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...
Electron-phonon interaction within classical molecular dynamics
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-01
We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.
The classical and quantum dynamics of molecular spins on graphene.
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices. PMID:26641019
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
Cleaning graphene: A first quantum/classical molecular dynamics approach
Delfour, L.; Davydova, A.; Despiau-Pujo, E.; Cunge, G.; Graves, D. B.; Magaud, L.
2016-03-01
Graphene outstanding properties created a huge interest in the condensed matter community and unprecedented fundings at the international scale in the hope of application developments. Recently, there have been several reports of incomplete removal of the polymer resists used to transfer as-grown graphene from one substrate to another, resulting in altered graphene transport properties. Finding a large-scale solution to clean graphene from adsorbed residues is highly desirable and one promising possibility would be to use hydrogen plasmas. In this spirit, we couple here quantum and classical molecular dynamics simulations to explore the kinetic energy ranges required by atomic hydrogen to selectively etch a simple residue—a CH3 group—without irreversibly damaging the graphene. For incident energies in the 2-15 eV range, the CH3 radical can be etched by forming a volatile CH4 compound which leaves the surface, either in the CH4 form or breaking into CH3 + H fragments, without further defect formation. At this energy, adsorption of H atoms on graphene is possible and further annealing will be required to recover pristine graphene.
International Nuclear Information System (INIS)
We present the first molecular dynamics simulation of the vacuum deposition of amorphous selenium films. We compare the classical, tight-binding and Hubbard-term corrected tight-binding molecular dynamics simulation methods. Densities, coordination defects, radial distribution functions, bond angles, dihedral angles, intrachain and interchain atomic correlations were investigated in the obtained amorphous films. Local atomic arrangements were compared to results of diffraction measurements
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.
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.
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.
Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics
International Nuclear Information System (INIS)
We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000 K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500 K
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.
Costandy, Joseph; Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G
2016-03-28
We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies. PMID:27036466
Quasi-classical description of molecular dynamics based on Egorov's theorem
Keller, Johannes
2014-01-01
Egorov's theorem on the classical propagation of quantum observables is related to prominent quasi-classical descriptions of quantum molecuar dynamics as the linearized semiclassical initial value representation (LSC-IVR), the Wigner phase space method or the statistical quasiclassical method. The error estimates show that different accuracies are achievable for the computation of expectation values and position densities. Numerical experiments for a Morse model of diatomic iodine and confined Henon-Heiles systems in various dimensions illustrate the theoretical results.
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
2010-11-01
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.
Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei
2016-10-01
Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. PMID:27144470
Gaussian Dynamics is Classical Dynamics
Habib, Salman
2004-01-01
A direct comparison of quantum and classical dynamical systems can be accomplished through the use of distribution functions. This is useful for both fundamental investigations such as the nature of the quantum-classical transition as well as for applications such as quantum feedback control. By affording a clear separation between kinematical and dynamical quantum effects, the Wigner distribution is particularly valuable in this regard. Here we discuss some consequences of the fact that when...
Isomorphic classical molecular dynamics model for an excess electron in a supercritical fluid
Miller III, Thomas F.
2009-01-01
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path integral statistics through the use of analytical continuation techniques. At low fluid densities, the RPMD model substantially underestimates the contribution of delocalized states to the dynamics of the excess electron. However, with increasing solvent density, ...
Carnevale, V.; Raugei, S.
2009-12-01
Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.
International Nuclear Information System (INIS)
Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.
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.
Marsalek, Ondrej; Markland, Thomas E
2016-02-01
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. PMID:26851913
International Nuclear Information System (INIS)
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
Energy Technology Data Exchange (ETDEWEB)
Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)
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.
Marsalek, Ondrej
2015-01-01
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 ab initio ring polymer contraction (AI-RPC) 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 pro...
Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe
2016-03-01
We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.
Sakko, Arto; Rossi, Tuomas P.; Nieminen, Risto M.
2014-08-01
The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na2 molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na2 molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na2 molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the backcoupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics.
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul
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(3)-10(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. PMID:25770527
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
International Nuclear Information System (INIS)
Very recently (Cai et al 2010 Phys. Rev. E 82 021921), a simple mechanism was presented by which a molecule subjected to forced oscillations, out of thermal equilibrium, can maintain quantum entanglement between two of its quantum degrees of freedom. Crucially, entanglement can be maintained even in the presence of very intense noise, so intense that no entanglement is possible when the forced oscillations cease. This mechanism may allow for the presence of nontrivial quantum entanglement in biological systems. Here we significantly enlarge the study of this model. In particular, we show that the persistent generation of dynamic entanglement is not restricted to the bosonic heat bath model, but can also be observed in other decoherence models, e.g. the spin gas model, and in non-Markovian scenarios. We also show how conformational changes can be used by an elementary machine to generate entanglement even in unfavorable conditions. In biological systems, similar mechanisms could be exploited by more complex molecular machines or motors. (paper)
International Nuclear Information System (INIS)
Using the multi-body Classical Molecular Dynamics simulation of 6Li+209Bi reaction it is shown that: (i) the breakup of a projectile fragment near the barrier leads to substantial increase in the ICF probabilities; (ii) the expected increase in σCF on relaxation of the rigid-body (RB) constraint on the projectile is compensated by reduction in the flux leading to CF, due to ICF events; (iii) the breakup probability increases with ECM and, for given ECM it also increases as b increases and peaks around some b>0, while cross sections σCF and σTF were calculated for b=0 only Therefore, we present the results of σCF (Complete Fusion) and σTF (Total Fusion) calculations which are obtained at critical impact parameter, bcr, where many ICF channels open up and compare with the calculations performed at b=0 only, where only few ICF channels open up
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…
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).
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.
International Nuclear Information System (INIS)
The first coordination sphere of trivalent lanthanum in a highly concentrated (14 M) lithium chloride solution is studied with a combination of classical molecular dynamics and density functional theory based first principle molecular dynamics. This method enables us to obtain a solvation shell of La3+ containing 2 chloride ions and 6 water molecules. After refinement using first principle molecular dynamics, the resulting cation-water and cation-anion distances are in very good agreement with experiment. The 2 Cl- and the 6 water molecules arrange in a square anti-prism around La3+. Exchange of water molecules was also observed in the first-principle simulation, with an intermediate structure comprising 7 water molecules stable for 2.5 ps. Finally, evaluation of dipole moments using maximally localized Wannier functions shows a substantial polarization of the chloride anions and the water molecules in the first solvation shell of trivalent lanthanum. (authors)
Vicent-Luna, Jose Manuel; Ortiz-Roldan, Jose Manuel; Hamad, Said; Tena-Zaera, Ramon; Calero, Sofia; Anta, Juan Antonio
2016-08-18
Compositional effects on the charge-transport properties of electrolytes for batteries based on room-temperature ionic liquids (RTILs) are well-known. However, further understanding is required about the molecular origins of these effects, in particular regarding the replacement of Li by Na. In this work, we investigate the use of RTILs in batteries, by means of both classical molecular dynamics (MD), which provides information about structure and molecular transport, and ab initio molecular dynamics (AIMD), which provides information about structure. The focus has been placed on the effect of adding either Na(+) or Li(+) to 1-methyl-1-butyl-pyrrolidinium [C4 PYR](+) bis(trifluoromethanesulfonyl)imide [Tf2 N](-) . Radial distribution functions show excellent agreement between MD and AIMD, which ensures the validity of the force fields used in the MD. This is corroborated by the MD results for the density, the diffusion coefficients, and the total conductivity of the electrolytes, which reproduce remarkably well the experimental observations for all studied Na/Li concentrations. By extracting partial conductivities, it is demonstrated that the main contribution to the conductivity is that of [C4 PYR](+) and [Tf2 N](-) . However, addition of Na(+) /Li(+) , although not significant on its own, produces a dramatic decrease in the partial conductivities of the RTIL ions. The origin of this indirect effect can be traced to the modification of the microscopic structure of the liquid as observed from the radial distribution functions, owing to the formation of [Na(Tf2 N)n ]((n-1)-) and [Li(Tf2 N)n ]((n-1)-) clusters at high concentrations. This formation hinders the motion of the large ions, hence reducing the total conductivity. We demonstrate that this clustering effect is common to both Li and Na, showing that both ions behave in a similar manner at a microscopic level in spite of their distinct ionic radii. This is an interesting finding for extending Li-ion and Li
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.
International Nuclear Information System (INIS)
We present converged quantum dynamics for the H + D2 reaction at a total energy high enough to produce HD in the v' = 3, j' = 7 vibrational-rotational state and for total angular momenta J = 0, 1, and 2. We compare state-to-state partial cross sections for H + D2 (v = 0-2, j = 0, J = 0-2) → HD (v' = 0-2, j') + H and H + D2 (v = 1, j = 6, J = 0-2) → HD (v' = 0-2, j') + H as calculated from classical trajectory calculations with quantized initial conditions, i.e., a quasiclassical trajectory (QCT) simulation, to the results of converged quantum dynamics calculations involving up to 654 coupled channels. Final states in the QCT calculations are assigned by the quadratic smooth sampling (QSS) method. Since the quasiclassical and quantal calculations are carried out with the same potential energy surface, the comparison provides a direct test of the accuracy of the quasiclassical simulations as a function of the initial vibrational-rotational state and the final vibrational-rotational state
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)
Energy Technology Data Exchange (ETDEWEB)
Rajput, Nav Nidhi; Qu, Xiaohuui; 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 (Mg2+ -> 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.
Efficiency optimization of the classical molecular heat pump
Zheng, Dong-Qin; Zhong, Wei-Rong
2011-07-01
We investigate a three-terminal heat pump through classical molecular dynamics simulations. It is reported an asymmetrical structure is necessary for the molecular heat pump. There exists an optimum pumping efficiency by controlling the asymmetry and the average temperature of the heat pump. The efficiency increases with the decreasing of the temperature difference between the hot and cold heat baths.
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.
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:
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.
Introduction to Accelerated Molecular Dynamics
Energy Technology Data Exchange (ETDEWEB)
Perez, Danny [Los Alamos National Laboratory
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
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 ...
Kwac, Kijeong; Geva, Eitan
2013-06-27
We present a mixed quantum-classical molecular dynamics study of the nonequilibrium hydrogen-bond dynamics following vibrational energy relaxation of the hydroxyl stretch in a 10 mol % methanol/carbon tetrachloride mixture and pure methanol. The ground and first-excited energy levels and wave functions are identified with the eigenvalues and eigenfunctions of the hydroxyl's adiabatic Hamiltonian and as such depend parametrically on the configuration of the remaining, classically treated, degrees of freedom. The dynamics of the classical degrees of freedom are in turn governed by forces obtained by taking the expectation value of the force with respect to the ground or excited vibrational wave functions. Polarizable force fields and nonlinear mapping relations between the hydroxyl transition frequencies and dipole moments and the electric field along the hydroxyl bond are used, which were previously shown to quantitatively reproduce the experimental infrared steady-state absorption spectra and excited state lifetime [Kwac, K.; Geva, E. J. Phys. Chem. B 2011, 115, 9184; 2012, 116, 2856]. The relaxation from the first-excited state to the ground state is treated as a nonadiabatic transition. Within the mixed quantum-classical treatment, relaxation from the excited state to the ground state is accompanied by a momentum-jump in the classical degrees of freedom, which is in turn dictated by the nonadiabatic coupling vector. We find that the momentum jump leads to breaking of hydrogen bonds involving the relaxing hydroxyl, thereby blue-shifting the transition frequency by more than the Stokes shift between the steady-state emission and absorption spectra. The subsequent nonequilibrium relaxation toward equilibrium on the ground state potential energy surface is thereby accompanied by red shifting of the transition frequency. The signature of this nonequilibrium relaxation process on the pump-probe spectrum is analyzed in detail. The calculated pump-probe spectrum is found
Guerreschi, Gian Giacomo; Popescu, Sandu; Briegel, Hans J
2011-01-01
Very recently [Phys. Rev. E 82, 021921 (2010)] a simple mechanism was presented by which a molecule subjected to forced oscillations, out of thermal equilibrium, can maintain quantum entanglement between two of its quantum degrees of freedom. Crucially, entanglement can be maintained even in the presence of very intense noise, so intense that no entanglement is possible when the forced oscillations cease. This mechanism may allow for the presence of non-trivial quantum entanglement in biological systems. Here we significantly enlarge the study of this model. In particular, we show that the persistent generation of dynamic entanglement is not restricted to the bosonic heat bath model, but it can also be observed in other decoherence models, e.g. the spin gas model, and in non-Markovian scenarios. We also show how conformational changes can be used by an elementary machine to generate entanglement even in unfavorable conditions. In biological systems, similar mechanisms could be exploited by more complex molecu...
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
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
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.
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
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.
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...
Classical dynamics of triatomic system: energized harmonic molecules
International Nuclear Information System (INIS)
The dynamical assumptions underlying the Slater and RRK classical-mechanical theories of unimolecular reaction rates are investigated. The predictions of these theories for several nonlinear, triatomic, harmonically-bonded molecular models are compared with the results obtained from the integration of the classical equations of motion. The accuracy of the small-vibration and weak-coupling assumptions are found to break down at energies above about one quarter of a bond dissociation energy. Nonetheless, the small-vibration approximation predicts reaction frequencies in good agreement with the exact results for the models. The effects of rotation on intramolecular energy exchange are examined and found to be significant
Quantum systems that follow classical dynamics
Manfredi, G; Feix, M R
1993-01-01
For a special class of potentials, the dynamical evolution of any quantum wavepacket is entirely determined by the laws of classical mechanics. Here, the properties of this class are investigated both from the viewpoint of the Ehrenfest theorem (which provides the evolution of the average position and momentum), and the Wigner representation (which expresses quantum mechanics in a phase space formalism). Finally, these results are extended to the case of a charged particle in a uniform magnetic field. (author)
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 ...
Kühne, Thomas D
2012-01-01
Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.
State-Dependent Molecular Dynamics
Directory of Open Access Journals (Sweden)
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Polymer friction Molecular Dynamics
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
2010-01-01
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to ...
Semi-classical molecular dynamics of photo induced isomerization of spiropyran%螺吡喃光控转变的半经验动力学研究
Institute of Scientific and Technical Information of China (English)
雷依波; 吴少美; 韩慧仙; 豆育升; 文振翼
2013-01-01
A semi-classical electron-radiation-ion dynamics simulation (SERID) has been employed to research the non-adiabatic dynamics process of the ring opening reaction of spiropyran molecule. The simplified model spiropyran (mSP) to simplify the calculation was used. The results show that mSP first passes through a conical intersecting (CD point into CTC-mMC (MC is the abbreviation of merocyanine, mMC is its simplified model) and then into the CTT-mMC, and the conversion reaction of the two isomers is the excited state reaction. These results is consistent with the fact that the first isomer formed after ring opening reaction of SP molecule is unstable and converts to CTC-mMC in a very short period of time. Simulation results indicate that CTT-mMC is more stable than CTC-mMC, so that the latter is rapidly back to lower energy CTT-mMC configuration on the excited state. The present results provide the real-time dynamics process of three C-C-C-C dihedral angle of mSP molecule turning around with the time, which verifies the reaction mechanism of theoretical speculation, and the lifetime of excited state on the typical trajectory is roughly consistent with the experimental result.%采用半经典的电子-辐射-离子动力学模拟(SERID)研究了螺吡喃分子开环反应的非绝热动力学过程.采用简化模型的螺吡喃(mSP)简化计算.开环过程中mSP分子首先经过一个圆锥相交点后变为顺式-反式-顺式-模型部花青(CTC-mMC)继而又变为顺式-反式-反式-模型部花青(CTT-mMC).这与实验中螺吡喃分子开环后由于第一个异构体顺式-顺式-顺式-模型部花青(CCC-mMC)不稳定而在很短时间内转变为CTC-mMC基本一致.模拟过程中亦发现CTC-mMC不如CTT-mMC稳定,体系经CTT-mMC后回到能量较低的CTT-mMC构型.mSP的3个C-C-C-C二面角随时间扭转的实时动力学过程验证了以前理论推测的反应机理,模拟得到的激发态寿命与实验值基本一致.
Observation of nondispersing classical-like molecular rotation
Korobenko, Aleksey; Milner, Valery
2014-01-01
Using the technique of an optical centrifuge, we produce rotational wave packets which evolve in time along either classical-like or non-classical trajectories. After releasing O2 and D2 molecules from the centrifuge, we track their field-free rotation by monitoring the molecular angular distribution with velocity map imaging. Due to the dispersion of the created rotational wave packets in oxygen, we observe a gradual transition between "dumbbell"-shaped and "cross"-shaped distributions, both rotating with a classical rotation frequency. In deuterium, a much narrower rotational wave packet is produced and shown to evolve in a truly classical non-dispersing fashion.
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.
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.
