insertion conditions. The binding energy of the C60 with the SWNT is due to Van der Waals interaction, and is found to be about 3.5 eV.
Pueyo, Adrián Gómez; Castro, Alberto
2016-01-01
We present an implementation of optimal control theory for the first-principles non-adiabatic Ehrenfest Molecular Dynamics model, which describes a condensed matter system by considering classical point-particle nuclei, and quantum electrons, handled in our case with time-dependent density-functional theory. The scheme is demonstrated by optimizing the Coulomb explosion of small Sodium clusters: the algorithm is set to find the optimal femtosecond laser pulses that disintegrate the clusters, for a given total pulse duration, fluence, and cut-off frequency. We describe the numerical details and difficulties of the methodology.
A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics
Morante, S.; Rossi, G. C.
2017-02-01
We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg-Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann-Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.
Analysis of Surface Texturization of Solar Cells by Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Hsiao-Yen Chung
2008-01-01
Full Text Available The purpose of this paper is to develop a simple new model, based on the classic molecular dynamics simulation (MD, alternative to complex electron-photon interactions to analyze the surface texturization of solar cells. This methodology can easily propose the absorptance differences between texturing and nontexturing solar cells. To verify model feasibility, this study simulates square, pyramidal, and semicircular texturization surfaces. Simulations show that surface texturization effectively increases the absorptance of incident light for solar cells, and this paper presents optimal texturization shapes. The MD model can also be potentially used to predict the efficiency promotion in any optical reflection-absorption cases.
Tracking and Motion Analysis of Crack Propagations in Crystals for Molecular Dynamics
Energy Technology Data Exchange (ETDEWEB)
Tsap, L V; Duchaineau, M; Goldgof, D B
2001-05-14
This paper presents a quantitative analysis for a discovery in molecular dynamics. Recent simulations have shown that velocities of crack propagations in crystals under certain conditions can become supersonic, which is contrary to classical physics. In this research, they present a framework for tracking and motion analysis of crack propagations in crystals. It includes line segment extraction based on Canny edge maps, feature selection based on physical properties, and subsequent tracking of primary and secondary wavefronts. This tracking is completely automated; it runs in real time on three 834-image sequences using forty 250 MHZ processors. Results supporting physical observations are presented in terms of both feature tracking and velocity analysis.
Beck, Tracy L; Takami, Michihiro; Pyo, Tae-Soo
2007-01-01
We present 2.0-2.4micron integral field spectroscopy at adaptive optics spatial resolution (~0.''1) obtained with the Near-infrared Integral Field Spectrograph (NIFS) at Gemini North Observatory of six Classical T Tauri stars: T Tau, DG Tau, XZ Tau, HL Tau, RW Aur and HV Tau C. In all cases, the v=1-0 S(1) (2.12 micron) emission is detected at spatially extended distances from the central stars. The bulk of the H_2 emission is typically not spatially coincident with the location of continuum flux. Multiple transitions detected in the K-band spectra show that H_2 level populations are typical of gas in thermal equilibrium with excitation temperatures in the 1800K-2300 K range. Three of the stars have H_2 velocity profiles that are centered at the stellar radial velocity, and three show velocity shifts with respect to the system. Each of the stars studied here show observed excitation temperatures, spatial extents, and kinematics of the H_2 that are most consistent with shock excited emission from the inner reg...
Staubach, Simon; Müller, Stefan; Pekmez, Murat; Hanisch, Franz-Georg
2017-02-03
Classical galactosemia, a hereditary metabolic disease caused by the deficiency of galactose-1-phosphate uridyltransferase (GALT; EC 2.7.712), results in an impaired galactose metabolism and serious long-term developmental affection of the CNS and ovaries, potentially related in part to endogenous galactose-induced protein dysglycosylation. In search for galactose-induced changes in membrane raft proteomes of GALT-deficient cells, we performed differential analyses of lipid rafts from patient-derived (Q) and sex- and age-matched control fibroblasts (H) in the presence or absence of the stressor. Label-based proteomics revealed of the total 454 (female) or 678 (male) proteins a proportion of ∼12% in at least one of four relevant ratios as fold-changed. GALT(-) cell-specific effects in the absence of stressor revealed cell-model-dependent affection of biological processes related to protein targeting to the plasma membrane (female) or to cellular migration (male). However, a series of common galactose-induced effects were observed, among them the strongly increased ER-stress marker GRP78 and calreticulin involved in N-glycoprotein quality control. The membrane-anchored N-glycoprotein receptor CD109 was concertedly decreased under galactose-stress together with cadherin-13, GLIPR1, glypican-1, and semaphorin-7A. A series of proteins showed opposite fold-changes in the two cell models, whereas others fluctuated in only one of the two models.
