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
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.
Classical molecular dynamics investigations of biphenyl-based carbon nanomembranes
Directory of Open Access Journals (Sweden)
Andreas Mrugalla
2014-06-01
Full Text Available Background: Free-standing carbon nanomembranes (CNM with molecular thickness and macroscopic size are fascinating objects both for fundamental reasons and for applications in nanotechnology. Although being made from simple and identical precursors their internal structure is not fully known and hard to simulate due to the large system size that is necessary to draw definite conclusions.Results: We performed large-scale classical molecular dynamics investigations of biphenyl-based carbon nanomembranes. We show that one-dimensional graphene-like stripes constitute a highly symmetric quasi one-dimensional energetically favorable ground state. This state does not cross-link. Instead cross-linked structures are formed from highly excited precursors with a sufficient amount of broken phenyls.Conclusion: The internal structure of the CNM is very likely described by a disordered metastable state which is formed in the energetic initial process of electron irradiation and depends on the process of relaxation into the sheet phase.
Passage from quantum to classical molecular dynamics in the presence of Coulomb interactions
Ambrosio, Luigi; Friesecke, Gero; Giannoulis, Jannis
2009-01-01
We present a rigorous derivation of classical molecular dynamics (MD) from quantum molecular dynamics (QMD) that applies to the standard Hamiltonians of molecular physics with Coulomb interactions. The derivation is valid away from possible electronic eigenvalue crossings.
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.
Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer
Casuyac Miqueas; Bantaculo Rolando
2016-01-01
This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNR)using the classical molecular dynamic (MD) simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H...
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.
Quasi-classical description of molecular dynamics based on Egorov's theorem
International Nuclear Information System (INIS)
Egorov's theorem on the classical propagation of quantum observables is related to prominent quasi-classical descriptions of quantum molecular dynamics as the linearized semiclassical initial value representation, the Wigner phase space method, or the statistical quasiclassical method. The error estimates show that different accuracies are achievable for the computation of expectation values and position densities. Numerical experiments for a Morse model of diatomic iodine and confined Henon–Heiles systems in various dimensions illustrate the theoretical results
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.
Floating-point performance of ARM cores and their efficiency in classical molecular dynamics
Nikolskiy, V.; Stegailov, V.
2016-02-01
Supercomputing of the exascale era is going to be inevitably limited by power efficiency. Nowadays different possible variants of CPU architectures are considered. Recently the development of ARM processors has come to the point when their floating point performance can be seriously considered for a range of scientific applications. In this work we present the analysis of the floating point performance of the latest ARM cores and their efficiency for the algorithms of classical molecular dynamics.
Srivastava, Deepak; Saini, Subhash (Technical Monitor)
1998-01-01
The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.
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
Transport properties of room temperature ionic liquids from classical molecular dynamics
Andreussi, Oliviero
2012-01-01
Room Temperature Ionic Liquids (RTILs) have attracted much of the attention of the scientific community in the past decade due the their novel and highly customizable properties. Nonetheless their high viscosities pose serious limitations to the use of RTILs in practical applications. To elucidate some of the physical aspects behind transport properties of RTILs, extensive classical molecular dynamics (MD) calculations are reported. Bulk viscosities and ionic conductivities of butyl-methyl-imidazole based RTILs are presented over a wide range of temperatures. The dependence of the properties of the liquids on simulation parameters, e.g. system size effects and choice of the interaction potential, is analyzed.
International Nuclear Information System (INIS)
Molecular dynamics simulations using a combined quantum/classical force field have been carried out to investigate the properties of hydrogen peroxide in aqueous solution. Radial distribution functions exhibit close similarities with those obtained for the OH radical. They show that H2O2 is a better proton donor than H2O but a weaker proton acceptor. Solvent effects modify the O-H bonds, which are weakened and elongated by 0.02 A. The HOOH dihedral angle decreases by 11 deg. and the dipole moment increases by 0.8 D. The O-O bond length and bond order do not change much. Fluctuations of the frontier orbital energies are analyzed in detail as a function of both, the HOOH geometry and the solvent configuration. Hydrogen-bonds with solvent molecules appear to have an opposite influence depending on their donor/acceptor character. Interconversion between energy minima always proceeds through a transoid transition state
Energy Technology Data Exchange (ETDEWEB)
Sewell, T. D. (Thomas D.); Gan, C. K. (Chee Kwan); Jaramillo, E. (Eugenio); Strachan, A. H. (Alejandro H.)
2004-01-01
We are using classical molecular dynamics and condensed phase electronic-structure methods to predict some of the thermophysical and mechanical properties that are needed as input to realistic mesoscale models for plastic-bonded explosives. The main materials studied to date are HMX, PETN, Estane copolymer, and bi(2,2-dinitropropyl) formal/acetal (BDNPF/A). Emphasis is placed on non-reactive properties and thermodynamic states relevant to cookoff and shock initiation phenomena. Both crystal and liquid-state properties are of interest. Typical simulation sizes and times are {approx}10{sup 2} molecules and 2-10 ns, respectively. The overarching goal is to develop internally consistent model thermodynamic and elastic mechanical descriptions for the materials. Prioritization among the set of properties amenable to atomistic simulation is made based on ongoing interactions with mesoscale modelers at Los Alamos and elsewhere. Recent work will be summarized and our view of profitable directions for future research will be discussed, including preliminary results for large-scale molecular dynamics simulations of shock response of crystalline HMX.
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
International Nuclear Information System (INIS)
Nonstationary heat conduction in a single-walled carbon nanotube was investigated by applying a local heat pulse with duration of subpicoseconds. The investigation was based on classical molecular dynamics simulations, where the heat pulse was generated as coherent fluctuations by connecting a thermostat to the local cell for a short duration. The heat conduction through the nanotube was observed in terms of spatiotemporal temperature profiles. Results of the simulations exhibit non-Fourier heat conduction where a distinct amount of heat is transported in a wavelike form. The geometry of carbon nanotubes allows us to observe such a phenomenon in the actual scale of the material. The resulting spatiotemporal profile was compared with the available macroscopic equations, the so-called non-Fourier heat conduction equations, in order to investigate the applicability of the phenomenological models to a quasi-one-dimensional system. The conventional hyperbolic diffusion equation fails to predict the heat conduction due to the lack of local diffusion. It is shown that this can be remedied by adopting a model with dual relaxation time. Further modal analyses using wavelet transformations reveal a significant contribution of the optical phonon modes to the observed wavelike heat conduction. The result suggests that, in carbon nanotubes with finite length where the long-wavelength acoustic phonons behave ballistically, even optical phonons can play a major role in the non-Fourier heat conduction
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
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, ...
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...
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.
Bryan, W A; King, R B; Nemeth, G R A J; Greenwood, J B; Williams, I D; Newell, W R
2010-01-01
A quasi-classical model (QCM) of molecular dynamics in intense femtosecond laser fields has been developed, and applied to a study of the effect of an ultrashort `control' pulse on the vibrational motion of a deuterium molecular ion in its ground electronic state. A nonadiabatic treatment accounts for the initial ionization-induced vibrational population caused by an ultrashort `pump' pulse. In the QCM, the nuclei move classically on the molecular potential as it is distorted by the laser-induced Stark shift and transition dipole. The nuclei then adjust to the modified potential, non-destructively shifting the vibrational population and relative phase. This shift has been studied as a function of control pulse parameters. Excellent agreement is observed with predictions of time-dependent quantum simulations, lending confidence to the validity of the model and permitting new observations to be made. The applicability of the QCM to more complex multi-potential energy surface molecules (where a quantum treatment...
Indian Academy of Sciences (India)
Y Pathania; P K Ahluwalla
2005-09-01
We have carried out a molecular dynamics simulation of two- and three- dimensional double Yukawa fluids near the triple point. We have compared some of the static and dynamic correlation functions with those of Lennard{Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good agreement. However, when repulsive and attractive parameters occurring in double Yukawa potential are varied, we found distinct differences in static and dynamic correlation functions. We have also compared the two-dimensional correlation functions with those of three-dimensional to study the effect of dimensionality, near the triple point region.
Deciphering mechanism of the 'myristoyl switch' with classical and accelerated molecular dynamics
Czech Academy of Sciences Publication Activity Database
Magarkar, Aniket; Kohagen, Miriam; Jungwirth, Pavel
2015-01-01
Roč. 44, Suppl 1 (2015), S169. ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * myristoyl switch * calcium ion binding Subject RIV: CF - Physical ; Theoretical Chemistry
International Nuclear Information System (INIS)
We derive the fundamental equations of an optimal control theory for systems containing both quantum electrons and classical ions. The system is modeled with Ehrenfest dynamics, a non-adiabatic variant of molecular dynamics. The general formulation, that needs the fully correlated many-electron wavefunction, can be simplified by making use of time-dependent density-functional theory. In this case, the optimal control equations require some modifications that we will provide. The abstract general formulation is complemented with the simple example of the H2+ molecule in the presence of a laser field. (paper)
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.
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.
Czech Academy of Sciences Publication Activity Database
Brown, E. C.; Mucha, Martin; Jungwirth, Pavel; Tobias, D. J.
2005-01-01
Roč. 109, - (2005), s. 7934-7940. ISSN 1520-6106 R&D Projects: GA MŠk(CZ) ME 644; GA MŠk(CZ) LC512 Grant ostatní: NSF(US) CHE 0431512 Institutional research plan: CEZ:AV0Z40550506 Keywords : vibrational spectroscopy * salt water * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.033, year: 2005
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.
International Nuclear Information System (INIS)
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. (paper)
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
Quantum emulation of classical dynamics
Margolus, Norman
2011-01-01
In statistical mechanics, it is well known that finite-state classical lattice models can be recast as quantum models, with distinct classical configurations identified with orthogonal basis states. This mapping makes classical statistical mechanics on a lattice a special case of quantum statistical mechanics, and classical combinatorial entropy a special case of quantum entropy. In a similar manner, finite-state classical dynamics can be recast as finite-energy quantum dynamics. This mapping...
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)
Minoshima, Yusuke; Seki, Yusuke; Takayanagi, Toshiyuki; Shiga, Motoyuki
2016-06-01
The dynamical process of electron attachment to a guanine-cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.
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 ...
International Nuclear Information System (INIS)
This paper calculates lattice thermal expansion (LTE) and thermal conductivity (TC) of Th1-xCexO2 (x=0.0, 0.0625 and 0.125) MOX using classical molecular dynamic simulations. The potential parameters of Coulomb-Buckingham function for Th-O, Ce-O and O-O were determined by fitting experimentally available LTE data for pure ThO2 and CeO2. The calculated linear thermal expansion coefficients in the temperature range 300-1500K for ThO2, CeO2, Th93.75Ce6.25O2 and Th87.5Ce12.5O2 are 10.61, 13.08, 10.78 and 10.93x10-6 K-1, respectively. The MD calculated LTE values of ThO2 and (Th,Ce)O2 MOX are slightly higher than the experimentally determined values. The MD calculated TC values of ThO2 and (Th,Ce)O2 MOX in the high temperature range (600 to 1200 K) our results accords very well with the experimental measurements and at the low temperature range (300-500 K) our results are slightly different from some experimental results as the difference comes from our presumption that the dominant mechanism for phonon scattering is the Umklapp process. (author)
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.
Classical Dynamics as Constrained Quantum Dynamics
Bartlett, Stephen D.; Rowe, David J.
2002-01-01
We show that the classical mechanics of an algebraic model are implied by its quantizations. An algebraic model is defined, and the corresponding classical and quantum realizations are given in terms of a spectrum generating algebra. Classical equations of motion are then obtained by constraining the quantal dynamics of an algebraic model to an appropriate coherent state manifold. For the cases where the coherent state manifold is not symplectic, it is shown that there exist natural projectio...
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)
International Nuclear Information System (INIS)
In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfer process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps−1, which is about 2.5 times faster than that in vacuum, 0.27 ps−1. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction
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
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 ...
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.
Orbital free molecular dynamics
International Nuclear Information System (INIS)
The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)
DEFF Research Database (Denmark)
Bhowmik, Arghya; Malik, R.; Prakash, S.;
2016-01-01
A high concentration of lithium, corresponding to charge capacity of ~4200 mAh/g, can be intercalated in silicon. Unfortunately, due to high intercalation strain leading to fracture and consequent poor cyclability, silicon cannot be used as anode in lithium ion batteries. But recently...... interconnected hollow nano-spheres of amorphous silicon have been found to exhibit high cyclability. The absence of fracture upon lithiation and the high cyclability has been attributed to reduction in intercalation stress due to hollow spherical geometry of the silicon nano-particles. The present work argues...... that the hollow spherical geometry alone cannot ensure the absence of fracture. Using classical molecular dynamics and density functional theory based simulations; satisfactory explanation to the absence of fracture has been explored at the atomic scale....
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.
Exceptional points in quantum and classical dynamics
Smilga, A V
2008-01-01
We notice that, when a quantum system involves exceptional points, i.e. the special values of parameters where the Hamiltonian loses its self-adjointness and acquires the Jordan block structure, the corresponding classical system also exhibits a singular behaviour associated with restructuring of classical trajectories. The system with the crypto-Hermitian Hamiltonian H = (p^2+z^2)/2 -igz^5 and hyper-ellictic classical dynamics is studied in details. Analogies with supersymmetric Yang-Mills dynamics are elucidated.