International Nuclear Information System (INIS)
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
Indeterminism in Classical Dynamics of Particle Motion
Eyink, Gregory; Vishniac, Ethan; Lalescu, Cristian; Aluie, Hussein; Kanov, Kalin; Burns, Randal; Meneveau, Charles; Szalay, Alex
2013-03-01
We show that ``God plays dice'' not only in quantum mechanics but also in the classical dynamics of particles advected by turbulent fluids. With a fixed deterministic flow velocity and an exactly known initial position, the particle motion is nevertheless completely unpredictable! In analogy with spontaneous magnetization in ferromagnets which persists as external field is taken to zero, the particle trajectories in turbulent flow remain random as external noise vanishes. The necessary ingredient is a rough advecting field with a power-law energy spectrum extending to smaller scales as noise is taken to zero. The physical mechanism of ``spontaneous stochasticity'' is the explosive dispersion of particle pairs proposed by L. F. Richardson in 1926, so the phenomenon should be observable in laboratory and natural turbulent flows. We present here the first empirical corroboration of these effects in high Reynolds-number numerical simulations of hydrodynamic and magnetohydrodynamic fluid turbulence. Since power-law spectra are seen in many other systems in condensed matter, geophysics and astrophysics, the phenomenon should occur rather widely. Fast reconnection in solar flares and other astrophysical systems can be explained by spontaneous stochasticity of magnetic field-line motion
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.
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)
Classical Hamiltonian Dynamics and Lie Group Algebras
Aycock, B; Silverberg, J L; Widom, A
2008-01-01
The classical Hamilton equations of motion yield a structure sufficiently general to handle an almost arbitrary set of ordinary differential equations. Employing elementary algebraic methods, it is possible within the Hamiltonian structure to describe many physical systems exhibiting Lie group symmetries. Elementary examples include magnetic moment precession and the mechanical orbits of color charged particles in classical non-abelian chromodynamics.
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....
Comparisons of classical and quantum dynamics for initially localized states
International Nuclear Information System (INIS)
We compare the dynamics of quantum wave packets with the dynamics of classical trajectory ensembles. The wave packets are Gaussian with expectation values of position and momenta which centers them in phase space. The classical trajectory ensembles are generated directly from the quantum wave packets via the Wigner transform. Quantum and classical dynamics are then compared using several quantum measures and the analogous classical ones derived from the Wigner equivalent formalism. Comparisons are made for several model potentials and it is found that there is generally excellent classical--quantum correspondence except for certain specific cases of tunneling and interference. In general, this correspondence is also very good in regions of phase space where there is classical chaos
BÄRBEL M. R. STADLER; Stadler, Peter F
2003-01-01
Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability...
Substructured multibody molecular dynamics.
Energy Technology Data Exchange (ETDEWEB)
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Controlling the sense of molecular rotation: classical vs quantum analysis
Khodorkovsky, Yuri; Hasegawa, Hirokazu; Ohshima, Yasuhiro; Averbukh, Ilya Sh
2010-01-01
Recently, it was predicted theoretically and verified experimentally that a pair of delayed and cross-polarized short laser pulses can create molecular ensembles with a well defined sense of rotation (clockwise or counterclockwise). Here we provide a comparative study of the classical and quantum aspects of the underlying mechanism for linear molecules and for symmetric tops, like benzene molecules, that were used for the first experimental demonstration of the effect. Very good quantitative agreement is found between the classical description of the process and the rigorous quantum mechanical analysis at the relevant experimental conditions. Both approaches predict the same optimal values for the delay between pulses and the angle between them, and deliver the same magnitude of the induced oriented angular momentum of the molecular ensemble. As expected, quantum and classical analysis substantially deviate when the delay between pulses is comparable with the period of quantum rotational revivals. However, ti...
Molecular dynamics for fermions
International Nuclear Information System (INIS)
The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)
Classical Dynamics of Free Electromagnetic Laser Pulses
Goto, S; Tucker, R. W.; Walton, T. J.
2015-01-01
We discuss a class of exact finite energy solutions to the vacuum source-free Maxwell field equations as models for multi- and single cycle laser pulses in classical interaction with relativistic charged test particles. These solutions are classified in terms of their chiral content based on their influence on particular charge configurations in space. Such solutions offer a computationally efficient parameterization of compact laser pulses used in laser-matter simulations and provide a poten...
Classical diffusive dynamics for the quasiperiodic kicked rotor
Lemarié, Gabriel; Delande, Dominique; Garreau, Jean Claude; Szriftgiser, Pascal
2010-01-01
We study the classical dynamics of a quasiperiodic kicked rotor, whose quantum counterpart is known to be an equivalent of the 3D Anderson model. Using this correspondence allowed for a recent experimental observation of the Anderson transition with atomic matter waves. In such a context, it is particularly important to assert the chaotic character of the classical dynamics of this system. We show here that it is a 3D anisotropic diffusion. Our simple analytical predictions for the associated...
A True Equation to Couple Classical and Quantum Dynamics
Diosi, Lajos
1995-01-01
Starting from the Schr\\"odinger-equation of a composite system, we derive unified dynamics of a classical harmonic system coupled to an arbitrary quantized system. The classical subsystem is described by random phase-space coordinates entangled with the quantized variables of the complementary subsystem. Our semiclassical equation is {\\it true} in a sense that its predictions are identical to those of the fully quantized composite dynamics. This exact method applies to a broad class of theori...
Classical Dynamics of Free Electromagnetic Laser Pulses
Goto, S; Walton, T J
2015-01-01
We discuss a class of exact finite energy solutions to the vacuum source-free Maxwell field equations as models for multi- and single cycle laser pulses in classical interaction with relativistic charged test particles. These solutions are classified in terms of their chiral content based on their influence on particular charge configurations in space. Such solutions offer a computationally efficient parameterization of compact laser pulses used in laser-matter simulations and provide a potential means for experimentally bounding the fundamental length scale in the generalized electrodynamics of Bopp, Lande and Podolsky.
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
2016-01-01
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. PMID:27546820
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.
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.
From Molecular Dynamics to Dissipative Particle Dynamics
Flekkoy, Eirik G.; Coveney, Peter V.
1999-01-01
A procedure is introduced for deriving a coarse-grained dissipative particle dynamics from molecular dynamics. The rules of the dissipative particle dynamics are derived from the underlying molecular interactions, and a Langevin equation is obtained that describes the forces experienced by the dissipative particles and specifies the associated canonical Gibbs distribution for the system.
On the classical dynamics of billiards on the sphere
Spina, M E
1999-01-01
We study the classical motion in bidimensional polygonal billiards on the sphere. In particular we investigate the dynamics in tiling and generic rational and irrational equilateral triangles. Unlike the plane or the negative curvature cases we obtain a complex but regular dynamics.
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
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...
Metamaterials: supra-classical dynamic homogenization
Caleap, Mihai; Drinkwater, Bruce W.
2015-12-01
Metamaterials are artificial composite structures designed for controlling waves or fields, and exhibit interaction phenomena that are unexpected on the basis of their chemical constituents. These phenomena are encoded in effective material parameters that can be electronic, magnetic, acoustic, or elastic, and must adequately represent the wave interaction behavior in the composite within desired frequency ranges. In some cases—for example, the low frequency regime—there exist various efficient ways by which effective material parameters for wave propagation in metamaterials may be found. However, the general problem of predicting frequency-dependent dynamic effective constants has remained unsolved. Here, we obtain novel mathematical expressions for the effective parameters of two-dimensional metamaterial systems valid at higher frequencies and wavelengths than previously possible. By way of an example, random configurations of cylindrical scatterers are considered, in various physical contexts: sound waves in a compressible fluid, anti-plane elastic waves, and electromagnetic waves. Our results point towards a paradigm shift in our understanding of these effective properties, and metamaterial designs with functionalities beyond the low-frequency regime are now open for innovation. Dedicated with gratitude to the memory of Prof Yves C Angel.
Pathology and molecular diagnosis of classical swine fever in Mizoram
Directory of Open Access Journals (Sweden)
David Malswamkima
2015-01-01
Full Text Available Aim: Clinical histopathological and molecular diagnosis of classical swine fever disease in pigs of Mizoram. Materials and Methods: Totally, 31 clinically suspected pigs from 6 districts of Mizoram were examined, and clinical symptoms were recorded. Detailed post mortem examination of all the 31 dead animals was conducted, and gross changes were recorded. Tissue samples were collected for histopathological examination and molecular diagnosis. The collected tissues (tonsil, lymph nodes, spleen were also processed for RNA extraction. Reverse transcription polymerase chain reaction (RT-PCR was performed to detect the specific gene fragments of classical swine fever virus (CSFV. Results: Clinical examination of all the 31 suspected pigs revealed typical clinical signs of CSF. All the animals also showed typical gross and microscopic lesions of CSF. RT-PCR on tissue samples amplified the 421bp, 449bp and 735bp region of 5´NCR, non-structural protein 5B and Erns gene regions of CSFV, respectively. Nested PCR for internal region of E2 gene also amplified the expected product of 271bp using PCR product of whole E2 region as template DNA. Conclusion: CSF is highly endemic disease in Mizoram. The viral strains circulating in this region are highly virulent. The disease can be diagnosed specifically using RT-PCR.
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
Akimov, Alexey V
2016-06-30
The "methodology discovery" library for quantum and classical dynamics simulations is presented. One of the major foci of the code is on nonadiabatic molecular dynamics simulations with model and atomistic Hamiltonians treated on the same footing. The essential aspects of the methodology, design philosophy, and implementation are discussed. The code capabilities are demonstrated on a number of model and atomistic test cases. It is demonstrated how the library can be used to study methodologies for quantum and classical dynamics, as well as a tool for performing detailed atomistic studies of nonadiabatic processes in molecular systems. The source code and additional information are available on the Web at http://www.acsu.buffalo.edu/~alexeyak/libra/index.html. © 2016 Wiley Periodicals, Inc. PMID:27016373
Continuous Finite Element Methods of Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Qiong Tang
2015-01-01
Full Text Available Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite element method is also a reliable method to simulate long-time classical trajectory of molecular systems.
Molecular machines operating on the nanoscale: from classical to quantum.
Goychuk, Igor
2016-01-01
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. PMID:27335728
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.
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
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...... for which isomorphs are only expected when the Coulomb interactions are relatively weak. We briefly discuss the consequences of the findings for theories of melting and crystallization...
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.
Decoherence and quantum-classical master equation dynamics
Grunwald, Robbie; Kapral, Raymond
2007-03-01
The conditions under which quantum-classical Liouville dynamics may be reduced to a master equation are investigated. Systems that can be partitioned into a quantum-classical subsystem interacting with a classical bath are considered. Starting with an exact non-Markovian equation for the diagonal elements of the density matrix, an evolution equation for the subsystem density matrix is derived. One contribution to this equation contains the bath average of a memory kernel that accounts for all coherences in the system. It is shown to be a rapidly decaying function, motivating a Markovian approximation on this term in the evolution equation. The resulting subsystem density matrix equation is still non-Markovian due to the fact that bath degrees of freedom have been projected out of the dynamics. Provided the computation of nonequilibrium average values or correlation functions is considered, the non-Markovian character of this equation can be removed by lifting the equation into the full phase space of the system. This leads to a trajectory description of the dynamics where each fictitious trajectory accounts for decoherence due to the bath degrees of freedom. The results are illustrated by computations of the rate constant of a model nonadiabatic chemical reaction.
Molecular dynamics study of cyclohexane interconversion
Wilson, Michael A.; Chandler, David
1990-12-01
Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.
Nonadiabatic Molecular Dynamics Based on Trajectories
Directory of Open Access Journals (Sweden)
Felipe Franco de Carvalho
2013-12-01
Full Text Available Performing molecular dynamics in electronically excited states requires the inclusion of nonadiabatic effects to properly describe phenomena beyond the Born-Oppenheimer approximation. This article provides a survey of selected nonadiabatic methods based on quantum or classical trajectories. Among these techniques, trajectory surface hopping constitutes an interesting compromise between accuracy and efficiency for the simulation of medium- to large-scale molecular systems. This approach is, however, based on non-rigorous approximations that could compromise, in some cases, the correct description of the nonadiabatic effects under consideration and hamper a systematic improvement of the theory. With the help of an in principle exact description of nonadiabatic dynamics based on Bohmian quantum trajectories, we will investigate the origin of the main approximations in trajectory surface hopping and illustrate some of the limits of this approach by means of a few simple examples.
Common Axioms for Inferring Classical Ensemble Dynamics and Quantum Theory
Parwani, R R
2005-01-01
Within a hamiltonian framework, the same set of physically motivated axioms is used to construct both the classical ensemble Hamilton-Jacobi equation and Schrodingers equation. Crucial roles are played by the assumptions of universality and simplicity (Occam's Razor) which restrict the number and type of of arbitrary constants that appear in the hamiltonian. In this approach, non-relativistic quantum theory is seen as the unique single parameter extension of the classical ensemble dynamics. The method is contrasted with other related constructions in the literature. Possible generalisation to the relativistic case, and some consequences of relaxing the axioms, are also discussed: for example, simple extensions of the linear Schrodinger equation lead to higher-derivative nonlinear corrections that are possibly related to gravity.
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
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.
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
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...
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...
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].
Classical and quantum stability of higher-derivative dynamics
Energy Technology Data Exchange (ETDEWEB)
Kaparulin, D.S.; Lyakhovich, S.L.; Sharapov, A.A. [Tomsk State University, Physics Faculty, Tomsk (Russian Federation)
2014-10-15
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 they keep the system stable. (orig.)
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.)
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 ...
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.
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.)
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.
Dynamics of mixed classical-quantum systems, geometric quantization and coherent states
Jauslin, H R
2011-01-01
We describe quantum and classical Hamiltonian dynamics in a common Hilbert space framework, that allows the treatment of mixed quantum-classical systems. The analysis of some examples illustrates the possibility of entanglement between classical and quantum systems. We give a summary of the main tools of Berezin-Toeplitz and geometric quantization, that provide a relation between the classical and the quantum models, based essentially on the selection of a subspace of the classical Hilbert space. Coherent states provide a systematic tool for the inverse process, called dequantization, that associates a classical Hamiltonian system to a given quantum dynamics through the choice of a complete set of coherent states.
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)
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.
Molecular machines operating on nanoscale: from classical to quantum
Goychuk, Igor
2015-01-01
The main physical features and operating principles of isothermal nanomachines in microworld are reviewed, which are common for both classical and quantum machines. Especial attention is paid to the dual and constructive role of dissipation and thermal fluctuations, 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 fe...
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.
Spin dynamics of quantum and classical Heisenberg dimers
Mentrup, D.; Schnack, J.; Luban, Marshall
1999-01-01
Analytical solutions for the time-dependent autocorrelation function of the classical and quantum mechanical spin dimer with arbitrary spin are presented and compared. For large spin quantum numbers or high temperature the classical and the quantum dimer become more and more similar, yet with the major difference that the quantum autocorrelation function is periodic in time whereas the classical is not.
Molecular quantum dynamics. From theory to applications
International Nuclear Information System (INIS)
An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the
Energy Technology Data Exchange (ETDEWEB)
Miller, William H., E-mail: millerwh@berkeley.edu; Cotton, Stephen J., E-mail: StephenJCotton47@gmail.com [Department of Chemistry and Kenneth S. Pitzer Center for Theoretical Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)
2015-04-07
It is noted that the recently developed symmetrical quasi-classical (SQC) treatment of the Meyer-Miller (MM) model for the simulation of electronically non-adiabatic dynamics provides a good description of detailed balance, even though the dynamics which results from the classical MM Hamiltonian is “Ehrenfest dynamics” (i.e., the force on the nuclei is an instantaneous coherent average over all electronic states). This is seen to be a consequence of the SQC windowing methodology for “processing” the results of the trajectory calculation. For a particularly simple model discussed here, this is shown to be true regardless of the choice of windowing function employed in the SQC model, and for a more realistic full classical molecular dynamics simulation, it is seen to be maintained correctly for very long time.
International Nuclear Information System (INIS)
It is noted that the recently developed symmetrical quasi-classical (SQC) treatment of the Meyer-Miller (MM) model for the simulation of electronically non-adiabatic dynamics provides a good description of detailed balance, even though the dynamics which results from the classical MM Hamiltonian is “Ehrenfest dynamics” (i.e., the force on the nuclei is an instantaneous coherent average over all electronic states). This is seen to be a consequence of the SQC windowing methodology for “processing” the results of the trajectory calculation. For a particularly simple model discussed here, this is shown to be true regardless of the choice of windowing function employed in the SQC model, and for a more realistic full classical molecular dynamics simulation, it is seen to be maintained correctly for very long time
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.
Dynamical fluctuations in classical adiabatic processes: General description and their implications
Zhang, Qi; Gong, Jiangbin; Oh, C. H.
2010-01-01
Dynamical fluctuations in classical adiabatic processes are not considered by the conventional classical adiabatic theorem. In this work a general result is derived to describe the intrinsic dynamical fluctuations in classical adiabatic processes. Interesting implications of our general result are discussed via two subtopics, namely, an intriguing adiabatic geometric phase in a dynamical model with an adiabatically moving fixed-point solution, and the possible "pollution" to Hannay's angle or...
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.
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)
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. PMID:27053964
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.
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.
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...
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.