Ono, Junichi; Ando, Koji
2012-11-01
A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many
Quantum dynamics of bio-molecular systems in noisy environments
Huelga S.F.; Plenio M.B.
2012-01-01
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...
Molecular Dynamics Simulation of Amyloid Beta Dimer Formation
Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V
2004-01-01
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...
A molecular superfluid: non-classical rotations in doped para-hydrogen clusters
Li, Hui; Roy, Pierre-Nicholas; McKellar, A R W; 10.1103/PhysRevLett.105.133401
2010-01-01
Clusters of para-hydrogen (pH2) have been predicted to exhibit superfluid behavior, but direct observation of this phenomenon has been elusive. Combining experiments and theoretical simulations, we have determined the size evolution of the superfluid response of pH2 clusters doped with carbon dioxide (CO2). Reduction of the effective inertia is observed when the dopant is surrounded by the pH2 solvent. This marks the onset of molecular superfluidity in pH2. The fractional occupation of solvation rings around CO2 correlates with enhanced superfluid response for certain cluster sizes.
Ananth, Nandini
2013-09-01
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral representation of the quantum Boltzmann operator using continuous Cartesian variables for both electronic states and nuclear degrees of freedom. We demonstrate the accuracy of the MV-RPMD approach in calculations of real-time, thermal correlation functions for a range of two-state single-mode model systems with different coupling strengths and asymmetries. Further, we show that the ensemble of classical trajectories employed in these simulations preserves the Boltzmann distribution and provides a direct probe into real-time coupling between electronic state transitions and nuclear dynamics.
Spellings, Matthew; Anderson, Joshua A; Glotzer, Sharon C
2016-01-01
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks-Chandler-Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method is a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.
Spellings, Matthew; Marson, Ryan L.; Anderson, Joshua A.; Glotzer, Sharon C.
2017-04-01
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks-Chandler-Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method is a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.
Molecular wave-packet dynamics on laser-controlled transition states
Fischer, Andreas; Cörlin, Philipp; Sperl, Alexander; Schönwald, Michael; Mizuno, Tomoya; Sansone, Giuseppe; Senftleben, Arne; Ullrich, Joachim; Feuerstein, Bernold; Pfeifer, Thomas; Moshammer, Robert
2016-01-01
Understanding and controlling the electronic as well as ro-vibrational motion and, thus, the entire chemical dynamics in molecules is the ultimate goal of ultrafast laser and imaging science. In photochemistry, laser-induced dissociation has become a valuable tool for modification and control of reaction pathways and kinetics. Here, we present a pump-probe study of the dissociation dynamics of H$_2^+$ using ultrashort extreme-ultraviolet (XUV) and near-infrared (IR) laser pulses. The reaction kinematics can be controlled by varying the pump-probe delay. We demonstrate that the nuclear motion through the transition state can be reduced to isolated pairs of initial vibrational states. The dynamics is well reproduced by intuitive semi-classical trajectories on a time-dependent potential curve. From this most fundamental scenario we gain insight in the underlying mechanisms which can be applied as design principles for molecular quantum control, particularly for ultrafast reactions involving protons.
Wang, Linjun; Akimov, Alexey V; Chen, Liping; Prezhdo, Oleg V
2013-11-07
The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.
Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions
Gkionis, Konstantinos
2014-07-23
The properties of liquids in a confined environment are known to differ from those in the bulk. Extending this knowledge to geometries defined by two metallic layers in contact with the ends of a carbon nanotube is important for describing a large class of nanodevices that operate in non-aqueous environments. Here we report a series of classical molecular dynamics simulations for gold-electrode junctions in acetone, cyclohexane and N,N-dimethylformamide solutions and analyze the structure and the dynamics of the solvents in different regions of the nanojunction. The presence of the nanotube has little effect on the ordering of the solvents along its axis, while in the transversal direction deviations are observed. Importantly, the orientational dynamics of the solvents at the electrode-nanotube interface differ dramatically from that found when only the electrodes are present.