Exceptional points in quantum and classical dynamics
Smilga, A. V.
2009-03-01
We note that when a quantum system involves exceptional points, i.e. the special values of parameters where the Hamiltonian loses its self-adjointness and acquires the Jordan block structure, the corresponding classical system also exhibits singular behaviour associated with the restructuring of classical trajectories. A system with the crypto-Hermitian Hamiltonian H = (p2 + z2)/2 - igz5 and hyper-elliptic classical dynamics is studied in detail. Analogies with supersymmetric Yang-Mills dynamics are elucidated.
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 ...
Collings Matthew D; Sherman David M
2002-01-01
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 aqueo...
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.
2015-01-01
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the `Classical Wigner' approximation. Here, we show that the further approximation of this `Matsubara dynamics' gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by disc...
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...
Dispersions in Semi-Classical Dynamics
International Nuclear Information System (INIS)
Dispersions around mean values of one-body observables are obtained by restoring classical many-body correlations in Vlasov and Landau-Vlasov dynamics. The method is applied to the calculation of fluctuations in mass, charge and linear momentum in heavy-ion collisions. Results are compared to those obtained by the Balian-Veneroni variational principle in semi-classical approximation
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.
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...
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
Effective dynamics of a classical point charges
Polonyi, Janos
2013-01-01
The effective Lagrangian of a point charge is derived by eliminating the electromagnetic field within the framework of the classical closed time path formalism. The short distance singularity of the electromagnetic field is regulated by an UV cutoff. The Abraham-Lorentz force is recovered and its similarity to anomalies is underlined. The full cutoff-dependent linearized equation of motion is obtained, no runaway trajectories are found but the effective dynamics shows acausality if the cutoff is beyond the classical charge radius. The strength of the radiation reaction force displays a pole in its cutoff-dependence in a manner reminiscent of the Landau-pole of perturbative QED. Similarity between the dynamical breakdown of the time reversal invariance and dynamical symmetry breaking is pointed out.
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
Molecular dynamics simulations
International Nuclear Information System (INIS)
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs
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)
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.
Kojima, H.; Yamada, A.; Okazaki, S.
2015-05-01
The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum-classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute-solvent interactions.
Energy Technology Data Exchange (ETDEWEB)
Kojima, H.; Yamada, A.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
2015-05-07
The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum–classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute–solvent interactions.
Accelerating Fermionic Molecular Dynamics
Clark, M. A.; Kennedy, A. D.
2004-01-01
We consider how to accelerate fermionic molecular dynamics algorithms by introducing n pseudofermion fields coupled with the nth root of the fermionic kernel. This reduces the maximum pseudofermionic force, and thus allows a larger molecular dynamics integration step size without hitting an instability in the integrator.
International Nuclear Information System (INIS)
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out
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.
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.
International Nuclear Information System (INIS)
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
Modeling the Hydrogen Bond within Molecular Dynamics
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
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
Nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
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
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Classical and semiclassical aspects of chemical dynamics
International Nuclear Information System (INIS)
Tunneling in the unimolecular reactions H2C2 → HC2H, HNC → HCN, and H2CO → H2 + 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 + + I- 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
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
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...
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.
A Survey on the Classical Limit of Quantum Dynamical Entropies
Cappellini, Valerio
2007-01-01
We analyze the behavior of quantum dynamical entropies production from sequences of quantum approximants approaching their (chaotic) classical limit. The model of the quantized hyperbolic automorphisms of the 2-torus is examined in detail and a semi-classical analysis is performed on it using coherent states, fulfilling an appropriate dynamical localization property. Correspondence between quantum dynamical entropies and the Kolmogorov-Sinai invariant is found only over time scales that are logarithmic in the quantization parameter.
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...
Open boundary molecular dynamics
Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.
2015-09-01
This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.
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 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...
Methane in carbon nanotube - molecular dynamics simulation
Bartuś, Katarzyna; Bródka, Aleksander
2011-01-01
Abstract The behaviour of methane molecules inside carbon nanotube at room temperature is studied using classical molecular dynamics simulations. A methane molecule is represented either by a shapeless super-atom or by rigid set of 5 interaction centres localised on atoms. Different loadings of methane molecules ranging from the dense gas density to the liquid density, and the influence of flexibility of the CNT on structural and dynamics properties of confined molecules are consid...
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.
Molecular Dynamics of Acetylcholinesterase
Energy Technology Data Exchange (ETDEWEB)
Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy
2002-06-01
Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.
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
Fundamental laws of relativistic classical dynamics revisited
International Nuclear Information System (INIS)
By stating that a linear differential form, whose coefficients are the components of the momentum and the energy of a particle, has an antiderivative, the basic equations of the dynamics of points are obtained, in the relativistic case. From the point of view of optimization theory, a connection between our condition and the Bellman-Isaacs equation of dynamic programming is discussed, with a view to extending the theory to relativistic wave mechanics
Quantum–classical correspondence and the role of the dipole function in molecular dissociation
International Nuclear Information System (INIS)
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
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
Point vortex dynamics: A classical mathematics playground
DEFF Research Database (Denmark)
Aref, Hassan
2007-01-01
integrability of the three-vortex problem, the interplay of relative equilibria of identical vortices and the roots of certain polynomials, addition formulas for the cotangent and the Weierstrass zeta function, projective geometry, and other topics. The hope and intent of the article is to garner further...... participation in the exploration of this intriguing dynamical system from the mathematical physics community....
Better, Cheaper, Faster Molecular Dynamics
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
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.
Relativistic and separable classical hamiltonian particle dynamics
International Nuclear Information System (INIS)
We show within the Hamiltonian formalism the existence of classical relativistic mechanics of N scalar particles interacting at a distance which satisfies the requirements of Poincare invariance, separability, world-line invariance and Einstein causality. The line of approach which is adopted here uses the methods of the theory of systems with constraints applied to manifestly covariant systems of particles. The study is limited to the case of scalar interactions remaining weak in the whole phase space and vanishing at large space-like separation distances of the particles. Poincare invariance requires the inclusion of many-body, up to N-body, potentials. Separability requires the use of individual or two-body variables and the construction of the total interaction from basic two-body interactions. Position variables of the particles are constructed in terms of the canonical variables of the theory according to the world-line invariance condition and the subsidiary conditions of the non-relativistic limit and separability. Positivity constraints on the interaction masses squared of the particles ensure that the velocities of the latter remain always smaller than the velocity of light
Opinion particles: Classical physics and opinion dynamics
International Nuclear Information System (INIS)
A model for Opinion Particles, based on Bayesian-inspired models of Opinion Dynamics such as the CODA model, is presented. By extending the discrete time characteristic of those models to continuous time, a theory for the movement of opinion particles is obtained, based only on inference ideas. This will allow inertia to be obtained as a consequence of an extended CODA model. For the general case, we will see that the likelihoods are associated with variables such as velocity and acceleration of the particles. Newtonian forces are easily defined and the relationship between a force and the equivalent likelihood provided. The case of the harmonic oscillator is solved as an example, to illustrate clearly the relationship between Opinion Particles and Mechanics. Finally, possible paths to apply these results to General Relativity are debated. - Highlights: • CODA model of Opinion Dynamics is extended to continuous time • The concept of Opinion Particles is introduced and inertia is obtained. • The relationship between opinion particle models and basic Physics is discussed. • Harmonic oscillator dynamics is obtained for opinion particles. • Possible equivalences to General Relativity are briefly discussed
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.
The nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments
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.
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Implementation of Accelerated Molecular Dynamics in NAMD
Wang, Yi; Harrison, Christopher B.; Schulten, Klaus; McCammon, J. Andrew
2011-01-01
Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Here we present the implementation of aMD in the parallel simulation program NAMD. We show that aMD simulations performed with NAMD have only a small overhead compared with classical MD simulations. Through example applications to the alanine dipeptide, we discuss the choice of acceleration parameters, the inte...
Low temperature spin wave dynamics in classical Heisenberg chains
Energy Technology Data Exchange (ETDEWEB)
Heller, P.; Blume, M.
1977-11-01
A detailed and quantitative study of the low-temperature spin-wave dynamics was made for the classical Heisenberg-coupled chain using computer simulation. Results for the spin-wave damping rates and the renormalization of the spin-wave frequencies are presented and compared with existing predictions.
Clifford algebras and the classical dynamical Yang-Baxter equation
Alekseev, Anton; Meinrenken, E.
2003-01-01
We describe a relationship of the classical dynamical Yang-Baxter equation with the following elementary problem for Clifford algebras: Given a vector space $V$ with quadratic form $Q_V$, how is the exponential of an element in $\\wedge^2(V)$ under exterior algebra multiplication related to its exponential under Clifford multiplication?
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
Dynamics in the quantum/classical limit based on selective use of the quantum potential
International Nuclear Information System (INIS)
A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction
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
A fermionic molecular dynamics technique to model nuclear matter
International Nuclear Information System (INIS)
Full text: At sub-nuclear densities of about 1014 g/cm3, nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)
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.
Quantum Gibbs distribution from dynamical thermalization in classical nonlinear lattices
International Nuclear Information System (INIS)
We study numerically time evolution in classical lattices with weak or moderate nonlinearity which leads to interactions between linear modes. Our results show that in a certain strength range a moderate nonlinearity generates a dynamical thermalization process which drives the system to the quantum Gibbs distribution of probabilities, or average oscillation amplitudes. The effective dynamical temperature of the lattice varies from large positive to large negative values depending on the energy of the initially excited modes. This quantum Gibbs distribution is drastically different from the usually expected energy equipartition over linear modes corresponding to a regime of classical thermalization. Possible experimental observations of this dynamical thermalization are discussed for cold atoms in optical lattices, nonlinear photonic lattices and optical fiber arrays. (paper)
Emergence of cooperative dynamics in fully packed classical dimers
Oakes, Tom; Garrahan, Juan P.; Powell, Stephen
2016-03-01
The classical dimer model on the square lattice is a paradigmatic example of a system subject to strong local constraints. We study its behavior under local stochastic dynamics, by means of Monte Carlo simulations and theoretical arguments. We observe clear signatures of correlated dynamics in both global and local observables and over a broad range of time scales, indicating a breakdown of the simple continuum description that approximates well the statics. We show that this collective dynamics can be understood in terms of one-dimensional "strings" of high mobility, which govern both local and long-wavelength dynamical properties. We introduce a coarse-grained description of the strings, based on the Edwards-Wilkinson model, which leads to exact results in the limit of low string density and provides a detailed qualitative understanding of the dynamics in all flux sectors. We discuss the implications of our results for the dynamics of constrained systems more generally.
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383
Mathematica for Theoretical Physics Classical Mechanics and Nonlinear Dynamics
Baumann, Gerd
2005-01-01
Mathematica for Theoretical Physics: Classical Mechanics and Nonlinear Dynamics This second edition of Baumann's Mathematica® in Theoretical Physics shows readers how to solve physical problems and deal with their underlying theoretical concepts while using Mathematica® to derive numeric and symbolic solutions. Each example and calculation can be evaluated by the reader, and the reader can change the example calculations and adopt the given code to related or similar problems. The second edition has been completely revised and expanded into two volumes: The first volume covers classical mechanics and nonlinear dynamics. Both topics are the basis of a regular mechanics course. The second volume covers electrodynamics, quantum mechanics, relativity, and fractals and fractional calculus. New examples have been added and the representation has been reworked to provide a more interactive problem-solving presentation. This book can be used as a textbook or as a reference work, by students and researchers alike. A...
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.
Mithen, James P.; Daligault, Jérôme; Gregori, G.
2011-01-01
The complementarity of the liquid and plasma descriptions of the classical one-component plasma (OCP) is explored by studying wavevector and frequency dependent dynamical quantities: the dynamical structure factor (DSF), and the dynamic local field correction (LFC). Accurate Molecular Dynamics (MD) simulations are used to validate/test models of the DSF and LFC. Our simulations, which span the entire fluid regime ($\\Gamma = 0.1 - 175$), show that the DSF is very well represented by a simple a...
The Computer Simulation of Liquids by Molecular Dynamics.
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
Physical adsorption and molecular dynamics
International Nuclear Information System (INIS)
Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.)
Nonadiabatic Molecular Dynamics Based on Trajectories
Directory of Open Access Journals (Sweden)
Felipe Franco de Carvalho
2013-12-01
Full Text Available Performing molecular dynamics in electronically excited states requires the inclusion of nonadiabatic effects to properly describe phenomena beyond the Born-Oppenheimer approximation. This article provides a survey of selected nonadiabatic methods based on quantum or classical trajectories. Among these techniques, trajectory surface hopping constitutes an interesting compromise between accuracy and efficiency for the simulation of medium- to large-scale molecular systems. This approach is, however, based on non-rigorous approximations that could compromise, in some cases, the correct description of the nonadiabatic effects under consideration and hamper a systematic improvement of the theory. With the help of an in principle exact description of nonadiabatic dynamics based on Bohmian quantum trajectories, we will investigate the origin of the main approximations in trajectory surface hopping and illustrate some of the limits of this approach by means of a few simple examples.
Molecular dynamics study of cyclohexane interconversion
Wilson, Michael A.; Chandler, David
1990-12-01
Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.