Topology of classical molecular optimal control landscapes for multi-target objectives
International Nuclear Information System (INIS)
This paper considers laser-driven optimal control of an ensemble of non-interacting molecules whose dynamics lie in classical phase space. The molecules evolve independently under control to distinct final states. We consider a control landscape defined in terms of multi-target (MT) molecular states and analyze the landscape as a functional of the control field. The topology of the MT control landscape is assessed through its gradient and Hessian with respect to the control. Under particular assumptions, the MT control landscape is found to be free of traps that could hinder reaching the objective. The Hessian associated with an optimal control field is shown to have finite rank, indicating an inherent degree of robustness to control noise. Both the absence of traps and rank of the Hessian are shown to be analogous to the situation of specifying multiple targets for an ensemble of quantum states. Numerical simulations are presented to illustrate the classical landscape principles and further characterize the system behavior as the control field is optimized
Topology of classical molecular optimal control landscapes for multi-target objectives
Energy Technology Data Exchange (ETDEWEB)
Joe-Wong, Carlee [Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544-1000 (United States); Ho, Tak-San; Rabitz, Herschel, E-mail: hrabitz@princeton.edu [Department of Chemistry, Princeton University, Princeton, New Jersey 08544-1009 (United States); Wu, Rebing [Department of Automation, Tsinghua University, Beijing (China)
2015-04-21
This paper considers laser-driven optimal control of an ensemble of non-interacting molecules whose dynamics lie in classical phase space. The molecules evolve independently under control to distinct final states. We consider a control landscape defined in terms of multi-target (MT) molecular states and analyze the landscape as a functional of the control field. The topology of the MT control landscape is assessed through its gradient and Hessian with respect to the control. Under particular assumptions, the MT control landscape is found to be free of traps that could hinder reaching the objective. The Hessian associated with an optimal control field is shown to have finite rank, indicating an inherent degree of robustness to control noise. Both the absence of traps and rank of the Hessian are shown to be analogous to the situation of specifying multiple targets for an ensemble of quantum states. Numerical simulations are presented to illustrate the classical landscape principles and further characterize the system behavior as the control field is optimized.
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...
Classicism and Romanticism : Dynamics of Jane Austen's Novels
Yamaneki, Kanako
1996-01-01
This dissertation explores Jane Austen's six completed novels, Northanger Abb~9y (1818), Sense and Sensibility(1811), Pride and Prejudice (1813), Mansfield Park (1814), Emma (1815), and Persuasion (1818), from the perspectives of classicism and romanticism. It is imperative to investigate her works from these perspectives because she historically belongs to the time of transition from the classical period to the romantic. Although many critics tend to see mainly the notable aspects of classic...
Power dissipation in nanoscale conductors: classical, semi-classical and quantum dynamics
International Nuclear Information System (INIS)
Modelling Joule heating is a difficult problem because of the need to introduce correct correlations between the motions of the ions and the electrons. In this paper we analyse three different models of current induced heating (a purely classical model, a fully quantum model and a hybrid model in which the electrons are treated quantum mechanically and the atoms are treated classically). We find that all three models allow for both heating and cooling processes in the presence of a current, and furthermore the purely classical and purely quantum models show remarkable agreement in the limit of high biases. However, the hybrid model in the Ehrenfest approximation tends to suppress heating. Analysis of the equations of motion reveals that this is a consequence of two things: the electrons are being treated as a continuous fluid and the atoms cannot undergo quantum fluctuations. A means for correcting this is suggested
Rheology via nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference
Rheology via nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.
Laser Controlled Molecular Orientation Dynamics
International Nuclear Information System (INIS)
Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation
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.
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.
Statistical and dynamical remastering of classic exoplanet systems
Nelson, Benjamin Earl
The most powerful constraints on planet formation will come from characterizing the dynamical state of complex multi-planet systems. Unfortunately, with that complexity comes a number of factors that make analyzing these systems a computationally challenging endeavor: the sheer number of model parameters, a wonky shaped posterior distribution, and hundreds to thousands of time series measurements. In this dissertation, I will review our efforts to improve the statistical analyses of radial velocity (RV) data and their applications to some renown, dynamically complex exoplanet system. In the first project (Chapters 2 and 4), we develop a differential evolution Markov chain Monte Carlo (RUN DMC) algorithm to tackle the aforementioned difficult aspects of data analysis. We test the robustness of the algorithm in regards to the number of modeled planets (model dimensionality) and increasing dynamical strength. We apply RUN DMC to a couple classic multi-planet systems and one highly debated system from radial velocity surveys. In the second project (Chapter 5), we analyze RV data of 55 Cancri, a wide binary system known to harbor five planetary orbiting the primary. We find the inner-most planet "e" must be coplanar to within 40 degrees of the outer planets, otherwise Kozai-like perturbations will cause the planet to enter the stellar photosphere through its periastron passage. We find the orbits of planets "b" and "c" are apsidally aligned and librating with low to median amplitude (50+/-6 10 degrees), but they are not orbiting in a mean-motion resonance. In the third project (Chapters 3, 4, 6), we analyze RV data of Gliese 876, a four planet system with three participating in a multi-body resonance, i.e. a Laplace resonance. From a combined observational and statistical analysis computing Bayes factors, we find a four-planet model is favored over one with three-planets. Conditioned on this preferred model, we meaningfully constrain the three-dimensional orbital
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.
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.
Scherer, Christoph
2015-01-01
Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industri...
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.
Molecular potentials and relaxation dynamics
International Nuclear Information System (INIS)
The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X1Σ+ and a3Σ+ states of LiH, NaH, KH, RbH, and CsH and the X2Σ+ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm-1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 5000K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy
Classical and Molecular Genetic Research on General Cognitive Ability.
McGue, Matt; Gottesman, Irving I
2015-01-01
Arguably, no psychological variable has received more attention from behavioral geneticists than what has been called "general cognitive ability" (as well as "general intelligence" or "g"), and for good reason. GCA has a rich correlational network, implying that it may play an important role in multiple domains of functioning. GCA is highly correlated with various indicators of educational attainment, yet its predictive utility is not limited to academic achievement. It is also correlated with work performance, navigating the complexities of everyday life, the absence of various social pathologies (such as criminal convictions), and even health and mortality. Although the causal basis for these associations is not always known, it is nonetheless the case that research on GCA has the potential to provide insights into the origins of a wide range of important social outcomes. In this essay, our discussion of why GCA is considered a fundamentally important dimension of behavior on which humans differ is followed by a look at behavioral genetics research on CGA. We summarize behavioral genetics research that has sought to identify and quantify the total contributions of genetic and environmental factors to individual differences in GCA as well as molecular genetic research that has sought to identify genetic variants that underlie inherited effects. PMID:26413945
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.
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.
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
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.
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.
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...
Emergent Phenomena via Molecular Dynamics
Rapaport, D. C.
Emergent phenomena are unusual because they are not obvious consequences of the design of the systems in which they appear, a feature no less relevant when they are being simulated. Several systems that exhibit surprisingly rich emergent behavior, each studied by molecular dynamics (MD) simulation, are described: (i) Modeling self-assembly processes associated with virus growth reveals the ability to achieve error-free assembly, where paradoxically, near-maximum yields are due to reversible bond formation. (ii) In fluids studied at the atomistic level, complex hydrodynamic phenomena in rotating and convecting fluids - the Taylor- Couette and Rayleigh-Bénard instabilities - can be reproduced, despite the limited length and time scales accessible by MD. (iii) Segregation studies of granular mixtures in a rotating drum reproduce the expected, but counterintuitive, axial and radial segregation, while for the case of a vertically vibrated layer a novel form of horizontal segregation is revealed.
Solhjoo, Soheil; Vakis, Antonis I.
2015-01-01
Abstract Using classical molecular dynamics, atomic scale simulations of normal contact between a nominally flat substrate and different atomistic and non-atomistic spherical particles were performed to investigate the applicability of classical contact theories at the nanoscale, and further elucida
The Dynamic Ebbinghaus: motion dynamics greatly enhance the classic contextual size illusion
Directory of Open Access Journals (Sweden)
Ryan E.B. Mruczek
2015-02-01
Full Text Available The Ebbinghaus illusion is a classic example of the influence of a contextual surround on the perceived size of an object. Here, we introduce a novel variant of this illusion called the Dynamic Ebbinghaus illusion in which the size and eccentricity of the surrounding inducers modulates dynamically over time. Under these conditions, the size of the central circle is perceived to change in opposition with the size of the inducers. Interestingly, this illusory effect is relatively weak when participants are fixating a stationary central target, less than half the magnitude of the classic static illusion. However, when the entire stimulus translates in space requiring a smooth pursuit eye movement to track the target, the illusory effect is greatly enhanced, almost twice the magnitude of the classic static illusion. A variety of manipulations including target motion, peripheral viewing, and smooth pursuit eye movements all lead to dramatic illusory effects, with the largest effect nearly four times the strength of the classic static illusion. We interpret these results in light of the fact that motion-related manipulations lead to uncertainty in the image size representation of the target, specifically due to added noise at the level of the retinal input. We propose that the neural circuits integrating visual cues for size perception, such as retinal image size, perceived distance, and various contextual factors, weight each cue according to the level of noise or uncertainty in their neural representation. Thus, more weight is given to the influence of contextual information in deriving perceived size in the presence of stimulus and eye motion. Biologically plausible models of size perception should be able to account for the reweighting of different visual cues under varying levels of certainty.
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...
Molecular dynamics of membrane proteins.
Energy Technology Data Exchange (ETDEWEB)
Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); Crozier, Paul Stewart; Stevens, Mark Jackson
2004-10-01
Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.
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.
2016-01-17
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.
Molecular Diagnosis of Classical Rabies Virus in Polar Foxes in Greeenland
DEFF Research Database (Denmark)
Rasmussen, Thomas Bruun; Strandbygaard, Bertel
Classical rabies virus continues to circulate in polar foxes in Greenland. Within the last 5 years more than 30 animals, mainly polar foxes have been tested positive for rabies. In this study, brain samples from this period were assessed for the presence of rabies viral RNA using molecular...
Hamiltonian Dynamics, Classical R-matrices and Isomonodromic Deformations
Harnad, J
1998-01-01
The Hamiltonian approach to the theory of dual isomonodromic deformations is developed within the framework of rational classical R-matrix structures on loop algebras. Particular solutions to the isomonodromic deformation equations appearing in the computation of correlation functions in integrable quantum field theory models are constructed through the Riemann-Hilbert problem method. The corresponding $\\tau$-functions are shown to be given by the Fredholm determinant of a special class of integral operators.
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.
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...
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.
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.
Molecular epidemiology of current classical swine fever virus isolates of wild boar in Germany
DEFF Research Database (Denmark)
Leifer, I; Hoffmann, B; Höper, D;
2010-01-01
Classical swine fever (CSF) has caused significant economic losses in industrialized pig production, and is still present in some European countries. Recent CSF outbreaks in Europe were mainly associated with strains of genogroup 2 (subgroup 2.3). Although there are extensive datasets regarding 2.......3 strains, there is very little information available on longer fragments or whole classical swine fever virus (CSFV) genomes. Furthermore, there are no detailed analyses of the molecular epidemiology of CSFV wild boar isolates available. Nevertheless, complete genome sequences are supportive...
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.
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 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
2012-08-01
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.
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.
Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions
Energy Technology Data Exchange (ETDEWEB)
Fattebert, J.-L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Richards, D.F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Glosli, J.N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2012-12-01
We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·10^{6} particles on 65,536 MPI tasks.
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.
Catalyst dynamics: consequences for classical kinetic descriptions of reactors
DEFF Research Database (Denmark)
Johannessen, Tue; Larsen, Jane Hvolbæk; Chorkendorff, Ib;
2001-01-01
in situ studies and surface science investigations has brought added attention to the fact that catalysts may behave in a dynamic manner and reconstruct depending on the reaction conditions. This feature severely limits traditional kinetic descriptions. In the present paper, we present examples...
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.
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...
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
Establishments Dynamics and Matching Frictions in Classical Competitive Equilibrium
Veracierto, Marcelo
2008-01-01
This paper develops a Walrasian equilibrium theory of establishment level dynamics and matching frictions and uses it to evaluate the effects of congestion externalities in the matching process and determine the government interventions that are needed to implement a Pareto optimal allocation. The optimal policy, which involves a tax on the creation of help-wanted ads and an unemployment subsidy, is highly contractionary. However, it leads to large welfare gains. The policy also plays an impo...
Real-time quantum trajectories for classically allowed dynamics in strong laser fields
Plimak, L I
2015-01-01
Both the physical picture of the dynamics of atoms and molecules in intense infrared fields and its theoretical description use the concept of electron trajectories. Here we address a key question which arises in this context: Are distinctly quantum features of these trajectories, such as the complex-valued coordinates, physically relevant in the classically allowed region of phase space, and what is their origin? First, we argue that solutions of classical equations of motion can account for quantum effects. To this end, we construct an exact solution to the classical Hamilton-Jacobi equation which accounts for dynamics of the wave packet, and show that this solution is physically correct in the limit $\\hbar \\to 0$. Second, we show that imaginary components of classical trajectories are directly linked to the finite size of the initial wavepacket in momentum space. This way, if the electronic wavepacket produced by optical tunneling in strong infrared fiels is localised both in coordinate and momentum, its m...
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.
Quantum dynamics of complex molecular systems
Miller, William H.
2005-01-01
This Perspective presents a broad overview of the present status of theoretical capabilities for describing quantum dynamics in molecular systems with many degrees of freedom, e.g., chemical reactions in solution, clusters, solids, or biomolecular environments.
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, 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.
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
Wayne Cheng-Wei Huang; Herman Batelaan
2013-01-01
In the past decades, Random Electrodynamics (also called Stochastic Electrodynamics) has been used to study the classical harmonic oscillator immersed in the classical electromagnetic zero-point radiation. Random Electrodynamics (RED) predicts an identical probability distribution for the harmonic oscillator compared to the quantum mechanical prediction for the ground state. Moreover, the Heisenberg minimum uncertainty relation is also recovered with RED. To understand the dynamics that gives...
Ab initio mass tensor molecular dynamics
Tsuchida, Eiji
2010-01-01
Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal ato...
Molecular Dynamic Simulation on High Performance Infrastrucutres
Bergant, Anže
2016-01-01
This thesis covers comparison between different computer platforms of high performance computing while performing molecular dynamics simulations, which falls under very complex problems and needs lots of processing power. Our goal was to critically evaluate different platforms while solving molecular dynamics, so we used 1 to 16 processor cores on a computer cluster and one and two graphics processing units (GPU) for simulations. The results will be used while planning on buying new computer ...
Fermionic molecular dynamics for ground states and collisions of nuclei
International Nuclear Information System (INIS)
The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)
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.
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.
Fermionic Molecular Dynamics for nuclear dynamics and thermodynamics
Hasnaoui, K H O; Gulminelli, F
2008-01-01
A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented
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
Programming an interpreter using molecular dynamics
J.A. Bergstra; C.A. Middelburg
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
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...
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.
Molecular dynamics calculations for sodium using pseudopotential theory
International Nuclear Information System (INIS)
The equation of state of sodium is studied using the molecular dynamics technique whereby the classical motion of a system of ions is solved with the aid of computers. The interaction potential between pairs of sodium ions consists of Coulomb and Born-Mayer repulsion terms and an effective ion-ion interaction derived from pseudopotential theory. This theory includes the effects of electron gas screening, exchange, and correlation. A model pseudopotential with parameters fit to experimental low-temperature data is used. By using this technique, an atomic description of a simple metal proceeds to the calculation of macroscopic thermodynamic properties
Molecular dynamic study of pressure fluctuations spectrum in plasma
Bystryi, R. G.
2015-11-01
Pressure of plasma is calculated by using classical molecular dynamics method. The formula based on virial theorem was used. Spectrum pressure's fluctuations of singly ionized non-ideal plasma are studied. 1/f-like spectrum behavior is observed. In other words, flicker noise is observed in fluctuations of pressure equilibrium non-ideal plasma. Relations between the obtained result and pressure fluctuations within the Gibbs and Einstein approaches are discussed. Special attention is paid to features of calculating the pressure in strongly coupled systems.
Quantum versus classical hyperfine-induced dynamics in a quantum dota)
Coish, W. A.; Loss, Daniel; Yuzbashyan, E. A.; Altshuler, B. L.
2007-04-01
In this article we analyze spin dynamics for electrons confined to semiconductor quantum dots due to the contact hyperfine interaction. We compare mean-field (classical) evolution of an electron spin in the presence of a nuclear field with the exact quantum evolution for the special case of uniform hyperfine coupling constants. We find that (in this special case) the zero-magnetic-field dynamics due to the mean-field approximation and quantum evolution are similar. However, in a finite magnetic field, the quantum and classical solutions agree only up to a certain time scale t <τc, after which they differ markedly.
International Nuclear Information System (INIS)
The advent of free electron lasers and high harmonic sources enables the investigation of electronic and nuclear dynamics of molecules and solids with atomic spatial resolution and femtosecond/attosecond time resolution, using bright and ultrashort laser pulses of frequency from terahertz to hard x-ray range. With the help of ultrashort laser pulses, the nuclear and electronic dynamics can be initiated, monitored and actively controlled at the typical time scale in the femtosecond to attosecond realm. Meanwhile, theoretical tools are required to describe the underlying mechanism. This doctoral thesis focuses on the development of theoretical tools based on full quantum mechanical multiconfiguration time-dependent Hartree (MCTDH) and mixed quantum classical approaches, which can be applied to describe the dynamical behavior of gas phase molecules and strongly correlated solids in the presence of ultrashort laser pulses. In the first part of this thesis, the focus is on the motion of electron holes in gas phase molecular ions created by extreme ultraviolet (XUV) photoionization and watched by spectroscopic approaches. The XUV photons create electron-hole in the valence orbitals of molecules by photoionization, the electron hole, as a positively charged quasi-particle, can then interact with the nuclei and the rest of electrons, leading to coupled non-Born-Oppenheimer dynamics. I present our study on electron-hole relaxation dynamics in valence ionized molecular ions of moderate size, using quantum wave packet and mixed quantum-classical approaches, using photoionized [H+(H2O)n]+ molecular ion as example. We have shown that the coupled motion of the electron-hole and the nuclei can be mapped out with femtosecond resolution by core-level x-ray transient absorption spectroscopy. Furthermore, in specific cases, the XUV photon can create a coherent electron hole, that can maintain its coherence to time scales of ∝ 1 picosecond. Employing XUV pump - IR probe spectroscopy
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).