Molecular dynamics with deterministic and stochastic numerical methods
Leimkuhler, Ben
2015-01-01
This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...
Dynamics of molecular superrotors in external magnetic field
Korobenko, Aleksey
2015-01-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of 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 the 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 in 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.
Hanford, Amanda D; O'Connor, Patrick D; Anderson, James B; Long, Lyle N
2008-06-01
In the current study, real gas effects in the propagation of sound waves are simulated using the direct simulation Monte Carlo method for a wide range of frequencies. This particle method allows for treatment of acoustic phenomena at high Knudsen numbers, corresponding to low densities and a high ratio of the molecular mean free path to wavelength. Different methods to model the internal degrees of freedom of diatomic molecules and the exchange of translational, rotational and vibrational energies in collisions are employed in the current simulations of a diatomic gas. One of these methods is the fully classical rigid-rotor/harmonic-oscillator model for rotation and vibration. A second method takes into account the discrete quantum energy levels for vibration with the closely spaced rotational levels classically treated. This method gives a more realistic representation of the internal structure of diatomic and polyatomic molecules. Applications of these methods are investigated in diatomic nitrogen gas in order to study the propagation of sound and its attenuation and dispersion along with their dependence on temperature. With the direct simulation method, significant deviations from continuum predictions are also observed for high Knudsen number flows.
Calculation of heat capacities of light and heavy water by path-integral molecular dynamics
Shiga, Motoyuki; Shinoda, Wataru
2005-10-01
As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2O at 300 K, 6.9 in the liquid H2O at 300 K, and 4.1 in the ice IhH2O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2O has been calculated to be 10% higher than that of H2O, while it is 13% higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions.
First principles molecular dynamics without self-consistent field optimization
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Souvatzis, Petros, E-mail: petros.souvatsiz@fysik.uu.se [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Niklasson, Anders M. N., E-mail: amn@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2014-01-28
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.
First principles molecular dynamics without self-consistent field optimization.
Souvatzis, Petros; Niklasson, Anders M N
2014-01-28
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.
Bianchi I model in terms of non-standard LQC: Classical dynamics
Dzierzak, Piotr
2009-01-01
The cosmological singularities of the Bianchi I universe are analyzed in the setting of loop geometry underlying the loop quantum cosmology. We solve the Hamiltonian constraint of the theory and find the Lie algebra of elementary observables. Physical compound observables are defined in terms of elementary ones. Modification of classical theory by holonomy around a loop removes the singularities. However, our model has a free parameter that cannot be determined within our method. Testing the model by the data of observational cosmology may be possible after quantization of our modified classical theory.
Gao, Yi; Neuhauser, Daniel
2013-05-14
We show how to obtain the correct electronic response of a large system by embedding; a small region is propagated by TDDFT (time-dependent density functional theory) simultaneously with a classical electrodynamics evolution using the Near-Field method over a larger external region. The propagations are coupled through a combined time-dependent density yielding a common Coulomb potential. We show that the embedding correctly describes the plasmonic response of a Mg(0001) slab and its influence on the dynamical charge transfer between an adsorbed H2O molecule and the substrate, giving the same spectral shape as full TDDFT (similar plasmon peak and molecular-dependent differential spectra) with much less computational effort. The results demonstrate that atomistic embedding electrodynamics is promising for nanoplasmonics and nanopolaritonics.
Dynamics Studies on Molecular Diffusion in Zeolites
Institute of Scientific and Technical Information of China (English)
王秋霞; 樊建芬; 肖鹤鸣
2003-01-01
A review about the applications of molecular dynamics（MD）simulation in zeolites is presented. MD simulation has been proved to be a useful tool due to its applications in this field for the recent two decades. The fundamental theory of MD is introduced and the hydrocarbon diffusion in zeolites is mainly focused on in this paper.
Molecular Dynamics Simulations of the Hydrogen Peroxyl Radical
2014-05-01
NOTES The original document contains color images . 14. ABSTRACT The first study of this dissertation is focused on the classical dynamics and rates of...enough to cause non-statistical unimolecular decay, an observation made earlier by Lemon and Hase76 based on an empirical PES. Marques and...the same total energy to within ≈1% for each of the PESs. We have repeated the Marque and 57 42 Varandas70 trajectory study of unimolecular
Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D
2015-01-01
Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis.