Molecular dynamics simulation for modelling plasma spectroscopy
Talin, B; Calisti, A; Gigosos, M A; González, M A; Gaztelurrutia, T R; Dufty, J W
2003-01-01
The ion-electron coupling properties for an ion impurity in an electron gas and for a two-component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely motivated by the study of radiator dipole relaxation in plasmas which makes a real link between models and experiments. Current radiative property models for plasmas include single electron collisions neglecting charge-charge correlations within the classical quasi-particle approach commonly used in this field. The dipole relaxation simulation based on electron-ion molecular dynamics proposed here will provide a means to benchmark and improve model developments. Benefiting from a detailed study of a single ion embedded in an electron plasma, the challenging two-component ion-electron molecular dynamics simulations are proved accurate. They open new possibilities of obtaining reference lineshape data.
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.
Hidden Symmetries of Dynamics in Classical and Quantum Physics
Cariglia, Marco
2014-01-01
This article reviews the role of hidden symmetries of dynamics in the study of physical systems, from the basic concepts of symmetries in phase space to the forefront of current research. Such symmetries emerge naturally in the description of physical systems as varied as non-relativistic, relativistic, with or without gravity, classical or quantum, and are related to the existence of conserved quantities of the dynamics and integrability. In recent years their study has grown intensively, due to the discovery of non-trivial examples that apply to different types of theories and different numbers of dimensions. Applications encompass the study of integrable systems such as spinning tops, the Calogero model, systems described by the Lax equation, the physics of higher dimensional black holes, the Dirac equation, supergravity with and without fluxes, providing a tool to probe the dynamics of non-linear systems.
Applications of Molecular Dynamics in Atmospheric and Solution Chemistry
Li, Xin
2011-01-01
This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial ch...
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...
Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations
Alkis, S.; Krause, J. L.; Fry, J. N.; Cheng, H.-P.
2009-03-01
We study the diffusion of silver nanoparticles on self-assembled monolayers (SAMs). Silver clusters Agn of sizes n=55 , 147, and 1289 were evolved in contact with an alkanethiol (12 carbon, dodecanethiol) SAM deposited on a gold (111) surface. Analysis based on classical molecular dynamics simulations reveals that these systems exhibit a rich variety of behaviors, from superdiffusive for the lightest cluster to pinned for the heaviest, evolution self-similar in lengths and times for the lightest cluster but with characteristic time scales and directional anisotropies emerging for the heavier clusters.
Galilei invariant molecular dynamics
International Nuclear Information System (INIS)
We construct a C*-dynamical model for a chemical reaction. Galilei invariance of our nonrelativistic model is demonstrated by defining it directly on a Galilean space-time fibrebundle with C*-algebra valued fibre, i.e. without reference to any coordinate system. The existence of equilibrium states in this model is established and some of their properties are discussed. (orig.)
Information dynamics and open systems classical and quantum approach
Ingarden, R S; Ohya, M
1997-01-01
This book aims to present an information-theoretical approach to thermodynamics and its generalisations On the one hand, it generalises the concept of `information thermodynamics' to that of `information dynamics' in order to stress applications outside thermal phenomena On the other hand, it is a synthesis of the dynamics of state change and the theory of complexity, which provide a common framework to treat both physical and nonphysical systems together Both classical and quantum systems are discussed, and two appendices are included to explain principal definitions and some important aspects of the theory of Hilbert spaces and operator algebras The concept of higher-order temperatures is explained and applied to biological and linguistic systems The theory of open systems is presented in a new, much more general form Audience This volume is intended mainly for theoretical and mathematical physicists, but also for mathematicians, experimental physicists, physical chemists, theoretical biologists, communicat...
Isomorph invariance of the structure and dynamics of classical crystals
DEFF Research Database (Denmark)
Albrechtsen, Dan; Olsen, Andreas Elmerdahl; Pedersen, Ulf Rørbæk; Schrøder, Thomas; Dyre, J. C.
2014-01-01
, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics of a......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...... defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles...
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.)
Classical and quantum dynamics of driven elliptical billiards
International Nuclear Information System (INIS)
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.)
A sampling of molecular dynamics
Sindhikara, Daniel Jon
The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel
Energy Technology Data Exchange (ETDEWEB)
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
Rapid learning dynamics in individual honeybees during classical conditioning
Directory of Open Access Journals (Sweden)
Evren Pamir
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 ...
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Progress in quantum molecular dynamics
International Nuclear Information System (INIS)
In this paper a microscopic simulation method of the quantum molecular dynamics (QMD) and its extensions to high- and low-energy regions are reported. Combined with the statistical decay calculation, QMD can reproduce experimental data with fixed and very few parameters. (J.P.N.)
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.
Classical dynamics and stability of collapsing thick shells of matter
International Nuclear Information System (INIS)
We study the collapse towards the gravitational radius of a macroscopic spherical thick shell surrounding an inner massive core. This overall electrically neutral macroshell is composed of many nested δ-like massive microshells which can bear non-zero electric charge, and a possibly non-zero cosmological constant is also included. The dynamics of the shells is described by means of Israel's (Lanczos) junction conditions for singular hypersurfaces and, adopting a Hartree (mean-field) approach, an effective Hamiltonian for the motion of each microshell is derived which allows us to check the stability of the matter composing the macroshell. We end by briefly commenting on the quantum effects which may arise from the extension of our classical treatment to the semiclassical level
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.)
Particle physics and dark energy. Beyond classical dynamics
International Nuclear Information System (INIS)
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.)
DYNAMIC AND CLASSICAL PRA: A BWR SBO CASE COMPARISON
Energy Technology Data Exchange (ETDEWEB)
Mandelli, Diego; Smith, Curtis L; Ma, Zhegang
2011-07-01
As part of the Light-Water Sustainability Program (LWRS), the purpose of the Risk Informed Safety Margin Characterization (RISMC) Pathway research and development is to support plant decisions for risk-informed margin management with the aim to improve economics, reliability, and sustain the safety of current NPPs. In this paper, we describe the RISMC analysis process illustrating how mechanistic (i.e., dynamic system simulators) and probabilistic (stochastic sampling strategies) approaches are combined in a dynamic PRA fashion in order to estimate safety margins. We use the scenario of a “station blackout” (SBO) wherein offsite power and onsite power are lost, thereby causing a challenge to plant safety systems. We describe the RISMC approach, illustrate the station blackout modeling, and compare this with traditional risk analysis modeling for this type of accident scenario. In the RISMC approach the dataset obtained consists of set of simulation runs (performed by using codes such as RELAP5/3D) where timing and ordering of events is changed accordingly to the stochastic sampling strategy adopted. On the other side, classical PRA methods, which are based on event-tree (FT) and fault-tree (FT) structures, generate minimal cut sets and probability values associated to each ET branch. The comparison of the classical and RISMC approaches is performed not only in terms of overall core damage probability but also considering statistical differences in the actual sequence of events. The outcome of this comparison analysis shows similarities and dissimilarities between the approaches but also highlights the greater amount of information that can be generated by using the RISMC approach.
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...
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.
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)
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.
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
International Nuclear Information System (INIS)
In this study either cluster fragmentation, using a time-dependent Hartree-Fock formulation, or cluster deposition, based on classical molecular dynamics, have been studied. An exhaustive analysis has been performed on the many parameters acting on the two processes. Fragmentation calculations show a primary dependence on the input energy whereas the interatomic forces play a primary role in deposition. However the central result of this study is the essential agreement between the classical and quantum mechanical calculation
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)
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...
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.
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
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.
Mithen, James P; Gregori, G
2011-01-01
The complementarity of the liquid and plasma descriptions of the classical one-component plasma (OCP) is explored by studying wavevector and frequency dependent dynamical quantities: the dynamical structure factor (DSF), and the dynamic local field correction (LFC). Accurate Molecular Dynamics (MD) simulations are used to validate/test models of the DSF and LFC. Our simulations, which span the entire fluid regime ($\\Gamma = 0.1 - 175$), show that the DSF is very well represented by a simple and well known memory function model of generalized hydrodynamics. On the other hand, the LFC, which we have computed using MD for the first time, is not well described by existing models.
Molecular Dynamics for Dense Matter
Maruyama, Toshiki; Chiba, Satoshi
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...
DMS: A Package for Multiscale Molecular Dynamics
Somogyi, Endre; Ortoleva, Peter J
2013-01-01
Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables...
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.
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
Wereszczynski, Jeff; McCammon, J. Andrew
2010-01-01
Accelerated molecular dynamics (aMD) has been shown to enhance conformational space sampling relative to classical molecular dynamics; however, the exponential reweighting of aMD trajectories, which is necessary for the calculation of free energies relating to the classical system, is oftentimes problematic, especially for systems larger than small poly peptides. Here, we propose a method of accelerating only the degrees of freedom most pertinent to sampling, thereby reducing the total accele...
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.
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
Molecular dynamics investigation of dynamic crack stability
International Nuclear Information System (INIS)
A series of molecular-dynamics simulations has been performed in order to evaluate the effects of several physical factors on dynamic crack stability. These factors are the crystalline structure and the interatomic interaction modeled by various empirical potentials. For brittle crack propagation at low temperature we find that steady-state crack velocities are limited to a band of accessible values. Increasing the overload beyond KIc, the crack can propagate with a steady-state velocity, which quickly reaches the terminal velocity of about 0.4 of the Rayleigh wave speed. The magnitude of the terminal velocity can be related to the nonlinearity of the interatomic interaction. Further increasing the overload does not change the steady-state velocity dramatically, but significantly increases the amplitude of acoustic emission from the crack tip. Loading the crack even further leads to instabilities which take the form of cleavage steps, dislocation emission, or branching. The instability is closely related to the buildup of a localized coherent, phononlike field generated by the bond-breaking events. The form of the instability depends critically on crystal structure and on the crystallographic orientation of the crack system but can also be correlated with the relative ease of dislocation generation (and motion). copyright 1997 The American Physical Society
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...
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Classical dynamical description of heavy ion sequential fission
International Nuclear Information System (INIS)
Sequential fission processes are investigated in a classical fragmentation model. Dissipative forces are included. In the fissioning process the recoupling of excitational degrees of freedom to kinetic degrees of freedom is found important. 6 figures
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
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
Energy Technology Data Exchange (ETDEWEB)
Hu, Zixuan; Ratner, Mark A.; Seideman, Tamar, E-mail: t-seideman@northwestern.edu [Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113 (United States)
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.
Hu, Zixuan; Ratner, Mark A.; Seideman, Tamar
2014-12-01
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.
International Nuclear Information System (INIS)
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
Ab initio molecular dynamics on the electronic Boltzmann equilibrium distribution
Energy Technology Data Exchange (ETDEWEB)
Alonso, J L; Echenique, P [Departamento de Fisica Teorica, Universidad de Zaragoza, Pedro Cerbuna 12, E-50009 Zaragoza (Spain); Castro, A; Polo, V [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, E-50018 Zaragoza (Spain); Rubio, A [Nano-Bio Spectroscopy group and ETSF Scientific Development Centre, Departamento de Fisica de Materiales, Universidad del PaIs Vasco, Centro de Fisica de Materiales, CSIC-UPV/EHU-MPC and DIPC, E-20018 San Sebastian (Spain); Zueco, D, E-mail: dzueco@unizar.e [Instituto de Ciencia de Materiales de Aragon and Departamento de Fisica de la Materia Condensada, CSIC-Universidad de Zaragoza, E-50009 Zaragoza (Spain)
2010-08-15
We prove that for a combined system of classical and quantum particles, it is possible to describe a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In addition, these molecular dynamics (MD) do not need to assume that the electrons immediately follow the nuclear motion (in contrast to any adiabatic approach) and do not present problems in the presence of crossing points between different potential energy surfaces (conical intersections or spin-crossings). A practical application of this MD to the study of the effect of temperature on molecular systems presenting (nearly) degenerate states-such as the avoided crossing in the ring-closure process of ozone-is presented.
The uncertainty principle enables non-classical dynamics in an interferometer
Dahlsten, Oscar C. O.; Garner, Andrew J. P.; Vedral, Vlatko
2014-08-01
The quantum uncertainty principle stipulates that when one observable is predictable there must be some other observables that are unpredictable. The principle is viewed as holding the key to many quantum phenomena and understanding it deeper is of great interest in the study of the foundations of quantum theory. Here we show that apart from being restrictive, the principle also plays a positive role as the enabler of non-classical dynamics in an interferometer. First we note that instantaneous action at a distance should not be possible. We show that for general probabilistic theories this heavily curtails the non-classical dynamics. We prove that there is a trade-off with the uncertainty principle that allows theories to evade this restriction. On one extreme, non-classical theories with maximal certainty have their non-classical dynamics absolutely restricted to only the identity operation. On the other extreme, quantum theory minimizes certainty in return for maximal non-classical dynamics.
Spin dynamics of an ultra-small nanoscale molecular magnet
Directory of Open Access Journals (Sweden)
Ciftja Orion
2007-01-01
Full Text Available AbstractWe present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high Heisenberg spins. We derive exact analytic expressions (in integral form for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail.