Gutierrez, R.; Caetano, R.; Woiczikowski, P. B.; Kubar, T.; Elstner, M; Cuniberti, G.
2009-01-01
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either fr...
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...
Dynamically consistent method for mixed quantum-classical simulations: A semiclassical approach.
Antipov, Sergey V; Ye, Ziyu; Ananth, Nandini
2015-05-14
We introduce a new semiclassical (SC) framework, the Mixed Quantum-Classical Initial Value Representation (MQC-IVR), that can be tuned to reproduce existing quantum-limit and classical-limit SC approximations to quantum real-time correlation functions. Applying a modified Filinov transformation to a quantum-limit SC formulation leads to the association of a Filinov parameter with each degree of freedom in the system; varying this parameter from zero to infinity controls the extent of quantization of the corresponding mode. The resulting MQC-IVR expression provides a consistent dynamic framework for mixed quantum-classical simulations and we demonstrate its numerical accuracy in the calculation of real-time correlation functions for a model 1D system and a model 2D system over the full range of quantum- to classical-limit behaviors. PMID:25978878
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
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... 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...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...
The effect of dynamics on damage spreading in the two-dimensional classical XY model
Energy Technology Data Exchange (ETDEWEB)
Chiu, J.; Teitel, S. (Univ. of Rochester, NY (United States))
1990-01-01
The authors study damage spreading in the classical two-dimensional XY model, using a dynamics and distance measure which preserve the rotational variance of the Hamiltonian. They find only a high temperature random phase and a lower temperature ordered phase, consistent with equilibrium results. Their results contrast to previous results of Golinelli and Derrida.
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.
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...
Real-time quantum trajectories for classically allowed dynamics in strong laser fields
Plimak, L. I.; Ivanov, Misha Yu.
2015-10-01
Both the physical picture of the dynamics of atoms and molecules in intense infrared fields and its theoretical description use the concept of electron trajectories. Here, we address a key question which arises in this context: Are distinctly quantum features of these trajectories, such as the complex-valued coordinates, physically relevant in the classically allowed region of phase space, and what is their origin? First, we argue that solutions of classical equations of motion can account for quantum effects. To this end, we construct an exact solution to the classical Hamilton-Jacobi equation which accounts for dynamics of the wave packet, and show that this solution is physically correct in the limit ?. Second, we show that imaginary components of classical trajectories are directly linked to the finite size of the initial wave packet in momentum space. This way, if the electronic wave packet produced by optical tunnelling in strong infrared fields is localised both in coordinate and momentum, its motion after tunnelling ipso facto cannot be described with purely classical trajectories - in contrast to popular models in the literature.
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.
Collective Molecular Dynamics in Proteins and Membranes
Rheinstadter, Maikel C
2008-01-01
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of membrane composition and properties and of structure and dynamics of the surrounding hydration water on protein function is an upcoming hot topic, which can be addressed by modern experimental and computational techniques. Correlated molecular motions might play a crucial role for the understanding of, for instance, transport processes and elastic properties, and might be relevant for protein function. Experimentally that involves determining dispersion relations for the different molecular components, i.e., the length scale dependent excitation frequencies and relaxation rates. Only very few experimental techniques can access dynamical properties in biological materials on the nanometer scale, and resolve dynamics of lipid molecules, hydration water molecules and proteins and t...
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.
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.
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.
De Martino, Salvatore; De Siena, Silvio; 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 m...
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.
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.)
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.
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.
Molecular dynamics simulations of weak detonations.
Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie
2011-12-01
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055
Gauge fixing and classical dynamical r-matrices in (2+1)-gravity
International Nuclear Information System (INIS)
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.
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.
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
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.
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.
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.
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.
Biological and molecular characterization of classical swine fever challenge virus from India
Directory of Open Access Journals (Sweden)
Parveen Kumar
2015-03-01
Full Text Available Aim: The aim of this study was biological and molecular characterization of classical swine fever (CSF challenge virus from India. Materials and Methods: CSF challenge virus maintained at Division of Biological standardization was experimentally infected to two seronegative piglets. The biological characterization was done by clinical sign and symptoms along with postmortem findings. For molecular characterization 5’-nontranslated region, E2 and NS5B regions were amplified by reverse transcription polymerase chain reaction and sequenced. The sequences were compared with that of reference strains and the local field isolates to establish a phylogenetic relation. Results: The virus produced symptoms of acute disease in the piglets with typical post-mortem lesions. Phylogenetic analysis of the three regions showed that the current Indian CSF Challenge virus is having maximum similarity with the BresciaX strain (USA and Madhya Pradesh isolate (India and is belonging to subgroup 1.2 under Group 1. Conclusion: Based on biological and molecular characterization of CSF challenge virus from India is described as a highly virulent virus belonging to subgroup 1.2 under Group 1 along with some field isolates from India and Brescia strain.
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.
Generalized microcanonical and Gibbs ensembles in classical and quantum integrable dynamics
Yuzbashyan, Emil A.
2016-04-01
We prove two statements about the long time dynamics of integrable Hamiltonian systems. In classical mechanics, we prove the microcanonical version of the Generalized Gibbs Ensemble (GGE) by mapping it to a known theorem and then extend it to the limit of infinite number of degrees of freedom. In quantum mechanics, we prove GGE for maximal Hamiltonians-a class of models stemming from a rigorous notion of quantum integrability understood as the existence of conserved charges with prescribed dependence on a system parameter, e.g. Hubbard U, anisotropy in the XXZ model etc. In analogy with classical integrability, the defining property of these models is that they have the maximum number of independent integrals. We contrast their dynamics induced by quenching the parameter to that of random matrix Hamiltonians.
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.
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.
Classical dynamics of a charged particle in a laser field beyond the dipole approximation
Jameson, Paul; Khvedelidze, Arsen
2008-01-01
The classical dynamics of a charged particle traveling in a laser field modeled by an elliptically polarized monochromatic electromagnetic plane wave is discussed within the time reparametrization invariant form of the non-relativistic Hamilton-Jacobi theory. The exact parametric representation for a particle's orbit in an arbitrary plane wave background beyond the dipole approximation and including effect of the magnetic field is derived. For an elliptically polarized monochromatic plane wav...
Ovaskainen, Otso; Hanski, Ilkka
2004-01-01
Spatially structured populations in patchy habitats show much variation in migration rate, from patchy populations in which individuals move repeatedly among habitat patches to classic metapopulations with infrequent migration among discrete populations. To establish a common framework for population dynamics in patchy habitats, we describe an individual-based model (IBM) involving a diffusion approximation of correlated random walk of individual movements. As an example, we apply the model t...
Quantum-classical transition in the electron dynamics of thin metal films
Jasiak, Rafal; Manfredi, Giovanni; Hervieux, Paul-Antoine; Haefele, Matthieu
2009-01-01
International audience 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 class...
A general solution for classical sequential growth dynamics of Causal Sets
Varadarajan, Madhavan; Rideout, David
2005-01-01
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 ...
Matthews, Charles
2013-01-01
Molecular dynamics (MD) computations aim to simulate materials at the atomic level by approximating molecular interactions classically, relying on the Born-Oppenheimer approximation and semi-empirical potential energy functions as an alternative to solving the difficult time-dependent Schrodinger equation. An approximate solution is obtained by discretization in time, with an appropriate algorithm used to advance the state of the system between successive timesteps. Modern MD s...
Boltzmann-conserving classical dynamics in quantum time-correlation functions: “Matsubara dynamics”
Energy Technology Data Exchange (ETDEWEB)
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C., E-mail: sca10@cam.ac.uk [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)
2015-04-07
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 → ∞, 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 ħ{sup 2} at ħ{sup 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 O(ħ{sup 2}) disappear from the Matsubara Liouvillian in the limit N → ∞) and conserves the quantum Boltzmann distribution because the Matsubara Hamiltonian is symmetric with respect to imaginary-time translation. Numerical tests show that the Matsubara approximation to the quantum time-correlation function converges with respect to the number of modes and gives better agreement than LSC-IVR with the exact quantum result. Matsubara dynamics is too computationally expensive to be applied to complex systems, but its further approximation may lead to practical methods.
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.)
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.
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...
International Nuclear Information System (INIS)
The explosion dynamics of small hydrogen clusters irradiated by intense femtosecond infrared laser pulses is investigated by classical molecular dynamics simulations. We find a spatial anisotropy in these explosions with proton energies enhanced along the laser polarization direction. Our simulations can identify the origin of this anisotropy: the interplay between the space charge separation in the early stage of cluster ionization and the Coulomb attraction between the rescattered electrons and protons during cluster explosion. (paper)
An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations
Tsuchida, Eiji
2016-08-01
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.
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.
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Towards the molecular bases of polymerase dynamics
International Nuclear Information System (INIS)
One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (rf) and RNA polymerase (rt). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking rf and rt suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin rt may depend on the length (λt) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs
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
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.
Simulating granular flow with molecular dynamics
Ristow, Gerald
1992-01-01
We investigate by means of Molecular Dynamics simulations an assembly of spheres to model a granular medium flowing from an upper rectangular chamber through a hole into a lower chamber. Two different two dimensional models are discussed one of them including rotations of the individual spheres. The outflow properties are investigated and compared to experimental data. The qualitative agreement suggests that our models contain the necessary ingredients to describe the outflow properties of gr...
Temperature Dependent Molecular Dynamic Simulation of Friction
Dias, R A; Coura, P Z; Costa, B V
2006-01-01
In this work we present a molecular dynamics simulation of a FFM experiment. The tip-sample interaction is studied by varying the normal force in the tip and the temperature of the surface. The friction force, cA, at zero load and the friction coefficient, $\\mu$, were obtained. Our results strongly support the idea that the effective contact area, A, decreases with increasing temperature and the friction coefficient presents a clear signature of the premelting process of the surface.
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 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. PMID:26871185
Optimally designed fields for controlling molecular dynamics
Rabitz, Herschel
1991-10-01
This research concerns the development of molecular control theory techniques for designing optical fields capable of manipulating molecular dynamic phenomena. Although is has been long recognized that lasers should be capable of manipulating dynamic events, many frustrating years of intuitively driven laboratory studies only serve to illustrate the point that the task is complex and defies intuition. The principal new component in the present research is the recognition that this problem falls into the category of control theory and its inherent complexities require the use of modern control theory tools largely developed in the engineering disciplines. Thus, the research has initiated a transfer of the control theory concepts to the molecular scale. Although much contained effort will be needed to fully develop these concepts, the research in this grant set forth the basic components of the theory and carried out illustrative studies involving the design of optical fields capable of controlling rotational, vibrational and electronic degrees of freedom. Optimal control within the quantum mechanical molecular realm represents a frontier area with many possible ultimate applications. At this stage, the theoretical tools need to be joined with merging laboratory optical pulse shaping capabilities to illustrate the power of the concepts.
A Concurrent Multiscale Micromorphic Molecular Dynamics. Part I. Theoretical Formulation
Li, Shaofan
2014-01-01
Based on a novel concept of multiplicative multiscale decomposition, we have derived a multiscale micromorphic molecular dynamics (MMMD)to extent the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and macroscale. The multiscale micromorphic molecular dynamics is a con-current three-scale particle dynamics that couples a fine scale molecular dynamics, a mesoscale particle dynamics of micromorphic medium, and a coarse scale nonlocal particle dynamics of nonlinear continuum. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and it is a special case of the proposed multiscale micromorphic molecular dynamics. The discovered mutiscale structure and the corresponding multiscale dynamics reveal a seamless transition channel from atomistic scale to continuum scale and the intrinsic coupling relation among them, and it can be used to solve finite size nanoscale sc...
Dynamical structure of fluid mercury: Molecular-dynamics simulations
Hoshino, Kozo; Tanaka, Shunichiro; Shimojo, Fuyuki
2007-01-01
We have carried out molecular-dynamics simulations for nonmetallic fluid mercury in liquid and vapor phases using a Lennard-Jones type effective potential and shown that the structure factors S(Q) and the dynamic structure factors S(Q, omega) of nonmetallic fluid mercury obtained by our MD simulations are in good agreement with recent X-ray diffraction and inelastic X-ray scattering experiments. We conclude from these results that, though the fluid mercury which shows a metal-nonmetal transit...
"Like-charge attraction" between anionic polyelectrolytes: molecular dynamics simulations.
Molnar, Ferenc; Rieger, Jens
2005-01-18
"Like-charge attraction" is a phenomenon found in many biological systems containing DNA or proteins, as well as in polyelectrolyte systems of industrial importance. "Like-charge attraction" between polyanions is observed in the presence of mobile multivalent cations. At a certain limiting concentration of cations, the negatively charged macroions cease to repel each other and even an attractive force between the anions is found. With classical molecular dynamics simulations it is possible to elucidate the processes that govern the attractive behavior with atomistic resolution. As an industrially relevant example we study the interaction of negatively charged carboxylate groups of sodium polyacrylate molecules with divalent cationic Ca2+ counterions. Here we show that Ca2+ ions initially associate with single chains of polyacrylates and strongly influence sodium ion distribution; shielded polyanions approach each other and eventually "stick" together (precipitate), contrary to the assumption that precipitation is initially induced by intermolecular Ca2+ bridging. PMID:15641856
Width spreading and tests of wave packet molecular dynamics
International Nuclear Information System (INIS)
Complete text of publication follows. We examine three aspects of wave packet molecular dynamics (WPMD): wave packet spreading, the versatility of the isotropic Gaussian basis, and the interpretation of WPMD data. It is commonly known in the WPMD community that at large temperatures isotropic Gaussian wave packets have divergent widths. We quantify the unphysicality of this behavior by calculating radial distribution functions at many temperatures and densities, and compare to quantum statistical potential and path integral Monte Carlo results. We also make direct comparisons with a numerically exact time-dependent Schroedinger equation solver to determine deficiencies in the basis by studying a single quantum electron traveling through a static classical dense plasma. Another aspect is the validity of standard calculation methods. Central to these quantum computations are the ensemble explored by WPMD and its ergodic properties.
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.
A census of the expected properties of classical Milky Way dwarfs in Milgromian dynamics
Lüghausen, Fabian; Kroupa, Pavel
2014-01-01
Prompted by the recent successful predictions of the internal dynamics of Andromeda's satellite galaxies (McGaugh & Milgrom 2013a,b), we revisit the classical Milky Way dwarf spheroidal satellites Draco, Sculptor, Sextans, Carina, and Fornax in the framework of Milgromian dynamics (MOND). We use for the first time a Poisson solver with adaptive mesh refinement in order to account simultaneously for the gravitational influence of the Milky Way and its satellites. This allows to rigorously model the important external field effect (EFE) of Milgromian dynamics, which can reduce the effective acceleration significantly. We make predictions on the dynamical mass-to-light ratio (Mdyn/L) expected to be measured by an observer who assumes Newtonian dynamics to be valid. We show that Milgromian dynamics predicts typical Mdyn/L ~ 10...50 Msun/Lsun. The results for the most luminous ones, Fornax and Sculptor, agree well with available velocity dispersion data. Moreover, the central power law slopes of the dynamical ...
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.
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.
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.
Generalized Langevin models of molecular dynamics simulations with applications to ion channels
Gordon, Dan; Krishnamurthy, Vikram; Chung, Shin-Ho
2009-10-01
We present a new methodology, which combines molecular dynamics and stochastic dynamics, for modeling the permeation of ions across biological ion channels. Using molecular dynamics, a free energy profile is determined for the ion(s) in the channel, and the distribution of random and frictional forces is measured over discrete segments of the ion channel. The parameters thus determined are used in stochastic dynamics simulations based on the nonlinear generalized Langevin equation. We first provide the theoretical basis of this procedure, which we refer to as "distributional molecular dynamics," and detail the methods for estimating the parameters from molecular dynamics to be used in stochastic dynamics. We test the technique by applying it to study the dynamics of ion permeation across the gramicidin pore. Given the known difficulty in modeling the conduction of ions in gramicidin using classical molecular dynamics, there is a degree of uncertainty regarding the validity of the MD-derived potential of mean force (PMF) for gramicidin. Using our techniques and systematically changing the PMF, we are able to reverse engineer a modified PMF which gives a current-voltage curve closely matching experimental results.
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.
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.
Molecular dynamic results on transport properties
Energy Technology Data Exchange (ETDEWEB)
Alder, B.J.; Alley, W.E.
1978-06-01
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so.
Electronic continuum model for molecular dynamics simulations.
Leontyev, I V; Stuchebrukhov, A A
2009-02-28
A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627
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
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
equation is solved analytically by Homotopy Analysis Methods. Present solution gives an expression which can be used in wide range of time for all domain of response. Comparisons of the obtained solutions with numerical results show that this method is effective and convenient for solving this problem.......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...
