Energy conservation in molecular dynamics simulations of classical systems
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
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
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...
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
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
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
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
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.
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
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
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.
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...
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
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
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
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., 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.
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
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.
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
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
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.
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 ...
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)
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...
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)
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 ...
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
Ganster, P
2004-10-15
A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
Rajput, Nav Nidhi; Qu, 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.
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
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)
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....
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
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
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
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
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
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
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.
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.
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
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.
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.
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
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Progress in quantum molecular dynamics
In this paper a microscopic simulation method of the quantum molecular dynamics (QMD) and its extensions to high- and low-energy regions are reported. Combined with the statistical decay calculation, QMD can reproduce experimental data with fixed and very few parameters. (J.P.N.)
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
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
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
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
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
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
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
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.
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.
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
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
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
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
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
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
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference
Rheology via nonequilibrium molecular dynamics
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.
Laser Controlled Molecular Orientation Dynamics
Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation
State-to-state dynamics of molecular energy transfer
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
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
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
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
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
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
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
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.
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
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
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
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
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
Henriksen, Niels Engholm
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic Mole...
Theoretical Concepts in Molecular Photodissociation Dynamics
Henriksen, Niels Engholm
1995-01-01
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
A classical reactive potential for molecular clusters of sulphuric acid and water
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
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.
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
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
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
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
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
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
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
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
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
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
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
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...