Molecular dynamics simulations of complex shaped particles using Minkowski operators
Galindo-Torres, Sergio-Andres; Alonso-Marroquin, Fernando
2008-01-01
The Minkowski operators (addition and substraction of sets in vectorial spaces) has been extensively used for Computer Graphics and Image Processing to represent complex shapes. Here we propose to apply those mathematical concepts to extend the Molecular Dynamics (MD) Methods for simulations with complex-shaped particles. A new concept of Voronoi-Minkowski diagrams is introduced to generate random packings of complex-shaped particles with tunable particle roundness. By extending the classical...
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.
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...
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Molecular dynamics studies of palladium
International Nuclear Information System (INIS)
Equilibrium bulk properties of Pd are examined using molecular dynamics technique based on the embedded atom potential. We calculate the total energy and the lattice parameter as a function of temperature. Melting temperature is determined from the discontinuous transition in the energy and lattice parameter. Specific heat and linear coefficient of thermal expansion are calculated from the energy and lattice parameters respectively and results show good agreement with experimental values. Finally the mean square displacements of thermal expansion are calculated form the energy and lattice parameters respectively and results show good agreement with the experimental values. Finally the mean square displacements of the atoms in bulk Pd are compared with the mean square displacements on the three low-index faces (100), (110) and (III). (author)
Theoretical Concepts in Molecular Photodissociation Dynamics
DEFF Research Database (Denmark)
Henriksen, Niels Engholm
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic Mole...
Theoretical Concepts in Molecular Photodissociation Dynamics
DEFF Research Database (Denmark)
Henriksen, Niels Engholm
1995-01-01
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
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.
Lesniak, Joseph; Behrman, Elizabeth; Zandler, Melvin; Kumar, Preethika
2008-03-01
Very few quantum algorithms are currently useable today. When calculating molecular energies, using a quantum algorithm takes advantage of the quantum nature of the algorithm and calculation. A few small molecules have been used to show that this method is possible. This method will be applied to larger molecules and compared to classical computer methods.
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...
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.
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.
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 simulation by atomic mass weighting
Mao, Boryeu; Friedman, Alan R.
1990-01-01
A molecular dynamics-based simulation method in which atomic masses are weighted is described. Results from this method showed that the capability for conformation search in molecular dynamics simulation of a short peptide (FMRF-amide) is significantly increased by mass weighting.
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...
Takatsuka, Kazuo; Matsumoto, Kentaro
2016-01-21
We present a basic theory to study real-time dynamics embedded in a large environment that is treated using a statistical method. In light of great progress in the molecular-level studies on time-resolved spectroscopies, chemical reaction dynamics, and so on, not only in the gas phase but also in condensed phases like liquid solvents and even in crowded environments in living cells, we need to bridge over a gap between statistical mechanics and microscopic real-time dynamics. For instance, an analogy to gas-phase dynamics in which molecules are driven by the gradient of the potential energy hyper-surfaces (PESs) suggests that particles in condensed phases should run on the free energy surface instead. The question is whether this anticipation is correct. To answer it, we here propose a mixed dynamics and statistical representation to treat chemical dynamics embedded in a statistical ensemble. We first define the entropy functional, which is a function of the phase-space position of the dynamical subsystem, being dressed with statistical weights from the statistical counterpart. We then consider the functionals of temperature, free energy, and chemical potential as their extensions in statistical mechanics, through which one can clarify the relationship between real-time microscopic dynamics and statistical quantities. As an illustrative example we show that molecules in the dynamical subsystem should run on the free-energy functional surface, if and only if the spatial gradients of the temperature functional are all zero. Otherwise, additional forces emerge from the gradient of the temperature functional. Numerical demonstrations are presented at the very basic level of this theory of molecular dissociation in atomic cluster solvents. PMID:26674298
A molecular dynamics simulation code ISIS
International Nuclear Information System (INIS)
Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)
Quantum molecular dynamics simulations of dense matter
Energy Technology Data Exchange (ETDEWEB)
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Quantum field theory of classically unstable Hamiltonian dynamics
International Nuclear Information System (INIS)
We study a class of dynamical systems for which the motions can be described in terms of geodesics on a manifold (ordinary potential models can be cast into this form by means of a conformal map). It is rigorously proven that the geodesic deviation equation of Jacobi, constructed with a second covariant derivative, is unitarily equivalent to that of a parametric harmonic oscillator, and we study the second quantization of this oscillator. The excitations of the Fock space modes correspond to the emission and absorption of quanta into the dynamical medium, thus associating unstable behavior of the dynamical system with calculable fluctuations in an ensemble with possible thermodynamic consequences
Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite
Van den Berg, A.W.C.; Bromley, S.T.; Flikkema, E.; Wojdel, J.; Maschmeyer, T; Jansen, J C
2004-01-01
In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the temperature range of 700–1200 K, the diffusion coefficient is found to range from 1.6⋅10−10 to 1.8⋅10−9 m2/s. The energy barrier for hydrogen diffusion is determined from the simulations allowing the applica...
Thermally driven molecular linear motors - A molecular dynamics study
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence
2009-01-01
We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...
Kinetic theory molecular dynamics and hot dense matter: Theoretical foundations
Graziani, F. R.; Bauer, J. D.; Murillo, M. S.
2014-09-01
Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD
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. PMID:22859479
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.
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
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.
Chaotic Dynamics and Transport in Classical and Quantum Systems
International Nuclear Information System (INIS)
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
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.
Cleaning graphene : a first quantum/classical molecular dynamics approach
Delfour, L.; Davydova, A.; Despiau-Pujo, E.; Cunge, G; Graves, D. B.; Magaud, L.
2015-01-01
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 promisi...
Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package
Dizkirici, Ayten; Tekpinar, Mustafa
2015-03-01
GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.
Quantum-Classical Nonadiabatic Dynamics: Coupled- vs Independent-Trajectory Methods.
Agostini, Federica; Min, Seung Kyu; Abedi, Ali; Gross, E K U
2016-05-10
Trajectory-based mixed quantum-classical approaches to coupled electron-nuclear dynamics suffer from well-studied problems such as the lack of (or incorrect account for) decoherence in the trajectory surface hopping method and the inability of reproducing the spatial splitting of a nuclear wave packet in Ehrenfest-like dynamics. In the context of electronic nonadiabatic processes, these problems can result in wrong predictions for quantum populations and in unphysical outcomes for the nuclear dynamics. In this paper, we propose a solution to these issues by approximating the coupled electronic and nuclear equations within the framework of the exact factorization of the electron-nuclear wave function. We present a simple quantum-classical scheme based on coupled classical trajectories and test it against the full quantum mechanical solution from wave packet dynamics for some model situations which represent particularly challenging problems for the above-mentioned traditional methods. PMID:27030209
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...
Catalyst dynamics: consequences for classical kinetic descriptions of reactors
DEFF Research Database (Denmark)
Johannessen, Tue; Larsen, Jane Hvolbæk; Chorkendorff, Ib; Livbjerg, Hans; Topsøe, Henrik
The modelling of catalytic reactions/reactors has undergone great improvements since the introduction of empirical power-law kinetics in chemical reaction engineering and micro-kinetic models based on insight into the nature of elementary steps have appeared for many reactions. However, recent 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 of the...... dynamical behaviour of some catalytic systems and discuss the corresponding Limitations in existing models for catalytic reactions and reactors. Catalytic reactors operated in non-steady-state are becoming more frequent in industry. The additional efforts needed to accurately simulate these types of...
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...
Quantum dynamics of complex molecular systems
Miller, William H.
2005-01-01
This Perspective presents a broad overview of the present status of theoretical capabilities for describing quantum dynamics in molecular systems with many degrees of freedom, e.g., chemical reactions in solution, clusters, solids, or biomolecular environments.
Dynamical processes in atomic and molecular physics
Ogurtsov, Gennadi
2012-01-01
Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece
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...
Mixed quantum-classical dynamics from the exact decomposition of electron-nuclear motion
Abedi, Ali; Gross, E K U
2014-01-01
We present a novel mixed quantum-classical approach to the coupled electron-nuclear dynamics based on the exact factorization of the electron-nuclear wave function, recently proposed in [A. Abedi, N. T. Maitra, and E. K. U. Gross, Phys. Rev. Lett. 105, 123002 (2010)]. In this framework, classical nuclear dynamics is derived as the lowest order approximation of the time dependent Schr\\"odinger equation that describes the evolution of the nuclei. The effect of the time dependent scalar and vector potentials, representing the exact electronic back-reaction on the nuclear subsystem, is consistently derived within the classical approximation. We examine with an example the performance of the proposed mixed quantum-classical scheme in comparison with exact calculations.
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.
Ab initio mass tensor molecular dynamics
Tsuchida, Eiji
2010-01-01
Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal ato...
Accelerated molecular dynamics simulations of protein folding
Miao, Y.; Feixas, F; Eun, C; McCammon, JA
2015-01-01
© 2015 Wiley Periodicals, Inc. Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native ...
Molecular Dynamic Simulation on High Performance Infrastrucutres
Bergant, Anže
2016-01-01
This thesis covers comparison between different computer platforms of high performance computing while performing molecular dynamics simulations, which falls under very complex problems and needs lots of processing power. Our goal was to critically evaluate different platforms while solving molecular dynamics, so we used 1 to 16 processor cores on a computer cluster and one and two graphics processing units (GPU) for simulations. The results will be used while planning on buying new computer ...
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...
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Jahn, S.; P. A. Madden
2008-01-01
The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q) from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω) from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the ...
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.
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
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.
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.
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
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.
Agostini, Federica; Abedi, Ali; Suzuki, Yasumitsu; Min, Seung Kyu; Maitra, Neepa T.; Gross, E. K. U.
2015-03-01
The Born-Oppenheimer (BO) approximation allows to visualize the coupled electron-nuclear dynamics in molecular systems as a set of nuclei moving on a single potential energy surface representing the effect of the electrons in a given eigenstate. Many interesting phenomena, however, such as vision or charge separation in organic photovoltaic materials, take place in conditions beyond its range of validity. Nevertheless, the basic construct of the adiabatic treatment, the BO potential energy surfaces, is employed to describe non-adiabatic processes and the full problem is represented in terms of adiabatic states and transitions among them in regions of strong non-adiabatic coupling. But the concept of single potential energy is lost. The alternative point of view arising in the framework of the exact factorization of the electron-nuclear wave function will be presented. A single, time-dependent, potential energy provides the force driving the nuclear motion and is adopted as starting point for the development of quantum-classical approximations to the full quantum mechanical problem.
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
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...
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... statistical mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular...
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...
Fast dynamics of molecular bridges
Czech Academy of Sciences Publication Activity Database
Špička, Václav; Kalvová, Anděla; Velický, B.
T151, č. 1 (2012), s. 1-17. ISSN 0031-8949 R&D Projects: GA ČR GAP204/12/0897 Institutional research plan: CEZ:AV0Z10100521; CEZ:AV0Z10100520 Keywords : time quantum dynamics * nonequilibrium Green-functions * Kadanoff-Baym equations * initial correlations * transportequations * mesoscopic systems Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.032, year: 2012
Magnetism on a Mesoscopic Scale: Molecular Nanomagnets Bridging Quantum and Classical Physics
Energy Technology Data Exchange (ETDEWEB)
Konstantinidis, Nikolaos P; Sundt, Alexander; Nehrkorn, Joscha; Machens, Anna; Waldmann, Oliver, E-mail: oliver.waldmann@physik.uni-freiburg.de [Physikalisches Institut, Universitaet Freiburg, 79104 Freiburg (Germany)
2011-07-06
In recent years polynuclear transition metal molecules have been synthesized and proposed for example as magnetic storage units or qubits in quantum computers. They are known as molecular nanomagnets and belong in the class of mesoscopic systems, which are large enough to display many-body effects but small enough to be away from the finite-size scaling regime. It is a challenge for physicists to understand their magnetic properties, and for synthetic chemists to efficiently tailor them by assembling fundamental units. They are complementary to artificially engineered spin systems for surface deposition, as they support a wider variety of complex states in their low energy spectrum. Here a few characteristic examples of molecular nanomagnets showcasing unusual many-body effects are presented. Antiferromagnetic wheels and chains can be described in classical terms for small sizes and large spins to a great extent, even though their wavefunctions do not significantly overlap with semiclassical configurations. Hence, surprisingly, for them the transition from the classical to the quantum regime is blurred. A specific example is the Fe18 wheel, which displays quantum phase interference by allowing Neel vector tunneling in a magnetic field. Finally, the Co{sub 5}Cl single-molecule magnet is shown to have an unusual anisotropic response to a magnetic field.
Magnetism on a Mesoscopic Scale: Molecular Nanomagnets Bridging Quantum and Classical Physics
International Nuclear Information System (INIS)
In recent years polynuclear transition metal molecules have been synthesized and proposed for example as magnetic storage units or qubits in quantum computers. They are known as molecular nanomagnets and belong in the class of mesoscopic systems, which are large enough to display many-body effects but small enough to be away from the finite-size scaling regime. It is a challenge for physicists to understand their magnetic properties, and for synthetic chemists to efficiently tailor them by assembling fundamental units. They are complementary to artificially engineered spin systems for surface deposition, as they support a wider variety of complex states in their low energy spectrum. Here a few characteristic examples of molecular nanomagnets showcasing unusual many-body effects are presented. Antiferromagnetic wheels and chains can be described in classical terms for small sizes and large spins to a great extent, even though their wavefunctions do not significantly overlap with semiclassical configurations. Hence, surprisingly, for them the transition from the classical to the quantum regime is blurred. A specific example is the Fe18 wheel, which displays quantum phase interference by allowing Neel vector tunneling in a magnetic field. Finally, the Co5Cl single-molecule magnet is shown to have an unusual anisotropic response to a magnetic field.