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 .
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...
Mortazavi, Bohayra; Rémond, Yves
2012-06-01
In this paper, we employed classical molecular dynamics simulations using the Tersoff potential for the evaluation of thermal conductivity and tensile response of single-layer boron-nitride sheets (SBNS). By carrying out uniaxial tension simulations, the elastic moduli of SBNS structures are predicted to be close to those of boron-nitride nanotubes in a range between 0.8 and 0.85 TPa for different chirality directions. Performing non-equilibrium molecular dynamics simulations, the thermal conductivity of SBNS is predicted to be around 80 W/m-K, which is shown to be independent of chirality directions.
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.
An ab initio molecular dynamics study of the roaming mechanism of the H2+HOC+ reaction
Yu, Hua-Gen
2011-08-01
We report here a direct ab initio molecular dynamics study of the p-/o-H2+HOC+ reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H2+HOC+ reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.
Ab initio based force field and molecular dynamics simulations of crystalline TATB.
Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E
2004-04-15
An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608
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: 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. PMID:26827606
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.
Ab Initio Molecular Dynamics: A Virtual Laboratory
Hobbi Mobarhan, Milad
2014-01-01
In this thesis, we perform ab initio molecular dynamics (MD) simulations at the Hartree-Fock level, where the forces are computed on-the-fly using the Born-Oppenheimer approximation. The theory behind the Hartree-Fock method is discussed in detail and an implementation of this method based on Gaussian basis functions is explained. We also demonstrate how to calculate the analytic energy derivatives needed for obtaining the forces acting on the nuclei. Hartree-Fock calculations on the ground s...
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
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...
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.
[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.
Fermionic Molecular Dynamics and short range correlations
Feldmeier, H; Roth, R S; Schnack, J
1998-01-01
Fermionic Molecular Dynamics (FMD) models a system of fermions by means of many-body states which are composed of antisymmetrized products of single-particle states. These consist of one or several Gaussians localized in coordinate and momentum space. The parameters specifying them are the dynamical variables of the model. As the repulsive core of the nucleon-nucleon interaction induces short range correlations which cannot be accommodated by a Slater determinant, a novel approach, the unitary correlation operator method (UCOM), is applied. The unitary correlator moves two particles away from each other whenever their relative distance is within the repulsive core. The time-dependent variational principle yields the equations of motion for the variables. Energies of the stationary ground states are calculated and compared to exact many-body results for nuclei up to Ca 48. Time-dependent solutions are shown for collisions between nuclei.
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.
Effect of Markov and Non-Markov Classical Noise on Entanglement Dynamics
Bordone, Paolo; Benedetti, Claudia
2012-01-01
We analyze the effect of a classical noise into the entanglement dynamics between two particles, initially entangled, subject to continuous time quantum walks in a one-dimensional lattice. The noise is modeled by randomizing the transition amplitudes from one site to another. Both Markovian and non-Markovian environments are considered. For the Markov regime an exponential decay of the initial quantum correlation is found, while the loss of coherence of the quantum state increases monotonically with time up to a saturation value depending upon the degrees of freedom of the system. For the non-Markov regime the presence or absence of entanglement revival and entanglement sudden death phenomena is found or deduced depending on the peculiar characteristics of the noise. Our results indicate that the entanglement dynamics in the non-Markovian regime is affected by the persistence of the memory effects of the environment and by its intrinsic features.
Communication: Adiabatic and non-adiabatic electron-nuclear motion: Quantum and classical dynamics
Albert, Julian; Kaiser, Dustin; Engel, Volker
2016-05-01
Using a model for coupled electronic-nuclear motion we investigate the range from negligible to strong non-adiabatic coupling. In the adiabatic case, the quantum dynamics proceeds in a single electronic state, whereas for strong coupling a complete transition between two adiabatic electronic states takes place. It is shown that in all coupling regimes the short-time wave-packet dynamics can be described using ensembles of classical trajectories in the phase space spanned by electronic and nuclear degrees of freedom. We thus provide an example which documents that the quantum concept of non-adiabatic transitions is not necessarily needed if electronic and nuclear motion is treated on the same footing.
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...
Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations
Byutner, Oleksiy; Smith, Grant
2001-03-01
In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.
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.
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.
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.
Sidles, John A; Jacky, Jonathan P; Picone, Rico A R; Harsila, Scott A
2010-01-01
The practical focus of this work is the dynamical simulation of polarization transport processes in quantum spin microscopy and spectroscopy. The simulation framework is built-up progressively, beginning with state-spaces (configuration manifolds) that are geometrically natural, introducing coordinates that are algebraically natural; and finally specifying dynamical potentials that are physically natural; in each respect explicit criteria are given for "naturality." The resulting framework encompasses Hamiltonian flow (both classical and quantum), quantum Lindbladian processes, and classical thermostatic processes. Constructive validation and verification criteria are given for metric and symplectic flows on classical, quantum, and hybrid state-spaces, with particular emphasis to tensor network state-spaces. Both classical and quantum examples are presented, including dynamic nuclear polarization (DNP). A broad span of applications and challenges is discussed, ranging from the design and simulation of quantum...
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.
Collective dynamics in noble-gas and other very simple classical fluids
Directory of Open Access Journals (Sweden)
U.Bafile
2008-03-01
Full Text Available Rare gases and their liquids are the simplest systems to study for accurate investigations of the collective dynamics of fluid matter. Much work has been done using different spectroscopic techniques, molecular-dynamics simulations, and theoretical developments, in order to gain insight into the microscopic processes involved, in particular, in the propagation of acoustic excitations in gases and liquids. Here we briefly review the interpretation schemes currently applied to the characterization of such excitations, and recall a few results obtained from the analysis of rare-gas fluids and other very simple systems.
Stochastic quantum molecular dynamics for finite and extended systems
International Nuclear Information System (INIS)
Graphical abstract: The figure illustrates the time-evolution as generated by the quantum jump algorithm. The lower track represents the piecewise deterministic propagation of the physical state which is intercepted at instances in time where the bath operator S-circumflex acts on the state. The points in time where this takes place are determined by sampling a waiting-time distribution. The sampling is performed by propagating an auxiliary state (represented in the upper track) with a non-Hermitian Hamiltonian. Uniformly distributed random numbers are drawn and once the norm of the auxiliary state drops below the current random number the propagation of the physical and the auxiliary state is suspended. At this point in time the action of the bath operator on the physical state results in a new state which is then also used to initialize the auxiliary state for the evolution. The simulation of both states is then resumed again. Highlights: ►In this study we present a detailed account of the technical aspects of stochastic quantum molecular dynamics. ► We consider both finite systems with and without ionic motion, as well as describe its applicability to extended systems. ► We give prospects of applying the method to decoherence and energy relaxation in the presence of time-dependent fields. - Abstract: We present a detailed account of the technical aspects of stochastic quantum molecular dynamics, an approach introduced recently by the authors [H. Appel, M. Di Ventra, Phys. Rev. B 80 (2009) 212303] to describe coupled electron–ion dynamics in open quantum systems. As example applications of the method we consider both finite systems with and without ionic motion, as well as describe its applicability to extended systems in the limit of classical ions. The latter formulation allows the study of important phenomena such as decoherence and energy relaxation in bulk systems and surfaces in the presence of time-dependent fields.
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
Energy Technology Data Exchange (ETDEWEB)
Belyaev, Andrey K., E-mail: belyaev@herzen.spb.ru [Department of Theoretical Physics, Herzen University, St. Petersburg 191186 (Russian Federation); Domcke, Wolfgang, E-mail: wolfgang.domcke@ch.tum.de [Department Chemie, Technische Universität München, D-85747 Garching (Germany); Lasser, Caroline, E-mail: classer@ma.tum.de; Trigila, Giulio, E-mail: trigila@ma.tum.de [Zentrum Mathematik, Technische Universität München, D-85747 Garching (Germany)
2015-03-14
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.
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
Detecting Allosteric Networks Using Molecular Dynamics Simulation.
Bowerman, S; Wereszczynski, J
2016-01-01
Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. PMID:27497176
Gauge fixing and classical dynamical r-matrices in ISO(2,1)-Chern-Simons theory
Meusburger, Catherine
2012-01-01
We apply Dirac's gauge fixing procedure to Chern-Simons theory with gauge group ISO(2,1) on manifolds RxS, where S is a punctured oriented surface of general genus. For all gauge fixing conditions that satisfy certain structural requirements, this yields an explicit description of the Poisson structure on the moduli space of flat ISO(2,1)-connections on S via the resulting Dirac bracket. The Dirac bracket is determined by classical dynamical r-matrices for ISO(2,1). We show that the Poisson structures and classical dynamical r-matrices arising from different gauge fixing conditions are related by dynamical ISO(2,1)-valued transformations that generalise the usual gauge transformations of classical dynamical r-matrices. By means of these transformations, it is possible to classify all Poisson structures and classical dynamical r-matrices obtained from such gauge fixings. Generically these Poisson structures combine classical dynamical r-matrices for non-conjugate Cartan subalgebras of ISO(2,1).
Photodesorption of water ice: a molecular dynamics study
Andersson, S
2008-01-01
Absorption of ultraviolet radiation by water ice coating interstellar grains can lead to dissociation and desorption of the ice molecules. These processes are thought to be important in the gas-grain chemistry in molecular clouds and protoplanetary disks, but very few quantitative studies exist. We compute the photodesorption efficiencies of amorphous water ice and elucidate the mechanisms by which desorption occurs. Classical molecular dynamics calculations were performed for a compact amorphous ice surface at 10 K thought to be representative of interstellar ice. Dissociation and desorption of H2O molecules in the top six monolayers are considered following absorption into the first excited electronic state with photons in the 1300-1500 Angstrom range. The trajectories of the H and OH photofragments are followed until they escape or become trapped in the ice. The probability for H2O desorption per absorbed UV photon is 0.5-1% in the top three monolayers, then decreases to 0.03% in the next two monolayers, a...
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 Dynamics Simulation Study of Carbon-Nanotube Oscillator in Graphene Nanoribbon Trench
Lee, Eunae; Kang, Jeong Won; Kim, Ki-Sub; Kwon, Oh-Kuen
2016-01-01
Graphene/carbon-nanotube (CNT) hybrid material can be useful in energy storage and nanoelectronic technologies. Here we address the CNT-oscillator encapsulated in a graphene-nanoribbon (GNR) trench as a novel design, and investigate its properties via classical molecular dynamics simulations. Since the energy barrier was very low while the CNT was encapsulated in the GNR trench, the CNT absorbed on the GNR surface could easily be encapsulated in the GNR trench. MD simulations showed that the ...
Quantum Chemical and Molecular Dynamics Study of the Coordination of Th(IV) in Aqueous Solvent
Réal, Florent; Trumm, Michael; Vallet, Valérie; Schimmelpfennig, Bernd; Masella, Michel; Flament, Jean-Pierre
2010-01-01
In this work, we investigate the solvation of tetravalent thorium Th(IV) in aqueous solution using classical molecular dynamics simulations at the 10 ns scale and based on polarizable force-field approaches, which treat explicitly the covalent character of the metal−water interaction (and its inherent cooperative character). We have carried out a thorough analysis of the accuracy of the ab initio data that we used to adjust the force-field parameters. In particular, we show that large atomic ...
Action-derived molecular dynamics in the study of rare events
Passerone, D.; Parrinello, M.
2001-01-01
We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by non-trivial examples. The algorithm lends itself to straightforward parallelization, and when combined with molecular dynamics (MD) it promises to offer a powerful tool for the study of che...
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.
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.
An efficient time-stepping scheme for ab initio molecular dynamics simulations
Tsuchida, Eiji
2015-01-01
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2x performance gain over the standard Verlet method for a given accuracy.
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
Dynamics of dewetting at the nanoscale using molecular dynamics.
Bertrand, E; Blake, T D; Ledauphin, V; Ogonowski, G; Coninck, J De; Fornasiero, D; Ralston, J
2007-03-27
Large-scale molecular dynamics simulations are used to model the dewetting of solid surfaces by partially wetting thin liquid films. Two levels of solid-liquid interaction are considered that give rise to large equilibrium contact angles. The initial length and thickness of the films are varied over a wide range at the nanoscale. Spontaneous dewetting is initiated by removing a band of molecules either from each end of the film or from its center. As observed experimentally and in previous simulations, the films recede at an initially constant speed, creating a growing rim of liquid with a constant receding dynamic contact angle. Consistent with the current understanding of wetting dynamics, film recession is faster on the more poorly wetted surface to an extent that cannot be explained solely by the increase in the surface tension driving force. In addition, the rates of recession of the thinnest films are found to increase with decreasing film thickness. These new results imply not only that the mobility of the liquid molecules adjacent to the solid increases with decreasing solid-liquid interactions, but also that the mobility adjacent to the free surface of the film is higher than in the bulk, so that the effective viscosity of the film decreases with thickness. PMID:17328565
International Nuclear Information System (INIS)
In this paper, we define and experimentally verify thermodynamic characteristics of the liquid-glass transition, taking into account a kinetic origin of the process. Using the density scaling law and the four-point measure of the dynamic heterogeneity of molecular dynamics of glass forming liquids, we investigate contributions of enthalpy, temperature, and density fluctuations to spatially heterogeneous molecular dynamics at the liquid-glass transition, finding an equation for the pressure coefficient of the glass transition temperature, dTg/dp. This equation combined with our previous formula for dTg/dp, derived solely from the density scaling criterion, implies a relationship among thermodynamic coefficients at Tg. Since this relationship and both the equations for dTg/dp are very well validated using experimental data at Tg, they are promising alternatives to the classical Prigogine-Defay ratio and both the Ehrenfest equations in case of the liquid-glass transition
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.
Statistical mechanics and dynamics of molecular fragmentation
Energy Technology Data Exchange (ETDEWEB)
Quack, M. (Goettingen Univ. (Germany, F.R.). Inst. fuer Physikalische Chemie)
1981-05-11
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored.
Statistical mechanics and dynamics of molecular fragmentation
International Nuclear Information System (INIS)
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored. (author)
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)
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
Molecular dynamics simulations of shock compressed graphite
International Nuclear Information System (INIS)
We present molecular dynamic simulations of the shock compression of graphite with the LCBOPII potential. The range of shock intensities covers the full range of available experimental data, including near-tera-pascal pressures. The results are in excellent agreement with the available DFT data and point to a graphite-diamond transition for shock pressures above 65 GPa, a value larger than the experimental data (20 to 50 GPa). The transition mechanism leads preferentially to hexagonal diamond through a diffusion-less process but is submitted to irreversible re-graphitization upon release: this result is in good agreement with the lack of highly ordered diamond observed in post-mortem experimental samples. Melting is found for shock pressures ranging from 200 to 300 GPa, close to the approximate LCBOPII diamond melting line. A good overall agreement is found between the calculated and experimental Hugoniot data up to 46% compression rate. (authors)
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...
Iterative quantum-classical path integral with dynamically consistent state hopping.
Walters, Peter L; Makri, Nancy
2016-01-28
We investigate the convergence of iterative quantum-classical path integral calculations in sluggish environments strongly coupled to a quantum system. The number of classical trajectories, thus the computational cost, grows rapidly (exponentially, unless filtering techniques are employed) with the memory length included in the calculation. We argue that the choice of the (single) trajectory branch during the time preceding the memory interval can significantly affect the memory length required for convergence. At short times, the trajectory branch associated with the reactant state improves convergence by eliminating spurious memory. We also introduce an instantaneous population-based probabilistic scheme which introduces state-to-state hops in the retained pre-memory trajectory branch, and which is designed to choose primarily the trajectory branch associated with the reactant at early times, but to favor the product state more as the reaction progresses to completion. Test calculations show that the dynamically consistent state hopping scheme leads to accelerated convergence and a dramatic reduction of computational effort. PMID:26827203
Iterative quantum-classical path integral with dynamically consistent state hopping
Energy Technology Data Exchange (ETDEWEB)
Walters, Peter L.; Makri, Nancy [Department of Chemistry, University of Illinois, Urbana, Illinois 61801 (United States)
2016-01-28
We investigate the convergence of iterative quantum-classical path integral calculations in sluggish environments strongly coupled to a quantum system. The number of classical trajectories, thus the computational cost, grows rapidly (exponentially, unless filtering techniques are employed) with the memory length included in the calculation. We argue that the choice of the (single) trajectory branch during the time preceding the memory interval can significantly affect the memory length required for convergence. At short times, the trajectory branch associated with the reactant state improves convergence by eliminating spurious memory. We also introduce an instantaneous population-based probabilistic scheme which introduces state-to-state hops in the retained pre-memory trajectory branch, and which is designed to choose primarily the trajectory branch associated with the reactant at early times, but to favor the product state more as the reaction progresses to completion. Test calculations show that the dynamically consistent state hopping scheme leads to accelerated convergence and a dramatic reduction of computational effort.
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.
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.)
Interplay of classical and quantum dynamics in a thermal ensemble of atoms
Warsi Laskar, Arif; Singh, Niharika; Mukherjee, Arunabh; Ghosh, Saikat
2016-05-01
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, Λ-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. 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 pumping drives the atoms to a steady state in a significantly longer time-scale that sustains superposed dark states. Eventual control turn-off leads to a sudden fall in transmission with an ubiquitous signature for identifying closed and open systems. Numerical simulations and toy-model predictions confirm our claims. These studies reveal new insights into a rich and complex dynamics associated with atoms in thermal ensemble, which are otherwise absent in state-prepared, cold atomic ensembles.