Petascale molecular dynamics simulation using the fast multipole method on K computer
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.
VUV studies of molecular photofragmentation dynamics
Energy Technology Data Exchange (ETDEWEB)
White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.
Sayad, Mohammad; Potthoff, Michael
2015-11-01
The real-time dynamics of a classical spin in an external magnetic field and local exchange coupled to an extended one-dimensional system of non-interacting conduction electrons is studied numerically. Retardation effects in the coupled electron-spin dynamics are shown to be the source for the relaxation of the spin in the magnetic field. Total energy and spin is conserved in the non-adiabatic process. Approaching the new local ground state is therefore accompanied by the emission of dispersive wave packets of excitations carrying energy and spin and propagating through the lattice with Fermi velocity. While the spin dynamics in the regime of strong exchange coupling J is rather complex and governed by an emergent new time scale, the motion of the spin for weak J is regular and qualitatively well described by the Landau-Lifschitz-Gilbert (LLG) equation. Quantitatively, however, the full quantum-classical hybrid dynamics differs from the LLG approach. This is understood as a breakdown of weak-coupling perturbation theory in J in the course of time. Furthermore, it is shown that the concept of the Gilbert damping parameter is ill-defined for the case of a one-dimensional system.
Directory of Open Access Journals (Sweden)
Debjyoti Paul
Full Text Available In contrast with normal cells, most of the cancer cells depend on aerobic glycolysis for energy production in the form of adenosine triphosphate (ATP bypassing mitochondrial oxidative phosphorylation. Moreover, compared to normal cells, cancer cells exhibit higher consumption of glucose with higher production of lactate. Again, higher rate of glycolysis provides the necessary glycolytic intermediary precursors for DNA, protein and lipid synthesis to maintain high active proliferation of the tumor cells. In this scenario, classical control theory based approach may be useful to explore the altered dynamics of the cancer cells. Since the dynamics of the cancer cells is different from that of the normal cells, understanding their dynamics may lead to development of novel therapeutic strategies.We have developed a model based on the state space equations of classical control theory along with an order reduction technique to mimic the actual dynamic behavior of mammalian central carbon metabolic (CCM pathway in normal cells. Here, we have modified Michaelis Menten kinetic equation to incorporate feedback mechanism along with perturbations and cross talks associated with a metabolic pathway. Furthermore, we have perturbed the proposed model to reduce the mitochondrial oxidative phosphorylation. Thereafter, we have connected proportional-integral (PI controller(s with the model for tuning it to behave like the CCM pathway of a cancer cell. This methodology allows one to track the altered dynamics mediated by different enzymes.The proposed model successfully mimics all the probable dynamics of the CCM pathway in normal cells. Moreover, experimental results demonstrate that in cancer cells, a coordination among enzymes catalyzing pentose phosphate pathway and intermediate glycolytic enzymes along with switching of pyruvate kinase (M2 isoform plays an important role to maintain their altered dynamics.
Energy Technology Data Exchange (ETDEWEB)
Yasuaki, Ichikawa; Somehai, Prayongphan [Nagoya Univ., Dpt. of Environmental Engineering and Architecture, Chikusa, Nagoya (Japan); Kazumi, Kitayama [NUMO, Minato, Tokyo (Japan); Katsuyuki, Kawamura [Tokyo Institute of Technology, Tokyo (Japan)
2005-07-01
The major scenario of transport of radioactive nuclides is due to groundwater flow in most HLW projects. The phenomena of water flow and diffusion of chemical species in a bentonite buffer and surrounding rock mass have been treated mainly based on the classical porous media theories under the Darcy law and Fick law. The classical theories involve the following difficulties: 1) True velocity field is hard to be identified, especially in microscale sense. Note that it essentially affects the transport of chemical species. 2) The classical theories are not applicable to the problems in which experimental data are not available. Thus, the very long time behavior cannot be proven. We commonly recognize that the water flow in bentonite and mud-stone is strongly retarded. It is highly doubtful whether the above classical theories are applicable for such very low permeable materials. In this work we first show that the velocity and diffusion fields in pure smectite bentonite can be calculated by a coupled molecular dynamics (MD) simulation and the homogenization analysis (HA). The true velocity field can be calculated by applying HA to the Navier-Stokes equation, and the local distribution of viscosity used in this HA is obtained by MD. The diffusion field is also calculated under the same procedure of MD/HA by using the local diffusion equation with diffusivity calculated by MD. (authors)
Wieser, Robert
2015-03-01
The classical Landau-Lifshitz equation has been derived from quantum mechanics. Starting point is the assumption of a non-Hermitian Hamilton operator to take the energy dissipation into account. The corresponding quantum mechanical spin dynamics along with the time dependent Schrödinger, Liouville and Heisenberg equation has been described and the similarities and differences between classical and quantum mechanical spin dynamics have been discussed. Furthermore, a time dependent Schrödinger equation corresponding to the classical Landau-Lifshitz-Gilbert equation and two ways to include temperature into the quantum mechanical spin dynamics have been proposed.