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.
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.
Molecular Scale Dynamics of Large Ring Polymers
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar
This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining...... the system size of the simulation box generally used in simulation. Therefore, a method is developed for extending the RDFs to arbitrary distances so that the integrals can be evaluated. The method, which was first used in the classical study of the Lennard-Jones fluid by Verlet (Verlet (1968), Phys. Rev...
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.
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamic simulation of directional crystal growth
Costa, B. V.; Coura, P. Z.; Mesquita, O. N.
1999-01-01
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach experimentally, being an important tool for further experimental and theoretical developments in the area of crystal growth.
Molecular dynamics - NMR experiments and simulations
Czech Academy of Sciences Publication Activity Database
Dračínský, Martin; Hodgkinson, P.; Kessler, Jiří; Bouř, Petr
Brno : Masaryk University Press, 2015 - (Sklenář, V.). s. 277-278 ISBN 978-80-210-7890-1. [EUROMAR 2015. 05.07.2015-10.07.2015, Praha] Institutional support: RVO:61388963 Keywords : molecular dynamics * NMR spectroscopy * MD simulations Subject RIV: CF - Physical ; Theoretical Chemistry
Reaction dynamics in polyatomic molecular systems
Energy Technology Data Exchange (ETDEWEB)
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
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...
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.
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
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.
International Nuclear Information System (INIS)
We investigated the characteristics of a capacitive nano-accelerometer based on a telescoping carbon nanotube by means of classical molecular dynamics simulations. The position of the telescoping nanotube was controlled by an externally applied force, and feedback sensing was based on the capacitance change. The capacitance variations, which were almost linearly proportional to the applied acceleration, were monitored within an error tolerance
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.
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.
Suzuki, Yasumitsu; Watanabe, Kazuyuki; Abedi, Ali; Agostini, Federica; Min, Seung Kyu; Maitra, Neepa; Gross, E. K. U.
The exact factorization of the electron-nuclear wave function allows to define the time-dependent potential energy surfaces (TDPESs) responsible for the nuclear dynamics and electron dynamics. Recently a novel coupled-trajectory mixed quantum-classical (CT-MQC) approach based on this TDPES has been developed, which accurately reproduces both nuclear and electron dynamics. Here we study the TDPES for laser-induced electron localization with a view to developing a MQC method for strong-field processes. We show our recent progress in applying the CT-MQC approach to the systems with many degrees of freedom.
Dynamical quenching of tunneling in molecular magnets
International Nuclear Information System (INIS)
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation
Dynamical quenching of tunneling in molecular magnets
Energy Technology Data Exchange (ETDEWEB)
José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)
2015-12-15
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.
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.
Long-Term Dynamics and the Orbital Inclinations of the Classical Kuiper Belt Objects
Kuchner, M J; Holman, M; Kuchner, Marc J.; Brown, Michael E.; Holman, Matthew
2002-01-01
We numerically integrated the orbits of 1458 particles in the region of the classical Kuiper Belt (41 AU < a < 47 AU) to explore the role of dynamical instabilities in sculpting the inclination distribution of the classical Kuiper Belt Objects (KBOs). We find that the selective removal of low-inclination objects by overlapping secular resonances (nu_17 and nu_18) acts to raise the mean inclination of the surviving population of particles over 4 billion years of interactions with Jupiter, Saturn, Uranus and Neptune, though these long-term dynamical effects do not themselves appear to explain the discovery of KBOs with inclinations near 30 degrees. Our integrations also imply that after 3 billion years of interaction with the massive planets, high inclination KBOs more efficiently supply Neptune-encountering objects, the likely progenitors of short-period comets, Centaurs, and scattered KBOs. The secular resonances at low inclinations may indirectly cause this effect by weeding out objects unprotected by ...
Hamiltonian Structure of the Schrödinger Classical Dynamical System
Tessarotto, Massimo; Mond, Michael; Batic, Davide
2016-05-01
The connection between quantum mechanics and classical statistical mechanics has motivated in the past the representation of the Schrödinger quantum-wave equation in terms of "projections" onto the quantum configuration space of suitable phase-space asymptotic kinetic models. This feature has suggested the search of a possible exact super-dimensional classical dynamical system (CDS), denoted as Schrödinger CDS, which uniquely determines the time-evolution of the underlying quantum state describing a set of N like and mutually interacting quantum particles. In this paper the realization of the same CDS in terms of a coupled set of Hamiltonian systems is established. These are respectively associated with a quantum-hydrodynamic CDS advancing in time the quantum fluid velocity and a further one the RD-CDS, describing the relative dynamics with respect to the quantum fluid.
Socio-Cultural Dynamics of Education in the Context of the Post-Non-Classical Science
Directory of Open Access Journals (Sweden)
V. A. Ignatova
2015-02-01
Full Text Available The paper deals with the interrelations between society, education and culture. Using the comparative analysis of classical approaches to defining the above spheres, the author comes to conclusion that the nature of socio-cultural processes can be explored and described most consistently by applying comprehensive models of the post-non-classical science and considering civilization, education and culture in the context of the unified dynamic flow of socio-cultural genesis. The research investigates the dialectics of socio-cultural processes in the light of systematic synergetic approach, the advancing role of education in socio-cultural dynamics being revealed and substantiated. The author emphasizes its inevitably rising priority due to sustained development of civilization bringing about the new environmentally-oriented meta-culture.The obtained results can be used in pedagogic research methodology, designing and modeling the educational process, its content, technology and organization.
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.
Nuclear alignment: classical dynamic model for 238U- 238U system
International Nuclear Information System (INIS)
Dynamical properties of 238U- 238U system at the classical turning point, specifically the distance of closest approach, the relative orientations of the nuclei and deformations have been studied at sub-coulomb energy of Elab = 6.07 MeV/nucleon using a classical dynamical model with a variable moment of inertia. Probability of favorable alignment for anomalous positron-electron pair emission through vacuum decay is calculated. The calculated small favorable alignment probability value of 0.116 is found to be enhanced by about 16% in comparison with the results of a similar study using a fixed moment of inertia as well as the results from a semiquantal calculation reported earlier. (author)
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...
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 ...
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...
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.)
Exciton dynamics in perturbed vibronic molecular aggregates.
Brüning, C; Wehner, J; Hausner, J; Wenzel, M; Engel, V
2016-07-01
A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840
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)
International Nuclear Information System (INIS)
The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories
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.
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
Molecular dynamics at constant Cauchy stress
Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio
2016-05-01
The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.
Simulation of Abrasive Machining Using Molecular Dynamics
Oluwajobi, Akinjide O.; Chen, Xun
2009-01-01
The development of ultra–precision processes which can achieve excellent surface finish and tolerance at nanometre level is now a critical requirement for many applications in medical, electronics and energy industry. Presently, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use of Molecular Dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis ...
Modelling abrasive machining techniques using molecular dynamics
Oluwajobi, Akinjide O.; Chen, Xun
2008-01-01
The development of ultra–precision processes which can achieve nanometre surface finishes and tolerances is now a critical requirement for many applications in medical, electronics and energy industry. Presently, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use Molecular Dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis of these processes at the nanometre scal...
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Molecular dynamics modelling of solidification in metals
Energy Technology Data Exchange (ETDEWEB)
Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)
1997-12-31
Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.
Molecular dynamics simulation of expanding infinite matter
International Nuclear Information System (INIS)
Multi-fragmentation occurred in an expanding infinite system is studied by using molecular dynamics simulation. To evaluate the secondary decay effect, the time evolution of expanding system is proceeded till all fragments are stabilized completely. The fragment mass distribution from the expansion is compared with a percolation model and the cause of the exponential shape is clarified. The cause of small critical temperature is also discussed. (author)
Molecular Dynamics with Helical Periodic Boundary Conditions
Czech Academy of Sciences Publication Activity Database
Kessler, Jiří; Bouř, Petr
2014-01-01
Roč. 35, č. 21 (2014), s. 1552-1559. ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant ostatní: GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014
Temperature Dependent Molecular Dynamic Simulation of Friction
Dias, R A; Coura, P Z; Costa, B V
2006-01-01
In this work we present a molecular dynamics simulation of a FFM experiment. The tip-sample interaction is studied by varying the normal force in the tip and the temperature of the surface. The friction force, cA, at zero load and the friction coefficient, $\\mu$, were obtained. Our results strongly support the idea that the effective contact area, A, decreases with increasing temperature and the friction coefficient presents a clear signature of the premelting process of the surface.
Simulating granular flow with molecular dynamics
Ristow, Gerald
1992-01-01
We investigate by means of Molecular Dynamics simulations an assembly of spheres to model a granular medium flowing from an upper rectangular chamber through a hole into a lower chamber. Two different two dimensional models are discussed one of them including rotations of the individual spheres. The outflow properties are investigated and compared to experimental data. The qualitative agreement suggests that our models contain the necessary ingredients to describe the outflow properties of gr...
Molecular dynamics simulations using graphics processing units
Baker, J.A.; Hirst, J.D.
2011-01-01
It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation com...
Molecular Dynamics Studies of Nanofluidic Devices
DEFF Research Database (Denmark)
Zambrano Rodriguez, Harvey Alexander
of transport mechanism to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe...... the molecular dynamics methodology. In the second part of this thesis, we present the results of three different research projects. Fristly, we present a computational study of thermophoresis as a suitable mechanism to drive water droplets confined in different types of carbon nanotubes. We observe a...... motion of the water droplet in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The...
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.
Control Volume Representation of Molecular Dynamics
Smith, E R; Dini, D; Zaki, T A
2012-01-01
A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of [1] Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' Transport Theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-Control-Volume (LCV) conversion function \\vartheta_{i}, for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the Volume Average (VA, [2] Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, [3] Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges natu...
Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.
Dybeck, Eric C; König, Gerhard; Brooks, Bernard R; Shirts, Michael R
2016-04-12
We examine methods to reweight classical molecular mechanics solvation calculations to more expensive QM/MM energy functions. We first consider the solvation free energy difference between ethane and methanol in a QM/MM Hamiltonian from configurations generated in a cheaper MM potential. The solute molecules in the QM/MM Hamiltonian are treated with B3LYP/6-31G*, and the solvent water molecules are treated classically. The free energy difference in the QM/MM Hamiltonian is estimated using Boltzmann reweighting with both the non-Boltzmann Bennett method (NBB) and the multistate Bennett acceptance ratio (MBAR), and the variance of each method is directly compared for an identical data set. For this system, MBAR-derived methods are found to produce smaller overall uncertainties than NBB-based methods. Additionally, we show that to reduce the variance in the overall free energy difference estimate in this system for a fixed amount of QM/MM calculations, the energy re-evaluations in the Boltzmann reweighting step should be concentrated on the physical MM states with the highest overlap to the QM/MM states, rather than allocated equally over all sampled MM states. We also show that reallocating the QM/MM re-evaluations can be used to diagnose poor overlap between the sampled and target state. The solvation free energies for molecules in the SAMPL4 solvation data set are also calculated in the QM/MM Hamiltonian with NBB and MBAR, and the variances are marginally smaller for MBAR. Overall, NBB and MBAR produce similar variances for systems with poor sampling efficiency, and MBAR provides smaller variances than NBB in systems with high sampling efficiency. Both NBB and MBAR converge to identical solvation free energy estimates in the QM/MM Hamiltonian, and the RMSD to experimental values for molecules in the SAMPL4 solvation data set decreases by approximately 28% when switching from the MM Hamiltonian to the QM/MM Hamiltonian. PMID:26928941
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Directory of Open Access Journals (Sweden)
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
Wigner's dynamical transition state theory in phase space: classical and quantum
International Nuclear Information System (INIS)
We develop Wigner's approach to a dynamical transition state theory in phase space in both the classical and quantum mechanical settings. The key to our development is the construction of a normal form for describing the dynamics in the neighbourhood of a specific type of saddle point that governs the evolution from reactants to products in high dimensional systems. In the classical case this is the standard Poincaré–Birkhoff normal form. In the quantum case we develop a normal form based on the Weyl calculus and an explicit algorithm for computing this quantum normal form. The classical normal form allows us to discover and compute the phase space structures that govern classical reaction dynamics. From this knowledge we are able to provide a direct construction of an energy dependent dividing surface in phase space having the properties that trajectories do not locally 're-cross' the surface and the directional flux across the surface is minimal. Using this, we are able to give a formula for the directional flux through the dividing surface that goes beyond the harmonic approximation. We relate this construction to the flux–flux autocorrelation function which is a standard ingredient in the expression for the reaction rate in the chemistry community. We also give a classical mechanical interpretation of the activated complex as a normally hyperbolic invariant manifold (NHIM), and further describe the structure of the NHIM. The quantum normal form provides us with an efficient algorithm to compute quantum reaction rates and we relate this algorithm to the quantum version of the flux–flux autocorrelation function formalism. The significance of the classical phase space structures for the quantum mechanics of reactions is elucidated by studying the phase space distribution of scattering states. The quantum normal form also provides an efficient way of computing Gamov–Siegert resonances. We relate these resonances to the lifetimes of the quantum activated
A Concurrent Multiscale Micromorphic Molecular Dynamics. Part I. Theoretical Formulation
Li, Shaofan
2014-01-01
Based on a novel concept of multiplicative multiscale decomposition, we have derived a multiscale micromorphic molecular dynamics (MMMD)to extent the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and macroscale. The multiscale micromorphic molecular dynamics is a con-current three-scale particle dynamics that couples a fine scale molecular dynamics, a mesoscale particle dynamics of micromorphic medium, and a coarse scale nonlocal particle dynamics of nonlinear continuum. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and it is a special case of the proposed multiscale micromorphic molecular dynamics. The discovered mutiscale structure and the corresponding multiscale dynamics reveal a seamless transition channel from atomistic scale to continuum scale and the intrinsic coupling relation among them, and it can be used to solve finite size nanoscale sc...