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 ...
International Nuclear Information System (INIS)
Quasiclassical trajectory calculations are compared, with classical and Wigner sampling of transition state (TS) energy levels, for C2H5F≠→HF+C2H4 product energy partitioning and [Cl···CH3···Cl]- central barrier dynamics. The calculations with Wigner sampling are reported here for comparison with the previously reported calculations with classical sampling [Y. J. Cho et al., J. Chem. Phys. 96, 8275 (1992); L. Sun and W. L. Hase, J. Chem. Phys. 121, 8831 (2004)]. The C2H5F≠ calculations were performed with direct dynamics at the MP2/6-31G* level of theory. Classical and Wigner sampling give post-transition state dynamics, for these two chemical systems, which are the same within statistical uncertainties. This is a result of important equivalences in these two sampling methods for selecting initial conditions at a TS. In contrast, classical and Wigner sampling often give different photodissociation dynamics [R. Schinke, J. Phys. Chem. 92, 3195 (1988)]. Here the sampling is performed for a vibrational state of the ground electronic state potential energy surface (PES), which is then projected onto the excited electronic state's PES. Differences between the ground and the excited PESs may give rise to substantially different excitations of the vibrational and dissociative coordinates on the excited state PES by classical and Wigner sampling, resulting in different photodissociation dynamics.
Classical dynamics of a charged particle in a laser field beyond the dipole approximation
Jameson, Paul
2008-01-01
The classical dynamics of a charged particle traveling in a laser field modeled by an elliptically polarized monochromatic electromagnetic plane wave is discussed within the time reparametrization invariant form of the non-relativistic Hamilton-Jacobi theory. The exact parametric representation for a particle's orbit in an arbitrary plane wave background beyond the dipole approximation and including effect of the magnetic field is derived. For an elliptically polarized monochromatic plane wave the particle's trajectory, as an explicit function of the laboratory frame's time, is given in terms of the Jacobian elliptic functions, whose modulus is proportional to the laser's intensity and depends on the polarization of radiation. It is shown that the system exposes the ``intensity duality'', correspondence between the motion in the backgrounds with various intensities. In virtue of the modular properties of the Jacobian functions, by starting with the representative ``fundamental solution'' and applying a certai...
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.
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.
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.
AMMARI, Zied; Falconi, Marco
2014-01-01
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-Schr\\"odinger equation. Also, we show that the ground state energy level of $N$ nucleons, when $N$ 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 elabor...
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.
Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules
International Nuclear Information System (INIS)
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wave packet calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics
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
2014-06-01
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. PMID:24908021
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
International Nuclear Information System (INIS)
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom
DEFF Research Database (Denmark)
Kaszuba, K.; Postila, P. A.; Cramariuc, O.;
2013-01-01
studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter...
Kreula, J. M.; Clark, S. R.; Jaksch, D.
2016-09-01
We propose a non-linear, hybrid quantum-classical scheme for simulating non-equilibrium dynamics of strongly correlated fermions described by the Hubbard model in a Bethe lattice in the thermodynamic limit. Our scheme implements non-equilibrium dynamical mean field theory (DMFT) and uses a digital quantum simulator to solve a quantum impurity problem whose parameters are iterated to self-consistency via a classically computed feedback loop where quantum gate errors can be partly accounted for. We analyse the performance of the scheme in an example case.
Dou, Wenjie; Subotnik, Joseph E
2016-01-14
A broadened classical master equation (BCME) is proposed for modeling nonadiabatic dynamics for molecules near metal surfaces over a wide range of parameter values and with arbitrary initial conditions. Compared with a standard classical master equation-which is valid in the limit of weak molecule-metal couplings-this BCME should be valid for both weak and strong molecule-metal couplings. (The BCME can be mapped to a Fokker-Planck equation that captures level broadening correctly.) Finally, our BCME can be solved with a simple surface hopping algorithm; numerical tests of equilibrium and dynamical observables look very promising. PMID:26772563
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.
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 of Gases H2, D2 and T2
Institute of Scientific and Technical Information of China (English)
YANG Chuan-Lu; ZHAO Yong-Kuan; ZHU Zheng-He; WANG Rong; ZHANG Zhi-Hong; REN Ting-Qi; WANG Ming-Da; ZHANG Yong-Ming; TANG Yong-Jian; ZHENG Zhi-Jian
2002-01-01
The classical molecular dynamics simulation has been used to study the equation of state of gas H2, D2and T2. It has also been investigated that the isotope mass affects on the accuracy of equation of state. Our calculatedresults show that the classical effect is principal and the isotope mass effects on the equation of state are obvious for themuch light gases. At the same time, some useful theoretical data of equation of state for these gases have been provided.It is found that the classical simulation is still effective to the quantum gas. However, the quantum mechanics simulationand the improvement of intermolecular interaction potential are necessary if more accurate computational results areexpected.
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.
Directory of Open Access Journals (Sweden)
Tang Bo
2011-05-01
Full Text Available Abstract Background Classical swine fever (CSF, caused by the Classical swine fever virus (CSFV, is an Office International des Epizooties (OIE notifiable disease. However, we are far from fully understand the distribution, tissue tropism, pathogenesis, replication and excretion of CSFV in pigs. In this report, we investigated the dynamic distribution and tissue tropism of the virus in internal organs of the experimentally infected pigs using real-time RT-PCR and immunohistochemistry (IHC. Results A relative quantification real-time PCR was established and used to detect the virus load in internal organs of the experimentally infected pigs. The study revealed that the virus was detected in all 21 of the internal organs and blood collected from pigs at day 1 to day 8 post infections, and had an increasing virus load from day 1 to day 8 post infections. However, there was irregular distribution virus load in most internal organs over the first 2 days post infection. Blood, lymphoid tissue, pancreas and ileum usually contain the highest viral loads, while heart, duodenum and brain show relatively low viral loads. Conclusions All the data suggest that CSFV had an increasing virus load from day 1 to day 8 post infections in experimentally infected pigs detected by real-time RT-PCR, which was in consistent with the result of the IHC staining. The data also show that CSFV was likely to reproduce in blood, lymphoid tissue, pancreas and the ileum, while unlikely to replicate in the heart, duodenum and brain. The results provide a foundation for further clarification of the pathogenic mechanism of CSFV in internal organs, and indicate that blood, lymphoid tissue, pancreas and ileum may be preferred sites of acute infection.
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.
Imaging the Breakdown of Molecular Frame Dynamics through Rotational Uncoupling
Zipp, Lucas J; Bucksbaum, Philip H
2016-01-01
We have observed directly in the time domain the uncoupling of electron motion from the molecular frame due to rotational-electronic coupling in a molecular Rydberg system. In contrast to Born- Oppenheimer dynamics, in which the electron is firmly fixed to the molecular frame, there exists a regime of molecular dynamics known as $l$-uncoupling where the motion of a non-penetrating Rydberg electron decouples from the instantaneous alignment of the molecular frame. We have imaged this unusual regime in time-dependent photoelectron angular distributions of a coherently prepared electron wave packet in the 4$f$ manifold of $N_2$.
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.
Fracture simulations via massively parallel molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Holian, B.L. [Los Alamos National Lab., NM (United States); Abraham, F.F. [IBM Research Div., San Jose, CA (United States). Almaden Research Center; Ravelo, R. [Texas Univ., El Paso, TX (United States)
1993-09-01
Fracture simulations at the atomistic level have heretofore been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 {mu}m on a side. We report on recent MD simulations of mode I crack extension under tensile loading at high strain rates. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. We found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly in this paper will be especially important to carrying out feasible massively parallel 3D simulations via MD.
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 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.
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.
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.
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.
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.
CLASSICAL AND MOLECULAR CYTOGENETIC STUDIES FOR BREEDING AND SELECTION OF TULIPS
Aurel Popescu; Anca Nicoleta Sutan
2012-01-01
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 ...
Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications.
Kolesov, Grigory; Grånäs, Oscar; Hoyt, Robert; Vinichenko, Dmitry; Kaxiras, Efthimios
2016-02-01
We present a method for real-time propagation of electronic wave functions, within time-dependent density functional theory (RT-TDDFT), coupled to ionic motion through mean-field classical dynamics. The goal of our method is to treat large systems and complex processes, in particular photocatalytic reactions and electron transfer events on surfaces and thin films. Due to the complexity of these processes, computational approaches are needed to provide insight into the underlying physical mechanisms and are therefore crucial for the rational design of new materials. Because of the short time step required for electron propagation (of order ∼10 attoseconds), these simulations are computationally very demanding. Our methodology is based on numerical atomic-orbital-basis sets for computational efficiency. In the computational package, to which we refer as TDAP-2.0 (Time-evolving Deterministic Atom Propagator), we have implemented a number of important features and analysis tools for more accurate and efficient treatment of large, complex systems and time scales that reach into a fraction of a picosecond. We showcase the capabilities of our method using four different examples: (i) photodissociation into radicals of opposite spin, (ii) hydrogen adsorption on aluminum surfaces, (iii) optical absorption of spin-polarized organic molecule containing a metal ion, and (iv) electron transfer in a prototypical dye-sensitized solar cell. PMID:26680129
Classical dynamics of a charged particle in a laser field beyond the dipole approximation
Jameson, Paul; Khvedelidze, Arsen
2008-05-01
The classical dynamics of a charged particle traveling in a laser field modeled by an elliptically polarized monochromatic electromagnetic plane wave is discussed within the time reparametrization invariant form of the nonrelativistic Hamilton-Jacobi theory. The exact parametric representation for a particle’s orbit in an arbitrary plane wave background beyond the dipole approximation and including effect of the magnetic field is derived. For an elliptically polarized monochromatic plane wave the particle’s trajectory, as an explicit function of the laboratory frame’s time, is given in terms of the Jacobian elliptic functions, whose modulus is proportional to the laser’s intensity and depends on the polarization of radiation. It is shown that the system exposes the intensity duality, correspondence between the motion in the backgrounds with various intensities. In virtue of the modular properties of the Jacobian functions, by starting with the representative “fundamental solution” and applying a certain modular transformation one can obtain the particle’s orbit in the monochromatic plane wave background with arbitrarily prescribed characteristics.
Dynamics of an electron spin in strong classical and quantized electromagnetic fields
Energy Technology Data Exchange (ETDEWEB)
Skoromnik, Oleg
2014-07-09
The electron motion in the presence of a strong classical and quantized pulse of an electromagnetic field is studied with a special emphasis on the spin degree of freedom. It is shown that the Hamiltonian of this system can be separated into two parts with the help of canonical transformations of the field variables, namely the interaction between an electron and a single collective mode of the field and fluctuations relatively to this collective mode. The application of perturbation theory to the fluctuations allows the conditions of applicability of the single-mode approximation for the quantized external field to be formulated. Furthermore, within this approximation the electron spin evolution is investigated. In addition to fast spin oscillations at the laser frequency, a second time scale is identified due to the intensity-dependent emissions and absorptions of field quanta, that is collapse and revival dynamics. The effect is observable at the experimentally feasible intensity of 10{sup 18} Wcm{sup 2}. After this, we switch to the regime of higher intensities, when the fluctuations of the external field can be neglected. We investigate the asymmetries in the electron scattering arising due to the electron polarization and pulse duration, and constrain the optimal conditions for the asymmetry observation.
Accretion dynamics in the classical T Tauri star V2129 Oph
Alencar, S H P; Walter, F M; Dougados, C; Donati, J -F; Kurosawa, R; Romanova, M; Bonfils, X; Lima, G H R A; Massaro, S; Ibrahimov, M; Poretti, E
2012-01-01
We analyze the photometric and spectroscopic variability of the classical T Tauri star V2129 Oph over several rotational cycles to test the dynamical predictions of magnetospheric accretion models. The photometric variability and the radial velocity variations in the photospheric lines can be explained by rotational modulation due to cold spots, while the radial velocity variations of the He I (5876 \\AA) line and the veiling variability are due to hot spot rotational modulation. The hot and cold spots are located at high latitudes and about the same phase, but the hot spot is expected to sit at the chromospheric level, while the cold spot is at the photospheric level. Using the dipole+octupole magnetic-field configuration previously proposed in the literature for the system, we compute 3D MHD magnetospheric simulations of the star-disk system. We use the simulation's density, velocity and scaled temperature structures as input to a radiative transfer code, from which we calculate theoretical line profiles at ...
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
Rosini, Massimiliano Daniele
2013-01-01
This monograph presents a systematic treatment of the theory for hyperbolic conservation laws and their applications to vehicular traffics and crowd dynamics. In the first part of the book, the author presents very basic considerations and gradually introduces the mathematical tools necessary to describe and understand the mathematical models developed in the following parts focusing on vehicular and pedestrian traffic. The book is a self-contained valuable resource for advanced courses in mathematical modeling, physics and civil engineering. A number of examples and figures facilitate a better understanding of the underlying concepts and motivations for the students. Important new techniques are presented, in particular the wave front tracking algorithm, the operator splitting approach, the non-classical theory of conservation laws and the constrained problems. This book is the first to present a comprehensive account of these fundamental new mathematical advances.
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)
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.
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
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...
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to
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.
Linear Scaling First-Principles Molecular Dynamics with Controlled Accuracy
Energy Technology Data Exchange (ETDEWEB)
Gygi, F; Fattebert, J
2004-03-10
In our quest for accurate linear scaling first-principles molecular dynamics methods for pseudopotential DFT calculations, we investigate the accuracy of real-space grid approaches, with finite differences and spherical localization regions. We examine how the positions of the localization centers affect the accuracy and the convergence rate of the optimization process. In particular we investigate the accuracy of the atomic forces computation compared to the standard O(N{sup 3}) approach. We show the exponential decay of the error on the energy and forces with the size of the localization regions for a variety of realistic physical systems. We propose a new algorithm to automatically adapt the localization centers during the ground state computation which allows for molecular dynamics simulations with diffusion processes. The combination of algorithms proposed lead to a genuine linear scaling First-Principles Molecular Dynamics method with controlled accuracy. We illustrate our approach with examples of microcanonical molecular dynamics with localized orbitals.
Stanyon, Roscoe; Wienberg, Johannes; Romagno, D; F. Bigoni; 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.
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding
Yaman Arkun; Mert Gur
2012-01-01
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding Yaman Arkun1*, Mert Gur2¤ 1 Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey, 2 Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey Abstract A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamic...
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.
Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G
2016-04-12
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features. PMID:26949976
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
Non-MarkovianDynamics of Quantum and Classical Correlations in the Presence of System-Bath Coherence
Institute of Scientific and Technical Information of China (English)
李传锋; 汪浩田; 袁弘渊; 葛荣春; 郭光灿
2011-01-01
We present a detailed study on the dynamics of two-qubit correlations in non-Markovian environments, applying the hierarchy equations approach. This treatment is free from the limitation of perturbative, Markovian or rotating wave approximations. It is shown that crossovers and sudden changes in the classical and quantum correlations can appear when the strength of the interaction between qubits is gradually reduced. For some special initial states, there are even sudden transitions between the classical and quantum correlations.%We present a detailed study on the dynamics of two-qubit correlations in non-Markovian environments,applying the hierarchy equations approach.This treatment is free from the limitation of perturbative,Markovian or rotating wave approximations.It is shown that crossovers and sudden changes in the classical and quantum correlations can appear when the strength of the interaction between qubits is gradually reduced.For some special initial states,there are even sudden transitions between the classical and quantum correlations.
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.
An ab initio molecular dynamics study of the roaming mechanism of the H{sub 2}+HOC{sup +} reaction
Energy Technology Data Exchange (ETDEWEB)
Yu Huagen, E-mail: hgy@bnl.gov [Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973 (United States)
2011-08-01
We report here a direct ab initio molecular dynamics study of the p-/o-H{sub 2}+HOC{sup +} reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H{sub 2}+HOC{sup +} reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.
International Nuclear Information System (INIS)
The solvated electron production by reaction between the H atom and the hydroxide anion was studied using Density Functional Theory based first-principles molecular dynamics. The simulation reveals a complex mechanism, controlled by proton transfers in the coordination sphere of the hydroxide and by the diffusion of the H atom in its solvent cavity. We formulate the hypothesis, based on a coupling between classical and first-principles molecular dynamics, that these two processes give rise to a lag time for the reaction that would explain the H atom extremely small reactivity compared to other radical species. Furthermore, the reaction observed gives an original insight in excess electron solvation. (authors)
Energy Technology Data Exchange (ETDEWEB)
Munoz, A.; Lopez-Pineiro, A.; Ramirez, M.
2009-07-01
Soil microbe ecology has lately become increasingly important in the study of soil microbe populations. direct extraction of soil bacteria DNA allows PCR and DGGE analyses for the microorganism identification of these complex samples, avoiding the need for time-consuming culture-dependent techniques. The aim of the present study was to compare the two techniques (culture-dependent and molecular culture-independent) in four different plots of maize (Zea mays L.) crop under irrigation in south-western Spain. (Author)
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.
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.
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.
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.