On the Hamiltonian and Lagrangian formulation of classical dynamics for particles with spin
Ruijgrok, Th.W.; Vlist, H. van der
1980-01-01
The classical mechanics of nonrelativistic particles is generalized by also considering the spin components as canonical variables. Poisson-brackets and canonical transformations are discussed. The Lagrangian equations of motion are given and it is shown how rotational invariance leads to well known
Visualizing global properties of a molecular dynamics trajectory.
Zhou, Hao; Li, Shangyang; Makowski, Lee
2016-01-01
Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule.
Durlak, Piotr; Morrison, Carole A.; Middlemiss, Derek S.; Latajka, Zdzislaw
2007-08-01
We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density functional. In the classical dynamics a clear reaction mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. This mechanism is considerably altered when quantum tunneling is permitted in the simulation. The introduction of path integrals leads to considerable changes in the thermally averaged molecular geometry, leading to shorter and more centered hydrogen bond linkages.
Nussinov, Zohar; Johnson, Patrick; Graf, Matthias J.; Balatsky, Alexander V.
2013-05-01
Many electronic systems (e.g., the cuprate superconductors and heavy fermions) exhibit striking features in their dynamical response over a prominent range of experimental parameters. While there are some empirical suggestions of particular increasing length scales that accompany such transitions in some cases, this identification is not universal and in numerous instances no large correlation length is evident. To better understand, as a matter of principle, such behavior in quantum systems, we extend a known mapping (earlier studied in stochastic or supersymmetric quantum mechanics) between finite temperature classical Fokker-Planck systems and related quantum systems at zero temperature to include general nonequilibrium dynamics. Unlike Feynman mappings or stochastic quantization methods in field theories (as well as more recent holographic type dualities), the classical systems that we consider and their quantum duals reside in the same number of space-time dimensions. The upshot of our very broad and rigorous result is that a Wick rotation exactly relates (i) the dynamics in general finite temperature classical dissipative systems to (ii) zero temperature dynamics in the corresponding dual many-body quantum systems. Using this correspondence, we illustrate that, even in the absence of imposed disorder, many continuum quantum fluid systems (and possible lattice counterparts) may exhibit a zero-point “quantum dynamical heterogeneity” wherein the dynamics, at a given instant, is spatially nonuniform. While the static length scales accompanying this phenomenon do not seem to exhibit a clear divergence in standard correlation functions, the length scale of the dynamical heterogeneities can increase dramatically. We further study “quantum jamming” and illustrate how a hard-core bosonic system can undergo a zero temperature quantum critical metal-to-insulator-type transition with an extremely large effective dynamical exponent z>4 that is consistent with
Tunneling Dynamics Between Atomic and Molecular Bose-Einstein Condensates
Institute of Scientific and Technical Information of China (English)
CHEN Chang-Yong
2004-01-01
Tunneling dynamics of multi-atomic molecules between atomic and multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated.It is indicated that the tunneling in the two Bose-Einstein condensates depends on not only the inter-atomic-molecular nonlinear interactions and the initial number of atoms in these condensates,but also the tunneling coupling between the atomic condensate and the multi-atomic molecular condensate.It is discovered that besides oscillating tunneling current between the atomic condensate and the multi-atomic molecular condensate,the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance:a macroscopic quantum self-trapping effect.The influence of de-coherence caused by non-condensate atoms on the tunneling dynamics is studied.It is shown that de-coherence suppresses the multi-atomic molecular tunneling.Moreover,the conception of the molecular Bose-Einstein condensate,which is different from the conventional single-atomic Bose-Einstein condensate,is specially emphasized in this paper.