Molecular Dynamics Studies of Initiation in Energetic Materials
Haskins, P.
1995-01-01
In this paper an overview of Molecular Dynamics simulations of chemically reacting systems is described. In particular, molecular dynamics simulations of shock initiation in a model energetic material are reported. The use of Molecular Dynamics to model thermal initiation and determine reactions rates in energetic materials is also discussed. Finally, the future potential of MD techniques for energetic materials applications is considered.
Dynamical structure of fluid mercury: Molecular-dynamics simulations
Hoshino, Kozo; Tanaka, Shunichiro; Shimojo, Fuyuki
2007-01-01
We have carried out molecular-dynamics simulations for nonmetallic fluid mercury in liquid and vapor phases using a Lennard-Jones type effective potential and shown that the structure factors S(Q) and the dynamic structure factors S(Q, omega) of nonmetallic fluid mercury obtained by our MD simulations are in good agreement with recent X-ray diffraction and inelastic X-ray scattering experiments. We conclude from these results that, though the fluid mercury which shows a metal-nonmetal transit...
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.
Molecular dynamics simulation of hydrogen isotope injection into graphene
International Nuclear Information System (INIS)
We reveal the hydrogen isotope effect of three chemical reactions, i.e., the reflection, the absorption and the penetration ratios, by classical molecular dynamics simulation with a modified Brenner's reactive empirical bond order (REBO) potential. We find that the reflection by π-electron does not depend on the mass of the incident isotope, but the peak of the reflection by nuclear moves to higher side of incident energy. In addition to the reflection, we also find that the absorption ratio in the positive z side of the graphene becomes larger, as the mass of the incident isotope becomes larger. On the other hand, the absorption ratio in the negative z side of the graphene becomes smaller. Last, it is found that the penetration ratio does not depend on the mass of the incident isotope because the graphene potential is not affected by the mass. (author)
"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
Application of optimal prediction to molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Barber IV, John Letherman
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
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.
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.
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 .
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.
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.
Molecular dynamic results on transport properties
Energy Technology Data Exchange (ETDEWEB)
Alder, B.J.; Alley, W.E.
1978-06-01
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so.
Molecular dynamic results on transport properties
International Nuclear Information System (INIS)
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so
Electronic continuum model for molecular dynamics simulations.
Leontyev, I V; Stuchebrukhov, A A
2009-02-28
A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627
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
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.
Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
2016-01-01
Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations. PMID:26733483
Molecular dynamics studies of aromatic hydrocarbon liquids
International Nuclear Information System (INIS)
This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules
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.
A study on melting process of perylene using molecular dynamics simulation
Directory of Open Access Journals (Sweden)
M Peyvasteh
2014-11-01
Full Text Available Melting process of perylene is investigated using molecular dynamics simulation. Some of thermodynamic properties such as potential energy and transition order parameter are calculated as a function of temperature in the range of 500 K-600 K. These calculations are performed by two different methods in NPT and NVT ensembles. The selected interaction potential is Re-squared and the simulations are performed by LAMMPS (a classic molecular dynamics code. The results show that NPT ensemble is more appropraite for the study of melting process than NVT ensemble and shows a good agreement with experimental melting temperature.
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
Continuous Finite Element Methods of Molecular Dynamics Simulations
Qiong Tang; Luohua Liu; Yujun Zheng
2015-01-01
Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite elemen...
Parallelization of quantum molecular dynamics simulation code
International Nuclear Information System (INIS)
A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)
Ab Initio Molecular Dynamics: A Virtual Laboratory
Hobbi Mobarhan, Milad
2014-01-01
In this thesis, we perform ab initio molecular dynamics (MD) simulations at the Hartree-Fock level, where the forces are computed on-the-fly using the Born-Oppenheimer approximation. The theory behind the Hartree-Fock method is discussed in detail and an implementation of this method based on Gaussian basis functions is explained. We also demonstrate how to calculate the analytic energy derivatives needed for obtaining the forces acting on the nuclei. Hartree-Fock calculations on the ground s...
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
Electrostatic Energy Calculations for Molecular Dynamics
Love, M J; Comment, Henri J.F. Jansen; Love, Michael J.
1995-01-01
The evaluation of Coulomb forces is a difficult task. The summations that are involved converge only conditionally and care has to be taken in selecting the appropriate procedure to define the limits. The Ewald method is a standard method for obtaining Coulomb forces, but this method is rather slow, since it depends on the square of the number of atoms in a unit cell. In this paper we have adapted the plane-wise summation method for the evaluation of Coulomb forces. The use of this method allows for larger computational cells in molecular dynamics calculations.
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
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.
Molecular dynamics at constant temperature and pressure
Toxvaerd, S.
1993-01-01
Algorithms for molecular dynamics (MD) at constant temperature and pressure are investigated. The ability to remain in a regular orbit in an intermittent chaotic regime is used as a criterion for long-time stability. A simple time-centered algorithm (leap frog) is found to be the most stable of the commonly used algorithms in MD. A model of N one-dimensional dimers with a double-well intermolecular potential, for which the distribution functions at constant temperature T and pressure P can be calculated, is used to investigate MD-NPT dynamics. A time-centered NPT algorithm is found to sample correctly and to be very robust with respect to volume scaling.
Fermionic Molecular Dynamics and short range correlations
Feldmeier, H; Roth, R S; Schnack, J
1998-01-01
Fermionic Molecular Dynamics (FMD) models a system of fermions by means of many-body states which are composed of antisymmetrized products of single-particle states. These consist of one or several Gaussians localized in coordinate and momentum space. The parameters specifying them are the dynamical variables of the model. As the repulsive core of the nucleon-nucleon interaction induces short range correlations which cannot be accommodated by a Slater determinant, a novel approach, the unitary correlation operator method (UCOM), is applied. The unitary correlator moves two particles away from each other whenever their relative distance is within the repulsive core. The time-dependent variational principle yields the equations of motion for the variables. Energies of the stationary ground states are calculated and compared to exact many-body results for nuclei up to Ca 48. Time-dependent solutions are shown for collisions between nuclei.
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.
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.
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.
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.
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
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
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.
Multiple branched adaptive steered molecular dynamics
Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
2014-08-01
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient "multiple branching" (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.
International Nuclear Information System (INIS)
This thesis develops a new model, and related numerical methods, to describe classical time-dependent many-body systems interacting through central forces, spin-orbit forces and spin-spin forces. The model is based on two-particle interactions. The two-body forces consist of attractive and repulsive parts. In this model the investigated multi-particle systems are self-bound. Also the total potential of the whole ensemble is derived from the two-particle potential and is not imposed 'from outside'. Each particle has the three degrees of freedom of its centre-of-mass motion and the spin degree of freedom. The model allows for the particles to be either charged or uncharged. Furthermore, each particle has an angular momentum, an intrinsic spin, and a magnetic dipole moment. Through the electromagnetic forces between these charges and moments there arise dynamical couplings between them. The internal interactions between the charges and moments are well described by electromagnetic coupling mechanisms. In fact, compared to conventional classical molecular dynamics calculations in van der Waals clusters, which have no spin degrees of freedom, or for Heisenberg spin Systems, which have no orbital degrees of freedom, the model presented here contains both types of degrees of freedom with a highly non-trivial coupling. The model allows to study the fundamental effects resulting from the dynamical coupling of the spin and the orbital-motion sub-systems. In particular, the dynamics of the particle mass points show a behaviour basically different from the one of particles in a potential with only central forces. Furthermore, a special type of quenching procedure was invented, which tends to drive the multi-particle Systems into states with highly periodic, non-ergodic behaviour. Application of the model to cluster simulations has provided evidence that the model can also be used to investigate items like solid-to-liquid phase transitions (melting), isomerism and specific heat
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.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
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.
The 2011 Dynamics of Molecular Collisions Conference
Energy Technology Data Exchange (ETDEWEB)
Nesbitt, David J. [JILA, NIST
2011-07-11
The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor
A scheme to combine molecular dynamics and dislocation dynamics
International Nuclear Information System (INIS)
Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake. (paper)
Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.
2009-01-01
Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and mu...
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
Color Molecular-Dynamics for High Density Matter
Maruyama, Toshiki; Hatsuda, Tetsuo
1999-01-01
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Statistical feature and the dynamical change between confinement and deconfinement phases are studied with this molecular dynamics simulation.
Dynamical structure factor and collective modes in classical one-component plasmas
International Nuclear Information System (INIS)
The dynamical structure factor and collective modes in classical one-component plasmas are studied by employing the memory-function formalism. A response function for density fluctuations of ions in the system is treated in a self-consistent manner to express it in terms of that of a free ion system and an effective potential. An exact formal expression for the effective potential is composed of two parts, static and dynamic, the latter originating from an interaction-part of a second order memory function (ISMF). By studying the properties of the effective potential and of dampings of collective modes, the latter of which are separated into Landau damping and collisional damping, a criterion for the appearance of collective modes in intermediate wave number and frequency domains is obtained as a simple inequality. The dynamical structure factor is calculated by evaluating characteristic frequencies associated with several elementary factors of dynamics of ions in the system and by taking the ISMF to be Gaussian. The result so obtained is compared with the computer-experimental data of Hansen et al. Fairly good agreement with the experimental data is obtained for the plasma parameters 0.993 <= GAMMA <= 152.4. (author)
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.
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
International Nuclear Information System (INIS)
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
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 ...
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 ...
Molecular dynamics study of solvation effects on acid dissociation in aprotic media
Laria, Daniel; Kapral, Raymond; Estrin, Dario; Ciccotti, Giovanni
1996-01-01
Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solven...
Molecular dynamics simulations of precursor-derived Si-C-N ceramics
Resta, Nicoletta
2005-01-01
The microscopic mechanisms behind the transformation from the amorphous Si-C-N ceramics to the polycrystalline material are studied by isolating its fundamental steps. Si-C-N amorphous ceramics, amorphous and crystalline silicon carbide, and carbon, are numerically modeled by means of classical molecular dynamics. The interatomic interactions are modeled by the Tersoff many-body empirical potential. In the first part amorphous Si-C-N materials are studied. We show how the atomic structures...
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...
Savin, Alexander V; Cantarero, Andres
2011-01-01
We present a detailed description of the semi-quantum approach to the molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian equations of motion in which the quantum effects are introduced through random Langevin-like forces with a specific power spectral density (the color noise). The color noise describes the interaction of the molecular system with the thermostat. We apply this technique to the simulation of the thermal properties of different low-dimensional nanostructures. Within this approach, we simulate the specific heat and heat transport in carbon nanotubes, as well as the thermal transport in a molecular nanoribbon with rough edges and in a nanoribbon with a strongly anharmonic periodic interatomic potential. We show that the existence of rough edges and quantum statistics of phonons change drastically the thermal conductivity of the rough-edge nanoribbon in comparis...
Molecular dynamics study of the mechanical loss in amorphous pure and doped silica
International Nuclear Information System (INIS)
Gravitational wave detectors and other precision measurement devices are limited by the thermal noise in the oxide coatings on the mirrors of such devices. We have investigated the mechanical loss in amorphous oxides by calculating the internal friction using classical, atomistic molecular dynamics simulations. We have implemented the trajectory bisection method and the non-local ridge method in the DL-POLY molecular dynamics simulation software to carry out those calculations. These methods have been used to locate the local potential energy minima that a system visits during a molecular dynamics trajectory and the transition state between any two consecutive minima. Using the numerically calculated barrier height distributions, barrier asymmetry distributions, relaxation times, and deformation potentials, we have calculated the internal friction of pure amorphous silica and silica mixed with other oxides. The results for silica compare well with experiment. Finally, we use the numerical calculations to comment on the validity of previously used theoretical assumptions
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.
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.
Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS
Astuti, A. D.; Mutiara, A. B.
2009-01-01
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example of molecular dynamics application developed by Groningen University. This application is a non-commercial and able to work in the operating system Linux. The main ability of Gromacs is to perform molecular dynamics simulation and minimization energy. In this...
Horner, Daniel A.
2008-01-01
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 at s...