Classical, non-linear, internal dynamics of large, isolated, vibrationally excited molecules
Papoular, R J
2002-01-01
This work reports numerical experiments intended to clarify the internal equilibration process in large molecules, following vibrational excitation. A model of amorphous and oxygenated hydrocarbon macromolecule (about 500 atoms)--simulating interstellar dust-- is built up by means of a chemical simulation code. Its structure is optimized, and its normal modes determined. About 4.5 eV of potential energy is then deposited locally by perturbing one of the C-H peripheral bonds, thus simulating the capture of a free H atom by a dangling C bond. The ensuing relaxation of the system is followed for up to 300 ps, using a molecular mechanics code. When steady state is reached, spectra and time correlation functions of kinetic energy and bond length fluctuations indicate that most normal modes have been activated, but the motion remains quasi-periodic or regular. By contrast, when the molecule is violently excited or embedded in a thermal bath (modelled by Langevin dynamics), the same markers clearly depict chaotic mo...
Bhaskar, Nimisha; Ravishankar, Chintu; Rajasekhar, R; Sumod, K; Sumithra, T G; John, Koshy; Mini, M; Ravindran, Reghu; Shaji, Shiju; Aishwarya, J
2015-12-01
Classical swine fever (CSF) is an economically important disease of pigs caused by CSF virus (CSFV) belonging to the genus Pestivirus within the family Flaviviridae. The disease is endemic in many countries including India. A comprehensive study was carried out to assess the type of CSFV circulating in the South Indian state of Kerala. During the period 2013-2014, clinical samples were collected from 19 suspected CSF outbreaks of domestic pigs in different districts of Kerala. The samples were tested using nested reverse transcription PCR (RT-PCR) targeting the E2 gene and RT-PCR for 5'UTR of the virus. Partial 5' UTR and E2 gene regions of six CSFV isolates were sequenced. Phylogenetic analysis revealed that all the CSFV isolates belonged to subgroup 2.2. The isolates showed close resemblance to the other CSFV isolates circulating in India. It was also observed that the CSFV viruses from Kannur district were distinct from those circulating in the other districts as evidenced by their divergence from other Kerala isolates in the phylogenetic tree. Close relationship was seen to the CSFV isolates from South East Asian countries. PMID:26645036
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...
Molecular simulations of Taxawallin I inside classical taxol binding site of β-tubulin.
Khan, Inamullah; Nisar, Muhammad; Ahmad, Manzoor; Shah, Hamidullah; Iqbal, Zafar; Saeed, Muhammad; Halimi, Syed Muhammad Ashhad; Kaleem, Waqar Ahmad; Qayum, Mughal; Aman, Akhter; Abdullah, Syed Muhammad
2011-03-01
A new taxoid Taxawallin I (1) along with two known taxoids (2-3) were isolated from methanolic bark extract of Taxus wallichiana Zucc. Structural characterization was confirmed by mass and NMR spectral techniques. Taxawallin I exhibited significant in-vitro anticancer activity against HepG2, A498, NCI-H226 and MDR 2780AD cancer lines. Tubulin binding assay was performed to assess its tubulin binding activity. Molecular docking analysis was performed to study the potential binding mode inside the taxol binding site of β-tubulin. PMID:20969934
Molecular Dynamics Simulation of Amyloid Beta Dimer Formation
Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V
2004-01-01
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...
Interfacial Molecular Searching Using Forager Dynamics
Monserud, Jon H.; Schwartz, Daniel K.
2016-03-01
Many biological and technological systems employ efficient non-Brownian intermittent search strategies where localized searches alternate with long flights. Coincidentally, molecular species exhibit intermittent behavior at the solid-liquid interface, where periods of slow motion are punctuated by fast flights through the liquid phase. Single-molecule tracking was used here to observe the interfacial search process of DNA for complementary DNA. Measured search times were qualitatively consistent with an intermittent-flight model, and ˜10 times faster than equivalent Brownian searches, suggesting that molecular searches for reactive sites benefit from similar efficiencies as biological organisms.
International Nuclear Information System (INIS)
Concentrated binary aqueous solutions of lanthanide (Nd3+ and Dy3+) salts (ClO4-, Cl-, and NO3-) have been studied by means of classical molecular dynamics (MD) simulations with explicit polarization and UV-visible spectroscopy. Pair interaction potentials, used for the MD simulations, have been developed in order to reproduce experimental hydration properties. Nd3+ and Dy3+ have been chosen because of their position in the lanthanide series: Nd3+ being a light lanthanide and Dy3+ a heavy one. They are respectively coordinated to nine and eight water molecules, in pure water, involving changes in their salt hydration structures. Both MD simulations and UV-visible experiments highlight the stronger affinity of nitrate anions toward Ln3+ compared to perchlorates and chlorides. Dissociation/association processes of Nd3+-Cl- and Nd3+-NO3- ion pairs in aqueous solution have been analyzed using potential of mean force profile calculations. Furthermore, from MD simulations, it appears that the affinity of anions (perchlorate, chloride, and nitrate. ) is stronger for Nd3+ than Dy3+. (authors)
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
Rotational dynamics of a diatomic molecular ion in a Paul trap.
Hashemloo, A; Dion, C M
2015-11-28
We present models for a heteronuclear diatomic molecular ion in a linear Paul trap in a rigid-rotor approximation, one purely classical and the other where the center-of-mass motion is treated classically, while rotational motion is quantized. We study the rotational dynamics and their influence on the motion of the center-of-mass, in the presence of the coupling between the permanent dipole moment of the ion and the trapping electric field. We show that the presence of the permanent dipole moment affects the trajectory of the ion and that it departs from the Mathieu equation solution found for atomic ions. For the case of quantum rotations, we also evidence the effect of the above-mentioned coupling on the rotational states of the ion. PMID:26627960
Rotational dynamics of a diatomic molecular ion in a Paul trap
Hashemloo, A
2015-01-01
We present models for a heteronuclear diatomic molecular ion in a linear Paul trap in a rigid-rotor approximation, one purely classical, the other where the center-of-mass motion is treated classically while rotational motion is quantized. We study the rotational dynamics and their influence on the motion of the center-of-mass, in the presence of the coupling between the permanent dipole moment of the ion and the trapping electric field. We show that the presence of the permanent dipole moment affects the trajectory of the ion, and that it departs from the Mathieu equation solution found for atomic ions. For the case of quantum rotations, we also evidence the effect of the above-mentioned coupling on the rotational states of the ion.
Rotational dynamics of a diatomic molecular ion in a Paul trap
Energy Technology Data Exchange (ETDEWEB)
Hashemloo, A.; Dion, C. M., E-mail: claude.dion@umu.se [Department of Physics, Umeå University, SE-901 87 Umeå (Sweden)
2015-11-28
We present models for a heteronuclear diatomic molecular ion in a linear Paul trap in a rigid-rotor approximation, one purely classical and the other where the center-of-mass motion is treated classically, while rotational motion is quantized. We study the rotational dynamics and their influence on the motion of the center-of-mass, in the presence of the coupling between the permanent dipole moment of the ion and the trapping electric field. We show that the presence of the permanent dipole moment affects the trajectory of the ion and that it departs from the Mathieu equation solution found for atomic ions. For the case of quantum rotations, we also evidence the effect of the above-mentioned coupling on the rotational states of the ion.
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.
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.
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.
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.
Goller, Katja V; Gabriel, Claudia; Dimna, Mireille Le; Le Potier, Marie-Frédérique; Rossi, Sophie; Staubach, Christoph; Merboth, Matthias; Beer, Martin; Blome, Sandra
2016-03-01
Classical swine fever is a viral disease of pigs that carries tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high-resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of classical swine fever virus strains over the years and no impact of vaccination on mutation rates. However, substitution rates varied amongst protein genes; furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers. PMID:26684209
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.
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.
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.
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.
International Nuclear Information System (INIS)
Charge and excitonic-energy transfer phenomena are fundamental for energy conversion in solar cells as well as artificial photosynthesis. Currently, much interest is being paid to light-harvesting and energy transduction processes in supramolecular structures, where nuclear dynamics has a major influence on electronic quantum dynamics. For this reason, the simulation of long range electron transfer in supramolecular structures, under environmental conditions described within an atomistic framework, has been a difficult problem to study. This work describes a coupled quantum mechanics/molecular mechanics method that aims at describing long range charge transfer processes in supramolecular systems, taking into account the atomistic details of large molecular structures, the underlying nuclear motion, and environmental effects. The method is applied to investigate the relevance of electron–nuclei interaction on the mechanisms for photo-induced electron–hole pair separation in dye-sensitized interfaces as well as electronic dynamics in molecular structures. (paper)
da Silva, Robson; Hoff, Diego A; Rego, Luis G C
2015-04-10
Charge and excitonic-energy transfer phenomena are fundamental for energy conversion in solar cells as well as artificial photosynthesis. Currently, much interest is being paid to light-harvesting and energy transduction processes in supramolecular structures, where nuclear dynamics has a major influence on electronic quantum dynamics. For this reason, the simulation of long range electron transfer in supramolecular structures, under environmental conditions described within an atomistic framework, has been a difficult problem to study. This work describes a coupled quantum mechanics/molecular mechanics method that aims at describing long range charge transfer processes in supramolecular systems, taking into account the atomistic details of large molecular structures, the underlying nuclear motion, and environmental effects. The method is applied to investigate the relevance of electron-nuclei interaction on the mechanisms for photo-induced electron-hole pair separation in dye-sensitized interfaces as well as electronic dynamics in molecular structures. PMID:25767107
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.
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 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 Mechanotransduction: how forces trigger cytoskeletal dynamics
Ehrlicher, Allen
2012-02-01
Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.
Diagnosis and molecular characterization of non-classic forms of Tay-Sachs disease in Brazil.
Rozenberg, R; Kok, F; Burin, M G; Sá Miranda, M C; Vasques, C; Henriques-Souza, A M M; Giugliani, R; Vainzof, Mariz; Pereira, L V
2006-06-01
Molecular analysis of five Brazilian families, including eight patients presenting with nonclassic Tay-Sachs disease, was performed to identify frequent causative mutations and their correlation with clinical course. Three patients were affected by the B1 subacute variant and were shown to carry the R178H mutation (the DN allele), which is also common among Portuguese patients. Two of them were compound heterozygotes, whereas the third presented with the mutation in both alleles. Since Brazil was a Portuguese colony for over two centuries, common ancestry might be the probable explanation. The fourth patient presented with a juvenile phenotype and carries the R499H mutation, which has been reported only once worldwide and is associated with residual enzyme activity, responsible for a slower clinical course. The fifth family, of an Ashkenazi Jewish background, showed an extensive intrafamilial clinical variability among three affected sibs presenting with muscle atrophy, ataxia, and psychiatric symptoms. They were first diagnosed as having atypical spinal muscular atrophy and, subsequently, spinocerebellar ataxia, but, recently, the diagnosis of late-onset Tay-Sachs disease was confirmed based on reduced plasma hexosaminidase A activity and the G269S/InsTATC1278 genotype. It is therefore highly recommended to test patients with a similar clinical history for Tay-Sachs disease. In the same family, one first cousin committed suicide at the age of 24 years, presenting with a clinical phenotype that suggested an undiagnosed case and highlighting the effect of the intrafamilial clinical variability in delaying a prompt diagnosis. It is now recognized that his parents are, in fact, a carrier couple. Additionally, another relative had been previously identified as a heterozygote in a Tay-Sachs disease screening program, but the information was not shared among the family. Since this information might anticipate diagnosis and genetic counseling, it is advisable that
Wolthers, M.; Di Tommaso, D.; Du, Z; de Leeuw, N. H.
2012-01-01
Calcite–water interactions are important not only in carbon sequestration and the global carbon cycle, but also in contaminant behaviour in calcite-bearing host rock and in many industrial applications. Here we quantify the effect of variations in surface structure on calcite surface reactivity. Firstly, we employ classical Molecular Dynamics simulations of calcite surfaces containing an etch pit and a growth terrace, to show that the local environment in water around structurally different s...
Molecular dynamics insights into human aquaporin 2 water channel.
Binesh, A R; Kamali, R
2015-12-01
In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney. PMID:26489820
Theoretical analysis of dynamic processes for interacting molecular motors
International Nuclear Information System (INIS)
Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. (paper)
Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos
2016-06-22
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560
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
Quantum molecular dynamics of methyl rotors in peptide links
International Nuclear Information System (INIS)
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 Ch3 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 many biological processes and structures is the peptide unit, -CONH-. Of particular significance are the intermolecular networks that are often formed by the NHO hydrogen bonds, the peptide links. The molecules were chosen for the research in this thesis to form a tractable model for polypeptides and alpha-helix proteins. Methyl rotor tunnelling frequencies have been used, which are very sensitive to the potential energy surface, as a probe of the electronic and molecular structure associated with the peptide links. Quantum chemistry calculations were then utilized to connect experiments to theory to learn about the hydrogen bond. (author)
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp
2012-06-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.
Deposition of Small Clusters on Surface: a Molecular Dynamics Simulation
Institute of Scientific and Technical Information of China (English)
DUAN Xiang-Mei; GONG Xin-Gao
2000-01-01
By using the molecular dynamics simulation, we have studied the dynamic behaviors of small energetic clusters deposited on the surface. We find that, at incident energy as low as 1.0eV/atom, the structure of the cluster is destroyed and cluster atoms form an epitaxial layer above the surface. At high energy incidence, the site exchange between cluster atom and surface atom is observed. The effects of the cluster size and orientation are discussed.
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation
International Nuclear Information System (INIS)
We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
Pabis, Anna; Geronimo, Inacrist; York, Darrin M.; Paneth, Piotr
2014-01-01
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specif...
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
Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers
Directory of Open Access Journals (Sweden)
Monisha Rastogi
2015-05-01
Full Text Available The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generated and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.
Visualizing protein interactions and dynamics: evolving a visual language for molecular animation.
Jenkinson, Jodie; McGill, Gaël
2012-01-01
Undergraduate biology education provides students with a number of learning challenges. Subject areas that are particularly difficult to understand include protein conformational change and stability, diffusion and random molecular motion, and molecular crowding. In this study, we examined the relative effectiveness of three-dimensional visualization techniques for learning about protein conformation and molecular motion in association with a ligand-receptor binding event. Increasingly complex versions of the same binding event were depicted in each of four animated treatments. Students (n = 131) were recruited from the undergraduate biology program at University of Toronto, Mississauga. Visualization media were developed in the Center for Molecular and Cellular Dynamics at Harvard Medical School. Stem cell factor ligand and cKit receptor tyrosine kinase were used as a classical example of a ligand-induced receptor dimerization and activation event. Each group completed a pretest, viewed one of four variants of the animation, and completed a posttest and, at 2 wk following the assessment, a delayed posttest. Overall, the most complex animation was the most effective at fostering students' understanding of the events depicted. These results suggest that, in select learning contexts, increasingly complex representations may be more desirable for conveying the dynamic nature of cell binding events.
Simplistic Coulomb Forces in Molecular Dynamics
DEFF Research Database (Denmark)
Hansen, Jesper Schmidt; Schrøder, Thomas; Dyre, J. C.
2012-01-01
In this paper we compare the Wolf method to the shifted forces (SF) method for efficient computer simulation of bulk systems with Coulomb forces, taking results from the Ewald summation and particle mesh Ewald methods as representing the true behavior. We find that for the Hansen–McDonald molten...... salt model the SF approximation overall reproduces the structural and dynamical properties as accurately as does the Wolf method. It is shown that the optimal Wolf damping parameter depends on the property in focus and that neither the potential energy nor the radial distribution function are useful...... measures for the convergence of the Wolf method to the Ewald summation method. The SF approximation is also tested for the SPC/Fw model of liquid water at room temperature, showing good agreement with both the Wolf and the particle mesh Ewald methods; this confirms previous findings [Fennell, C. J...
Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics
International Nuclear Information System (INIS)
The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ''demon,'' which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations
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.
Superspreading: molecular dynamics simulations and experimental results
Theodorakis, Panagiotis; Kovalchuk, Nina; Starov, Victor; Muller, Erich; Craster, Richard; Matar, Omar
2015-11-01
The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Recently, we have observed that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. Here, we present the structural characteristics and kinetics of the droplet spreading during the different stages of this process, and we compare our results with experimental data for trisiloxane and poly oxy ethylene surfactants. In this way, we highlight and explore the differences between surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting. EPSRC Platform Grant MACIPh (EP/L020564/).
Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations.
Monti, Susanna; Carravetta, Vincenzo; Ågren, Hans
2016-07-14
The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system. The covalent attachments of the molecules to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be observed. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption. PMID:27305447
Systematic study of 16O-induced fusions with the improved quantum molecular dynamics model
Wang, Ning; Li, Zhuxia
2014-01-01
The heavy-ion fusion reactions with 16O bombarding on 62Ni, 65Cu, 74Ge, 148Nd, 180Hf, 186W, 208Pb, 238U are systematically investigated with the improved quantum molecular dynamics (ImQMD) model. The fusion cross sections at energies near and above the Coulomb barriers can be reasonably well reproduced by using this semi-classical microscopic transport model with the parameter sets SkP* and IQ3a. The dynamical nucleus-nucleus potentials and the influence of Fermi constraint on the fusion process are also studied simultaneously. In addition to the mean field, the Fermi constraint also plays a key role for the reliable description of fusion process and for improving the stability of fragments in heavy-ion collisions.