On the stochastic dynamics of molecular conformation
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.
Molecular dynamics insights into human aquaporin 2 water channel.
Binesh, A R; Kamali, R
2015-12-01
In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney.
Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.
Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem
2015-02-13
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.
Maxwell-Lorentz Dynamics for Rigid Charges - Classical Absorber Electrodynamics Part I
Bauer, G; Dürr, D
2010-01-01
This is the first part of our mathematical survey on the equations of motion of classical absorber electrodynamics, which shall be introduced and discussed briefly. Its basic equations of motion are the Maxwell-Lorentz (ML) equations of classical electrodynamics excluding the self-interaction term. We briefly explain that it is capable of describing the phenomenon of radiation reaction as well as the irreversible effect of radiation. We provide a global existence and uniqueness result for solutions to the ML equations (with as well as without self-interaction) which allows for finitely many non-rotating, rigid charges with possibly negative masses and a class of infinite energy (i.e. not square-integrable) fields. This result is the foundation of the second part (Part II) where it is applied to prove an existence theorem of the famous Wheeler-Feynman (WF) delay differential equations on finite but arbitrarily large time intervals.
Prototyping Bio-Nanorobots using Molecular Dynamics Simulation
Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos
2005-01-01
Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...
Femtochemistry and femtobiology ultrafast dynamics in molecular science
Douhal, Abderrazzak
2002-01-01
This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol
Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective
Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge
2013-03-01
Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.
Nanoscopic spontaneous motion of liquid trains: non-equilibrium molecular dynamics simulation
Bahrami, Amir Houshang
2009-01-01
Macroscale experiments show that a train of two immiscible liquid drops, a bislug, can spontaneously move in a capillary tube because of surface tension asymmetries. We use molecular dynamics simulation of Lennard-Jones fluids to demonstrate this phenomenon for NVT ensembles in sub-micron tubes. We deliberately tune the strength of intermolecular forces and control the velocity of bislug in different wetting and viscosity conditions. We compute the velocity profile of particles across the tube, and explain the origin of deviations from the classical parabolae. We show that the self-generated molecular flow resembles the Poiseuille law when the ratio of the tube radius to its length is less than a critical value.
Energy Technology Data Exchange (ETDEWEB)
Costa, Diogo Ricardo da, E-mail: drcosta@usp.br [Instituto de Física, Universidade de São Paulo, Rua do Matão, Cidade Universitária, 05314-970 São Paulo, SP (Brazil); School of Mathematics, University of Bristol, Bristol BS8 1TW (United Kingdom); Caldas, I.L. [Instituto de Física, Universidade de São Paulo, Rua do Matão, Cidade Universitária, 05314-970 São Paulo, SP (Brazil); Leonel, Edson D. [Departamento de Física, UNESP – Universidade Estadual Paulista, Av. 24A, 1515, 13506-900 Rio Claro, SP (Brazil)
2013-10-30
We consider dynamical properties for an ensemble of classical particles confined to an infinite box of potential and containing a time-dependent potential well described by different nonlinear functions. For smooth functions, the phase space contains chaotic trajectories, periodic islands and invariant spanning curves preventing the unlimited particle diffusion along the energy axis. Average properties of the chaotic sea are characterised as a function of the control parameters and exponents describing their behaviour show no dependence on the perturbation functions. Given invariant spanning curves are present in the phase space, a sticky region was observed and show to modify locally the diffusion of the particles.
2016-01-01
Mixtures of ethylene glycol with water are a prominent example of media with variable viscosity. Classical molecular dynamics simulations at room temperature were performed for mixtures of ethylene glycol (EG) and water with EG mole fractions of xE = 0.0, 0.1, 0.2, 0.4, 0.6, 0.9, 1.0. The calculated dielectric loss spectra were in qualitative agreement with experiment. We found a slightly overestimated slowdown of the dynamics with increasing EG concentration compared to experimental data. Statistics of the hydrogen bond network and hydrogen bond lifetimes were derived from suitable time correlation functions and also show a slowdown in the dynamics with increasing xE. A similar picture is predicted for the time scales of EG conformer changes and for molecular reorientation. A slight blue shift was obtained for the power spectra of the molecular center of mass motion. The results were used to give a qualitative interpretation of the origin of three different relaxation times that appear in experimental complex dielectric spectra and of their change with xE. PMID:27649083