Molecular dynamics simulations of shock compressed graphite
International Nuclear Information System (INIS)
We present molecular dynamic simulations of the shock compression of graphite with the LCBOPII potential. The range of shock intensities covers the full range of available experimental data, including near-tera-pascal pressures. The results are in excellent agreement with the available DFT data and point to a graphite-diamond transition for shock pressures above 65 GPa, a value larger than the experimental data (20 to 50 GPa). The transition mechanism leads preferentially to hexagonal diamond through a diffusion-less process but is submitted to irreversible re-graphitization upon release: this result is in good agreement with the lack of highly ordered diamond observed in post-mortem experimental samples. Melting is found for shock pressures ranging from 200 to 300 GPa, close to the approximate LCBOPII diamond melting line. A good overall agreement is found between the calculated and experimental Hugoniot data up to 46% compression rate. (authors)
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
Schwabe, Tobias
2015-08-20
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
Molecular dynamics simulation of laser shock phenomena
Energy Technology Data Exchange (ETDEWEB)
Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).
2001-10-01
Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)
Statistical mechanics and dynamics of molecular fragmentation
Energy Technology Data Exchange (ETDEWEB)
Quack, M. (Goettingen Univ. (Germany, F.R.). Inst. fuer Physikalische Chemie)
1981-05-11
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored.
Statistical mechanics and dynamics of molecular fragmentation
International Nuclear Information System (INIS)
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored. (author)
Cell list algorithms for nonequilibrium molecular dynamics
Dobson, Matthew; Fox, Ian; Saracino, Alexandra
2016-06-01
We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.
Superdeformed $\\Lambda$ hypernuclei with antisymmetrized molecular dynamics
Isaka, Masahiro; Kimura, Masaaki; Hiyama, Emiko; Sagawa, Hiroyuki; Yamamoto, Yasuo
2014-01-01
The response to the addition of a $\\Lambda$ hyperon is investigated for the deformed states such as superdeformation in $^{41}_\\Lambda$Ca, $^{46}_\\Lambda $Sc and $^{48}_\\Lambda$Sc. In the present study, we use the antisymmetrized molecular dynamics (AMD) model. It is pointed out that many kinds of deformed bands appear in $^{45}$Sc and $^{47}$Sc. Especially, it is found that there exists superdeformed states in $^{45}$Sc. By the addition of a $\\Lambda$ particle to $^{40}$Ca, $^{45}$Sc and $^{47}$Sc, it is predicted, for the first time, that the superdeformed states exist in the hypernuclei $^{41}_\\Lambda$Ca and $^{46}_\\Lambda$Sc. The manifestation of the dependence of the $\\Lambda$-separation energy on nuclear deformation such as spherical, normal deformation and superdeformation is shown in the energy spectra of $^{41}_\\Lambda$Ca, $^{46}_\\Lambda $Sc and $^{48}_\\Lambda$Sc hypernuclei.
Molecular Dynamics Simulations for Predicting Surface Wetting
Directory of Open Access Journals (Sweden)
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Nonequilibrium molecular dynamics: The first 25 years
International Nuclear Information System (INIS)
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments
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
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
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
International Nuclear Information System (INIS)
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
Iterative quantum-classical path integral with dynamically consistent state hopping
Walters, Peter L.; Makri, Nancy
2016-01-01
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.
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.
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
International Nuclear Information System (INIS)
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, Cesar D. [Comision Nacional de Energia Atomica, Centro Atomico Bariloche, Instituto Balseiro, Bariloche (Argentina); Lombardo, Fernando C. [Ciudad Universitaria, Departamento de Fisica Juan Jose Giambiagi, FCEyN UBA y IFIBA CONICET-UBA, Facultad de Ciencias Exactas y Naturales, Buenos Aires (Argentina)
2015-12-15
We study the properties of the classical electromagnetic radiation produced by two physically different yet closely related systems, which may be regarded as classical analogues of the dynamical Casimir effect. They correspond to two flat, infinite, parallel planes, one of them static and imposing perfect-conductor boundary conditions, while the other performs a rigid oscillatory motion. The systems differ just in the electrical properties of the oscillating plane: one of them is just a planar dipole layer (representing, for instance, a small-width electret). The other, instead, has a dipole layer on the side which faces the static plane, but behaves as a conductor on the other side: this can be used as a representation of a conductor endowed with patch potentials (on the side which faces the conducting plane). We evaluate, in both cases, the dissipative flux of energy between the system and its environment, showing that, at least for small mechanical oscillation amplitudes, it can be written in terms of the dipole layer autocorrelation function. We show that there are resonances as a function of the frequency of the mechanical oscillation. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Fosco, César D. [Centro Atómico Bariloche, Instituto Balseiro, Comisión Nacional de Energía Atómica, R8402AGP, Bariloche (Argentina); Lombardo, Fernando C., E-mail: lombardo@df.uba.ar [Departamento de Física Juan José Giambiagi, FCEyN UBA and IFIBA CONICET-UBA, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Pabellón I, 1428, Buenos Aires (Argentina)
2015-12-17
We study the properties of the classical electromagnetic radiation produced by two physically different yet closely related systems, which may be regarded as classical analogues of the dynamical Casimir effect. They correspond to two flat, infinite, parallel planes, one of them static and imposing perfect-conductor boundary conditions, while the other performs a rigid oscillatory motion. The systems differ just in the electrical properties of the oscillating plane: one of them is just a planar dipole layer (representing, for instance, a small-width electret). The other, instead, has a dipole layer on the side which faces the static plane, but behaves as a conductor on the other side: this can be used as a representation of a conductor endowed with patch potentials (on the side which faces the conducting plane). We evaluate, in both cases, the dissipative flux of energy between the system and its environment, showing that, at least for small mechanical oscillation amplitudes, it can be written in terms of the dipole layer autocorrelation function. We show that there are resonances as a function of the frequency of the mechanical oscillation.
Molecular Dynamic Simulation of Failure of Ettringite
International Nuclear Information System (INIS)
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
Molecular Dynamic Simulation of Failure of Ettringite
Sun, W.; Wang, D.; Wang, L.
2013-03-01
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
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 ...
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.
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.
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.
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...
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...
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
Molecular dynamics studies on nanoscale gas transport
Barisik, Murat
Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the
Junghans, Christoph; Perez, Danny; Vogel, Thomas
2014-01-01
We show direct formal relationship between the Wang-Landau iteration [PRL 86, 2050 (2001)], metadynamics [PNAS 99, 12562 (2002)] and statistical temperature molecular dynamics [PRL 97, 050601 (2006)], the major Monte Carlo and molecular dynamics work-horses for sampling from a generalized, multicanonical ensemble. We demonstrate that statistical temperature molecular dynamics (which is formally derived from the Wang-Landau method), augmented by the introduction of kernel updates of the statis...
Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules
International Nuclear Information System (INIS)
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wave packet calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics
Horner, D A; Miyabe, S; Rescigno, T N; McCurdy, C W; Morales, F; Martín, F
2008-10-31
Recent experiments on double photoionization of H2 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 at substantially higher photon energies. At the energies considered in the experiment we offer an alternative explanation based on the mixing of two nondiffractive contributions by circularly polarized light. PMID:18999826
Molecular Dynamics Investigated by Neutron Scattering
International Nuclear Information System (INIS)
A short review of the present state of the problem of applicability of the Krieger-Nelkin theory as well as of the Griffing theory to gases is made. Then, on the basis of experiments with liquid methane, the applicability of the mass-tensor concept to molecules in condensed states is criticized. Strong arguments against the application of the Krieger-Nelkin theory to condensed states are: a shift of neutron energy distribution after scattering towards higher energies and the lack of dependence of the Inelastic part on the scattering angle. Further sections deal with the rotational dynamics of ammonium groups in ammonium compounds. Most of the experimental material is discussed in connection with ammonium halides on the basis of experiments by different authors. For some substances a freedom of rotation of NH4 groups was obtained from neutron measurements, whereas for some others the rotation goes over into torsional vibration. In this case, frequencies of torsional vibrations obtained by various authors from neutron experiments were compared with those obtained from infrared spectroscopy and specific heat measurements. The barrier-to-rotation evaluation from total neutron cross-section measurements is also discussed. Further a comparison is made of the rotational dynamics of NH4 groups in NH4CIO4 and H3O groups in H3OCIO4 on the basis of neutron inelastic scattering experiments. A free rotation of the NH4 group in ammonium perchlorate was obtained even at temperatures as low as liquid nitrogen temperature. For H3OCIO4 a torsional vibration of the H3O group with a frequency of 497 cm-1 was obtained. So in spite of the identity of the crystal lattices of NH4CIO4 and H3OCIO4 the dynamics of the NH4 and H3O groups are different. The results are compared with those known from Raman spectroscopy and nuclear magnetic resonance. Finally, a number of other substances is discussed from the point of view of molecular dynamics. (author)
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
International Nuclear Information System (INIS)
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom
Classic and molecular cytogenetic analysis regarding human reactivity to beta radiation
International Nuclear Information System (INIS)
Complete text of publication follows. One of the most important mutagen agents in developing different types of cancer is the action of ionizing radiation. The main events induced by irradiation are: chromosome breakage, chromosome rearrangements and genomic instability. The chromosomal aberrations are very useful biomarkers as intermediate end points in evaluating harmful biological effects of ionizing radiation. So, the main objectives of this work were: the study of human genome reactivity to beta radiation by classic microscopy; the study of the integrity/modification of the telomeres after irradiation and the analysis of the amplification of the RNA telomerase compound by FISH technique. Irradiations were performed at Electron Accelerators Laboratory, National Institute for Laser, Plasma and Radiation Physics, Magurele-Bucharest, Romania. The samples were irradiated using an ALIN 10 linear electron accelerator. ALIN 10 is a travelling wave type linac operating at 2.998 GHz, 6.5 MeV mean energy, with a 0.1 mm Al foil exit window. Improved Fricke, ferrous sulphate, cupric sulphate and sulphuric acid in triple distilled water dosimetry system has been used to perform preliminary dose measurements. The conventional Hungerford method on short-term cultures for 72 hrs was adapted for human chromosome investigation. The peripheral blood was collected from aged 27, healthy, non-smoker donor. The doses used to irradiate human blood cultures were: 4, 6, 8 and 10 Gy. The slides for optic microscopy were prepared by air-drying and stained with a 10% Giemsa solution. For FISH technique was used Chromosome In Situ Hybridization Kit. The probes were: one satellite probe - for revealing the telomere and the second one for the RNA telomerase compound. A large spectrum of chromosomal rearrangements was induced by beta irradiation in humans in vitro: complex chromosomal interchange involving at least two nonhomologous chromosomes, double minutes (DM), acentric fragments
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
Rakesh, L.
2009-09-01
Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the
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
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 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...
How Dynamic Visualization Technology Can Support Molecular Reasoning
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
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.
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.
Imaging the Breakdown of Molecular Frame Dynamics through Rotational Uncoupling
Zipp, Lucas J; Bucksbaum, Philip H
2016-01-01
We have observed directly in the time domain the uncoupling of electron motion from the molecular frame due to rotational-electronic coupling in a molecular Rydberg system. In contrast to Born- Oppenheimer dynamics, in which the electron is firmly fixed to the molecular frame, there exists a regime of molecular dynamics known as $l$-uncoupling where the motion of a non-penetrating Rydberg electron decouples from the instantaneous alignment of the molecular frame. We have imaged this unusual regime in time-dependent photoelectron angular distributions of a coherently prepared electron wave packet in the 4$f$ manifold of $N_2$.
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
International Nuclear Information System (INIS)
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed. (c) 1999 American Institute of Physics
The MOLDY short-range molecular dynamics package
Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.
2011-12-01
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as
Ab initio molecular dynamics calculations of ion hydration free energies
International Nuclear Information System (INIS)
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or 'λ-path' technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (φ) contributions, we obtain absolute AIMD hydration free energies (ΔGhyd) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model φ predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD ΔGhyd, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+→Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of ΔGhyd for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.
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.
Behavior of sodium borosilicate glasses under compression using molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Kilymis, D. A.; Ispas, S., E-mail: simona.ispas@univ-montp2.fr [Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Université de Montpellier, F-34095 Montpellier (France); Delaye, J.-M. [CEA, DEN, DTCD, SECM, F-30207 Bagnols-sur-Cèze (France)
2015-09-07
We have performed classical molecular dynamics simulations in order to study the changes under compression in the local and medium range structural properties of three sodium borosilicate glasses with varying sodium content. These glasses have been isostatically compressed up to 20 GPa and then decompressed in order to analyze the different mechanisms that affect densification, alongside with the permanent modifications of the structure after a full compression/decompression cycle. The results show that the atomic packing is the prominent characteristic that governs the amount of densification in the glass, as well as the setup of the permanent densification. During compression, the bulk modulus increases linearly up to approximately 15 GPa and more rapidly for higher pressures, a behavior which is reflected on the rate of increase of the average coordination for B and Na. Radial distribution functions at different pressures during the cycle help to quantify the amount of distortions in the elementary structural units, with a pronounced shortening of the Na–Na and Na–O bond lengths during compression. A subsequent decomposition of the glassy matrix into elementary Voronoi volumes verifies the high compressibility of Na-rich regions.
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...
Force field development for molecular dynamics simulations of clay minerals
International Nuclear Information System (INIS)
Document available in extended abstract form only. Clay minerals and their interfaces with aqueous solutions play an important role in many subsurface processes, including the retention and transport of aqueous species. Molecular simulations provide atomistic details of structural and dynamic properties of these fine-grained minerals that are difficult to obtain experimentally. Our research focus has been classical simulations of bulk clay minerals and their basal surfaces and interfaces using the fully flexible Clayff energy force field. Clayff is compatible with other force fields based on electrostatic and van der Waals interactions, permitting the study of a wide range of inorganic and organic solute at clay interfaces. Trends in clay swelling and ion adsorption onto the basal surfaces of clays are accurately described using this force field approach. Adsorption at pH-dependent edge sites is beyond the original scope of Clayff but is critical to a complete understanding of radionuclide transport near radioactive waste repositories. The application of Clayff to such edge sites requires three-body angle bend terms, and our recent work has involved parameterizing the hydroxylated edge site species (Mg-O-H, Al-O-H, and Si-O-H) found in end member models. (authors)
International Nuclear Information System (INIS)
We investigate a two-level atom interacting with a quantized cavity field and a classical driving field in the presence of phase decoherence and find that a stationary quantum discord can arise in the interaction of the atom and cavity field as the time turns to infinity. We also find that the stationary quantum discord can be increased by applying a classical driving field. Furthermore, we explore the quantum discord dynamics of two identical non-interacting two-level atoms independently interacting with a quantized cavity field and a classical driving field in the presence of phase decoherence. Results show that the quantum discord between two atoms is more robust than entanglement under phase decoherence and the classical driving field can help to improve the amount of quantum discord of the two atoms. (general)
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
International Nuclear Information System (INIS)
Research highlights: → Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. → Half height widths are used in modeling of Lorentzian doublets. → Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Energy Technology Data Exchange (ETDEWEB)
Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy)
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
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 ...
Rodríguez-Lara, B M
2012-01-01
The stability analysis of a generalized Dicke model, in the semi-classical limit, describing the interaction of a two-species Bose-Einstein condensate driven by a quantized field in the presence of Kerr and spontaneous parametric processes is presented. The transitions from Rabi to Josephson dynamics are identified depending on the relative value of the involved parameters. Symmetry-breaking dynamics are shown for both types of coherent oscillations due to the quantized field and nonlinear optical processes.
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 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.
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 ...
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.
Modeling shockwave deformation via molecular dynamics
International Nuclear Information System (INIS)
Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too
Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics
Lin, Lin; Shao, Sihong
2013-01-01
We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition as well as the accuracy of TRBOMD for computing physical properties such as the phonon frequency obtained from the molecular dynamic simulation. We connect and compare TRBOMD with the Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one dimensional model for Kohn-Sham density functional theory.
Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics
Directory of Open Access Journals (Sweden)
Lin Lin
2013-12-01
Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.
Nonadiabatic nuclear dynamics of atomic collisions based on branching classical trajectories
International Nuclear Information System (INIS)
The branching classical trajectory method for inelastic atomic collision processes is proposed. The approach is based on two features: (i) branching of a classical trajectory in a nonadiabatic region and (ii) the nonadiabatic transition probability formulas particularly adapted for a classical trajectory treatment. In addition to transition probabilities and inelastic cross sections, the proposed approach allows one to calculate incoming and outgoing currents. The method is applied to inelastic Na + H collisions providing the results in reasonable agreement with full quantum calculations.
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.
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
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.
Molecular Dynamics Studies of Structure, Dynamics and Dielectric Response in a Relaxor Ferroelectric
Grinberg, Ilya
2012-02-01
Since the first synthesis of the classic PbMg1/3Nb2/3O3 (PMN) material in 1961, relaxor ferroelectrics have been the subject of ongoing experimental and theoretical investigation due to their fundamental scientific interest and their importance in technological applications. We use atomistic molecular dynamics simulations to study relaxor behavior in the 0.75PMN-0.25PT material. Even for a fairly small simulation size of 1000 atoms, the system exhibits frequency dispersion and deviation from the Curie-Weiss law typical of relaxor materials. Analysis of the time autocorrelation functions for individual atoms allows us to identify the Nb atoms with a high concentration of neighboring Ti atoms as the nucleation sites for the relaxor behavior. This is due to the higher coupling between the cation displacements induced by the presence of overbonded oxygen atoms. We also analyze local structure and dynamics in PMN-PT using instantaneous, time-averaged and frequency resolved pair distribution functions (PDF). We find that dynamic Pb and Ti off-centering is present even in the paraelectric phase, below Tb the rate of growth of local Pb off-centering increases, followed by the freezing in of the local displacement direction at an intermediate temperature Tc and a transition to a ferroelectric-like phase at Tf. Thus there is a sequence of four phases, PE, dynamic relaxor, mixed dynamic and frozen phase, and the non-ergodic frozen relaxor phase. We identify the average instantaneous local cation off-centering as the order parameter for the dynamic relaxor phase, and the time-averaged local cation off-centering as the order parameter for the two lower-temperatures relaxor phases. Examination of the dynamic PDF data reveals the shape and the range of correlation between the cation displacements. We also show that the relaxor phase is characterized by the appearance of strong nearest-neighbor correlation between the off-center displacements along the Cartesian directions.
Modelling of Spectroscopic and Structural Properties using Molecular Dynamics
Francesco Muniz Miranda
2013-01-01
The following dissertation is about the study that I performed at the Chemistry Department of the University of Florence and at the European Laboratory for Non- Linear Spectroscopy (LENS) to recover and elucidate structural, dynamical, and spectroscopic molecular features adopting computer simulations. In particular, here ab initio molecular dynamics simulations and time-frequency analysis are the most employed “tools”, in order to have a better understanding of the origins ...
Multi CPU clusters and calculations by molecular dynamics method
International Nuclear Information System (INIS)
The technical characteristics of multi CPU (Central Processor Unit) clusters in Institute of Ion-Plasma and Laser Technologies AS RUz and Institute of Mathematics and Information Technologies AS RUz are described. There is detail information about cluster s architecture, installed programs and their productivity for decision of molecular dynamics tasks. Molecular dynamics program packages GROMACS, OPENMX and AutoDock-4.2.3 are described. The results of calculations using these program packages are presented. (author)
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
International Nuclear Information System (INIS)
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)
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)
Current-driven dynamics in molecular-scale devices
International Nuclear Information System (INIS)
We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)
Statistical Properties of the Dense Hydrogen Plasma an ab initio Molecular Dynamics Investigation
Kohanoff, J J; Kohanoff, Jorge; Hansen, Jean-Pierre
1996-01-01
The metallic regime of the hydrogen plasma is studied by ab initio Molecular Dynamics simulations, for classical protons and fully degenerate electrons, in the strong coupling regime of the protons. The breakdown of linear screening observed for decreasing density gives rise to a surprisingly rich low-temperature phase diagram, showing in particular a dramatic drop of the melting temperature of the proton crystal. Extensive dynamical simulations reveal the remarkable persistence of a weakly damped high-frequency ion acoustic mode (plasmon-like), even under conditions of strong electron screening. This collective mode should disappear in the molecular phase, thus providing a probe for the metal-insulator transition in a region of parameters where experiment is difficult to achieve. Finite-size effects arising in the simulation of liquid metals are discussed. The status of the dense Hydrogen matter is extensively reviewed in the introduction.
International Nuclear Information System (INIS)
We have investigated the radius dependence of the melting temperature of single-walled carbon nanotubes (SWCNTs) by classical molecular-dynamics (MD) simulations using the environment-dependent interatomic potential (EDIP) proposed by Marks. Here we define the 'melting temperature' as a temperature at which there occurs a thermal instability of SWCNTs. We have carried out molecular-dynamics simulations at several temperatures for carbon nanotubes with various radii and estimated the 'melting temperature' based on the temperature dependence of the radial distribution functions, mean-square displacements and atomic configurations. It is shown that the 'melting temperature' of SWCNTs decreases with decreasing radius. The origin of this radius dependence of the melting temperature of SWCNTs is discussed in relation to the stability of SWCNTs energetically based on the strain energy of carbon nanotubes
Directory of Open Access Journals (Sweden)
K.G.S. Dilrukshi
2015-07-01
Full Text Available A thorough understanding on the mechanical properties of carbon nanotube (CNT is essential in extending the advanced applications of CNT based systems. However, conducting experiments to estimate mechanical properties at this scale is extremely challenging. Therefore, development of mechanistic models to estimate the mechanical properties of CNTs along with the integration of existing continuum mechanics concepts is critically important. This paper presents a comprehensive molecular dynamics simulation study on the size dependency and potential function influence of mechanical properties of CNT. Commonly used reactive bond order (REBO and adaptive intermolecular reactive bond order (AIREBO potential functions were considered in this regard. Young’s modulus and shear modulus of CNTs are derived by integrating classical continuum mechanics concepts with molecular dynamics simulations. The results indicate that the potential function has a significant influence on the estimated mechanical properties of CNTs, and the influence of potential field is much higher when studying the torsional behaviour of CNTs than the tensile behaviour.
Dynamics of the molecular and atomic mechanisms for the hydrogen-iodine exchange reaction.
Raff, L. M.; Thompson, D. L.; Sims, L. B.; Porter, R. N.
1972-01-01
The molecular and atomic mechanisms for the hydrogen-iodine exchange reaction are treated theoretically by means of extensive classical trajectories calculated on a reasonable potential energy surface on which the single adjustable parameter is the iodine-core effective charge. The analysis shows the molecular mechanism to be dynamically forbidden, but gives an over-all rate constant for the atomic mechanism that is in agreement with the experimental values. It is indicated that the formation of a weak H2I complex plays an important dynamical role if the atomic mechanism is limited to reactions with collision complexes involving no more than two hydrogen atoms and two iodine atoms. Excellent agreement with experiment is obtained for the rate constant for the recombination I+I+H2 yields I2+H2 and its negative temperature coefficient.
Unified rotational dynamics of molecular crystals with orientational phase transition
Michel, K.H.; Raedt, H. De
1976-01-01
A unified theory for the rotational dynamics of molecular crystals with orientational phase transitions is given. As basic secular variables one takes symmetry adapted functions, which describe the molecular orientations, and the angular momenta of the molecules. Using Mori’s projection operator tec
Elucidation of molecular dynamics of invasive species of rice
Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...
International Nuclear Information System (INIS)
We consider symmetry properties of differential equations in non-relativistic quantum mechanics and classical mechanics. Special emphasis is given to periodically driven systems. For a model system connections between symmetries of corresponding classical and quantal systems are established. The fundamental difference between variational symmetries and symmetries of the Euler-Lagrange-equations is discussed for the special case of classical mechanics. For nonintegrable systems with quasiregular regions in phase space we introduce the notion of approximate symmetry. As an example, we demonstrate the accuracy of such symmetry properties in certain domains of phase space for a periodically driven anharmonic oscillator. (orig.)
Shapiro like steps reveals molecular nanomagnets' spin dynamics
Babak Abdollahipour; Jahanfar Abouie; Navid Ebrahimi
2015-01-01
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junct...
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
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)
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.
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.
Current Status of Protein Force Fields for Molecular Dynamics
Lopes, Pedro E.M.; Guvench, Olgun
2015-01-01
Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958
Current Status of Protein Force Fields for Molecular Dynamics
Lopes, Pedro E. M.; Guvench, Olgun; MacKerell, Alexander D.
2015-01-01
The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.
Current status of protein force fields for molecular dynamics simulations.
Lopes, Pedro E M; Guvench, Olgun; MacKerell, Alexander D
2015-01-01
The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958
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.
Tunable Interfacial Thermal Conductance by Molecular Dynamics
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1
Molecular 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
Czech Academy of Sciences Publication Activity Database
Orosová, Martina; Oros, A. M.
2012-01-01
Roč. 110, č. 5 (2012), s. 1397-1944. ISSN 0932-0113 R&D Projects: GA MŠk LC522; GA ČR GA524/08/0885 Institutional research plan: CEZ:AV0Z60220518 Keywords : TAPEWORMS PLATYHELMINTHES * RIBOSOMAL DNA * CHROMOSOME S * EVOLUTION * FISH * RDNA * PSEUDOPHYLLIDEA * LOCATION * GENES * DIFFERENTIATION Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.852, year: 2012 http://link.springer.com/content/pdf/10.1007%2Fs00436-011-2720-x
Non-existence of Physical Classical Solutions to Euler's Equations of Rigid Body Dynamics
Wilkinson, Mark
2015-01-01
We prove that one cannot construct, for arbitrary initial data, global-in-time physical classical solutions to Euler's equations of continuum rigid body mechanics when the constituent rigid bodies are not perfect spheres. By 'physical' solutions, we mean those that conserve the total linear momentum, angular momentum and kinetic energy of any given initial datum. The reason for absence of classical solutions is due to the non-existence of velocity scattering maps which resolve a collision bet...
Molecular Dynamics Simulations of Protein Dynamics and their relevance to drug discovery
Salsbury, Freddie R.
2010-01-01
Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery.
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.
Role of molecular dynamics on descriptions of shock-front processes
International Nuclear Information System (INIS)
By means of a computational approach based on classical molecular dynamics, we can begin to form a realistic picture of shock-induced processes occurring at the shock front and resulting from the detailed, violent motion associated with shock motion on an atomic scale. Prototype studies of phase transitions will be discussed. We will also examine the interaction of the shock front with defects, surfaces, voids, and inclusions, and across grain boundaries. We will focus on the critical question of how mechanical energy imparted to a condensed material by shock loading is converted to the activation energy required to overcome some initial energy barrier in an initiation process