Sorella, Sandro
2016-01-01
We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix $S$. Here we apply this technique, within a Quantum Monte Carlo (QMC) based wavefuntion approach and within the Born-Oppheneimer approximation, for determining the phase diagram of high-pressure Hydrogen with simulations much longer than the autocorrelation time. With the proposed method, we are able to equilibrate in few hundreds steps even close to the liquid-liquid phase transition (LLT). Within our approach we find that the LLT transition is consistent with recent density functionals predicting a much larger transition pressures when the long range dispersive forces are taken into account.
Reddy, Sandeep K; Bajaj, Pushp; Pham, C Huy; Riera, Marc; Moberg, Daniel R; Morales, Miguel A; Knight, Chris; Gotz, Andreas W; Paesani, Francesco
2016-01-01
The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulations as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly inc...
From Classical to Quantum: New Canonical Tools for the Dynamics of Gravity
Höhn, P.A.
2012-01-01
In a gravitational context, canonical methods offer an intuitive picture of the dynamics and simplify an identification of the degrees of freedom. Nevertheless, extracting dynamical information from background independent approaches to quantum gravity is a highly non-trivial challenge. In this thesi
Semiquantum molecular dynamics simulation of liquid water by time-dependent Hartree approach.
Kim, Hyeon-Deuk; Ando, Koji
2009-08-14
Semiquantum liquid water molecular dynamics simulation was developed using the time-dependent Hartree approach. The classical intra- and intermolecular potential functions of water were extended to describe the wave packet (WP) hydrogen atoms. The equations of motion with an extended phase space including auxiliary coordinates and momenta representing the hydrogen WP widths were derived and solved. The molecular dynamics simulation of semiquantum water demonstrated that the semiquantum hydrogen atoms make the liquid water less structured and the hydrogen bonds weakened. The poor structurization in liquid water was inferred from the increased mobility of a water molecule and the redshift of OH stretching frequency. The zero-point energy introduced by the semiquantum hydrogens enhances the anharmonic potential effects and contributes to the redshifted OH stretching vibration. We found a significant peak around 4400 cm(-1) in the absorption spectrum resulting from the energy exchange between the WP width dynamics and the coupling of the OH stretching mode and the rotational motion of each water. We proposed that a liquid free energy landscape is smoothed due to semiquantum hydrogen atoms, and influences the liquid structure and dynamics. PMID:19691391
Neptune on tiptoes: dynamical histories that preserve the cold classical Kuiper belt
Wolff, Schuyler; Murray-Clay, Ruth A
2011-01-01
The current dynamical structure of the Kuiper belt was shaped by the orbital evolution of the giant planets, especially Neptune, during the era following planet formation, when the giant planets may have undergone planet-planet scattering and/or planetesimal-driven migration. Numerical simulations of this process, while reproducing many properties of the belt, fail to generate the high inclinations and eccentricities observed for some objects while maintaining the observed dynamically "cold" population. We present the first of a three-part parameter study of how different dynamical histories of Neptune sculpt the planetesimal disk. Here we identify which dynamical histories allow an in situ planetesimal disk to remain dynamically cold, becoming today's cold Kuiper belt population. We find that if Neptune undergoes a period of elevated eccentricity and/or inclination, it secularly excites the eccentricities and inclinations of the planetesimal disk. We demonstrate that there are several well-defined regimes fo...
Probing Molecular Dynamics by Laser-Induced Backscattering Holography
Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B.
2016-04-01
We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H2 and D2 molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H2 and D2 with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules.
THE REFINEMENT OF NMR STRUCTURES BY MOLECULAR-DYNAMICS SIMULATION
TORDA, AE; VANGUNSTEREN, WF
1991-01-01
We discuss the use of molecular dynamics simulations as a tool for the refinement of structures based on NMR data. The procedure always involves the construction of a pseudo-energy term to model the experimental data and we consider the various approaches to this problem. We detail recent work where
Thermodynamics of small clusters of atoms: A molecular dynamics simulation
DEFF Research Database (Denmark)
Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J
1974-01-01
The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...
C60 molecular dynamics studied by muon spin relaxation
International Nuclear Information System (INIS)
In muonium-substituted organic radicals, the muon spin can serve as a probe of molecular dynamics. The motional perturbation induces transitions between the coupled spin states of muon and unpaired electron. Studies of the resultant muon spin relaxation in C60Mu, the species formed by muon implantation in solid C60, yield the correlation time characteristic of the reorientational motion
Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting tr
Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations
Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.
2013-01-01
Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules.
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
Menon, Madhu
1998-01-01
In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.
Active site modeling in copper azurin molecular dynamics simulations
Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R
2004-01-01
Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po
MOLECULAR DYNAMICS SIMULATION OF STRUCTURE STABILITY OF SILVER NANOCLUSTERS
Institute of Scientific and Technical Information of China (English)
W.H. Qi
2006-01-01
The structures of Ag clusters with sizes n=13 to 1157 are studied by tight binding molecular dynamics simulation. It is found that the stable structures of Ag clusters follow the sequence amorphous-crystalline-amorphous-crystalline with the cluster size increasing from 13 to 1157.Furthermore, all the shells of Ag clusters are different from the structure of the corresponding bulk Ag.
Metal cluster fission: jellium model and Molecular dynamics simulations
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia;
2004-01-01
Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18^2+ ...
Open boundary molecular dynamics of sheared star-polymer melts.
Sablić, Jurij; Praprotnik, Matej; Delgado-Buscalioni, Rafael
2016-02-28
Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution. PMID:26820315
Molecular Dynamics ofa Coulomb System with Deformable Periodic Boundary Conditions
Totsuji, Hiroo; Shirokoshi, Hideki; Nara, Shigetoshi
1991-01-01
Variable shape molecular dynamics is formulated for the one-component plasma and the structural transition from the fcc lattice to the bcc lattice has been observed. It is emphasized that the condition of constant volume should be imposed when deformations of periodic boundary conditions are taken into account.
Simulations of boundary migration during recrystallization using molecular dynamics
DEFF Research Database (Denmark)
Godiksen, Rasmus Brauner; Trautt, Z.T.; Upmanyu, M.;
2007-01-01
We have applied an atomistic simulation methodology based on molecular dynamics to study grain boundary migration in crystalline materials, driven by the excess energy of dislocation arrangements. This method is used to simulate recrystallization in metals. The simulations reveal that the migrati...
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
Directory of Open Access Journals (Sweden)
Renata De Paris
2015-01-01
Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.
Molecular dynamics simulation of a charged biological membrane
López Cascales, J.J.; García de la Torre, J.; Marrink, S.J.; Berendsen, H.J.C.
1996-01-01
A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as counterions and water molecules. The behavior of this membrane differs from that was shown by other me
Molecular dynamics simulations on PGLa using NMR orientational constraints
Energy Technology Data Exchange (ETDEWEB)
Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)
2015-11-15
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics
Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de
1997-01-01
The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.
Molecular dynamics simulations on PGLa using NMR orientational constraints
International Nuclear Information System (INIS)
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide
Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations
Monti, Susanna; Carravetta, Vincenzo; Ågren, Hans
2016-06-01
The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system. The covalent attachments of the molecules to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be observed. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption.The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system. The covalent attachments of the molecules to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be observed. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption. Electronic supplementary information (ESI) available: Different views of the AuNP surface coverage. Distance map describing the position of each molecule in relation to the others on the AuNP (alpha carbon distances). See DOI: 10.1039/C
Sieffert, Nicolas; Wipff, Georges
2006-10-01
We report a molecular dynamics (MD) study of the interfacial behavior of key partners involved in the Cs(+) cation extraction by a calix[4]arene-crown-6 host (L), comparing an ionic liquid (IL) to a classical molecular solvent (chloroform) as receiving "oil" phase. The IL is composed of hydrophobic 1-butyl-3-methylimidazolium cations (BMI(+)) and bis(trifluoromethylsulfonyl)imide anions (Tf(2)N(-)) and forms a biphasic system with water. The simulations reveal similarities but also interesting differences between the two types of interfaces. Much longer times are needed to "equilibrate" IL systems, compared to classical liquid mixtures, and there is more intersolvent mixing with the IL than with chloroform, especially concerning the water-in-oil content. There is also some excess of the BMI(+) cations over the Tf(2)N(-) anions in the aqueous phase. Simulations on the Na(+)NO(3)(-) and Cs(+)NO(3)(-) ions show that they sometimes interact at the interface with the IL ions, forming hydrated intimate ion pairs, whereas they are "repelled" by the classical interface. The LCs(+) complex and L ligand also behave differently, depending on the "oil phase". They are better solvated by the IL than by chloroform and thus poorly attracted at the IL interface, whereas they adsorb at the chloroform interface, adopting well-defined amphiphilic orientations. The results are discussed in the context of assisted ion transfer and provide a number of arguments explaining the specificity and efficiency of IL based, compared to classical extraction systems.
Directory of Open Access Journals (Sweden)
Dimitrios Vlachakis
2013-06-01
Full Text Available The Classical Swine Fever virus (CSFV is a major pathogen of livestock and belongs to the flaviviridae viral family. Even though there aren’t any verified zoonosis cases yet, the outcomes of CSFV epidemics have been devastating to local communities. In an effort to shed light to the molecular mechanisms underlying the structural and drug design potential of the viral helicase, the three dimensional structure of CSFV helicase has been modeled using conventional homology modeling techniques and the crystal structure of the Hepatitis C virus (HCV as a template. The established structure of the CSFV helicase has been in silico evaluated for its viability using a repertoire of in silico tools. The ultimate goal of this study is to introduce the 3D conformation of the CSFV helicase as a reliable structure that may be used as the designing platform for de novo, structure-based drug design experiments. In this direction using the modeled structure of CSVF helicase, a 3D pharmacophore was designed. The pharmacophore comprises of a series of key characteristics that molecular inhibitors must satisfy in order to achieve maximum predicted affinity for the given enzyme. Overall, invaluable insights and conclusions are drawn from this structural study of the CSFV helicase, which may provide the scientific community with the founding plinth in the fight against CSFV infections through the perspective of the CSFV helicase as a potential pharmacological target. Notably, to date no antiviral agent is available against the CSFV nor is expected soon. Subsequently, there is urgent need for new modern and state-of-the-art antiviral strategies to be developed.
Ice Formation on Kaolinite: Insights from Molecular Dynamics Simulations
Sosso, Gabriele C; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos
2016-01-01
The formation of ice affects many aspects of our everyday life as well as technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even via state-of-the-art experimental techniques. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long timescales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaol...
Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description
Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco
2015-01-01
A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...
Intramolecular and nonlinear dynamics
Energy Technology Data Exchange (ETDEWEB)
Davis, M.J. [Argonne National Laboratory, IL (United States)
1993-12-01
Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.
Lachet, V; Teuler, J-M; Rousseau, B
2015-01-01
A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems.
Mixed convolved action for classical and fractional-derivative dissipative dynamical systems.
Dargush, G F
2012-12-01
The principle of mixed convolved action provides a new rigorous weak variational formalism for a broad range of initial value problems in mathematical physics and mechanics. Here, the focus is initially on classical single-degree-of-freedom oscillators incorporating either Kelvin-Voigt or Maxwell dissipative elements and then, subsequently, on systems that utilize fractional-derivative constitutive models. In each case, an appropriate mixed convolved action is formulated, and a corresponding weak form is discretized in time using temporal shape functions to produce an algorithm suitable for numerical solution. Several examples are considered to validate the mixed convolved action principles and to investigate the performance of the numerical algorithms. For undamped systems, the algorithm is found to be symplectic and unconditionally stable with respect to the time step. In the case of dissipative systems, the approach is shown to be robust and to be accurate with good convergence characteristics for both classical and fractional-derivative based models. As part of the derivations, some interesting results in the calculus of Caputo fractional derivatives also are presented.
Influence of conformational molecular dynamics on matter wave interferometry
Gring, Michael; Eibenberger, Sandra; Nimmrichter, Stefan; Berrada, Tarik; Arndt, Markus; Ulbricht, Hendrik; Hornberger, Klaus; Müri, Marcel; Mayor, Marcel; Böckmann, Marcus; Doltsinis, Nikos
2014-01-01
We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum object, our experiment demonstrates that the translational quantum phase is sensitive to dynamic conformational state changes inside the diffracted molecules. The structural flexibility of tailor-made hot organic particles is sufficient to admit a mixture of strongly fluctuating dipole moments. These modify the electric susceptibility and through this the quantum interference pattern in the presence of an external electric field. Detailed molecular dynamics simulations combined with density functional theory allow us to quantify the time-dependent structural reconfigurations and to predict the ensemble-averaged square of the dipole moment which is found to be in good agreement with the interferometric result. The experiment thus opens a new perspective on matter wave interfe...
Reaction dynamics of molecular hydrogen on silicon surfaces
DEFF Research Database (Denmark)
Bratu, P.; Brenig, W.; Gross, A.;
1996-01-01
Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...... of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective...
A large scale molecular dynamics calculation of a lipid bilayer
Energy Technology Data Exchange (ETDEWEB)
Okazaki, Susumu [Tokyo Inst. of Tech. (Japan)
1998-03-01
Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such a atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2 chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (author)
Discrete Dynamical Systems Meet the Classic Monkey-and-the-Bananas Problem.
Gannon, Gerald E.; Martelli, Mario U.
2001-01-01
Presents a solution of the three-sailors-and-the-bananas problem and attempts a generalization. Introduces an interesting way of looking at the mathematics with an idea drawn from discrete dynamical systems. (KHR)
Molecular dynamics computer simulation of permeation in solids
Energy Technology Data Exchange (ETDEWEB)
Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States)
1997-12-31
In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Chiappori, Federica; Merelli, Ivan; Colombo, Giorgio; Milanesi, Luciano; Morra, Giulia
2012-01-01
Author Summary Allostery, or the capability of proteins to respond to ligand binding events with a variation in structure or dynamics at a distant site, is a common feature for biomolecular function and regulation in a large number of proteins. Intra-protein connections and inter-residue coordinations underlie allosteric mechanisms and react to binding primarily through a finely tuned modulation of motions and structures at the microscopic scale. Hence, all-atom molecular dynamics simulations...
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik
2010-03-17
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
A New Approach to the Classical and Quantum Dynamics of Branes
Pavšič, Matej
2016-01-01
It is shown that the Dirac-nambu-Goto brane can be described as a point particle in an infinite dimensional brane space with a particular metric. This suggests a generalization to brane spaces with arbitrary metric, including the "flat" metric. Then quantization of such a system is straightforward: it is just like quantization of a bunch of non interacting particles. This leads us to a system of a continuous set of scalar fields. For a particular choice of the metric in the space of fields we find that the classical Dirac-Nambu-Goto brane theory arises as an effective theory of such an underlying quantum field theory. Quantization of branes is important for the brane world scenarios, and thus for "quantum gravity".
A new approach to the classical and quantum dynamics of branes
Pavšič, Matej
2016-07-01
It is shown that the Dirac-Nambu-Goto brane can be described as a point particle in an infinite-dimensional brane space with a particular metric. This suggests a generalization to brane spaces with arbitrary metric, including the “flat” metric. Then quantization of such a system is straightforward: it is just like quantization of a bunch of noninteracting particles. This leads us to a system of a continuous set of scalar fields. For a particular choice of the metric in the space of fields we find that the classical Dirac-Nambu-Goto brane theory arises as an effective theory of such an underlying quantum field theory. Quantization of branes is important for the brane world scenarios, and thus for “quantum gravity.”
Zimanyi, Eric N; Silbey, Robert J
2010-10-14
Recent experiments on resonance energy transfer (RET) in photosynthetic systems have found evidence of quantum coherence between the donor and the acceptor. Under these conditions, Förster's theory of RET is no longer applicable and no theory of coherent RET advanced to date rivals the intuitive simplicity of Förster's theory. Here, we develop a framework for understanding RET that is based on classical electrodynamics but still captures the essence of the quantum coherence between the molecules. Our theory requires only a knowledge of the complex polarizabilities of the two molecules participating in the transfer as well as the distance between them. We compare our results to quantum mechanical calculations and show that the results agree quantitatively.
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.
Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo
2015-12-15
Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to
Liu, Hao; Kang, Wei; Zhang, Ping; Duan, Huiling; He, X T
2016-01-01
We present a molecular dynamics simulation of shock waves propagating in dense deuterium with the electron force field method [J. T. Su and W. A. Goddard, Phys. Rev. Lett. 99, 185003 (2007)], which explicitly takes the excitation of electrons into consideration. Non-equilibrium features associated with the excitation of electrons are systematically investigated. We show that chemical bonds in D$_2$ molecules lead to a more complicated shock wave structure near the shock front, compared with the results of classical molecular dynamics simulation. Charge separation can bring about accumulation of net charges on the large scale, instead of the formation of a localized dipole layer, which might cause extra energy for the shock wave to propagate. In addition, the simulations also display that molecular dissociation at the shock front is the major factor corresponding to the "bump" structure in the principal Hugoniot. These results could help to build a more realistic picture of shock wave propagation in fuel mater...
Molecular dynamics analysis on impact behavior of carbon nanotubes
Energy Technology Data Exchange (ETDEWEB)
Seifoori, Sajjad, E-mail: sajjad.seifoori@vru.ac.ir
2015-01-30
Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.
Molecular dynamics analysis on impact behavior of carbon nanotubes
International Nuclear Information System (INIS)
Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation