Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

PubMed

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

2018-04-05

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Molecular Dynamics Simulations of Simple Liquids

ERIC Educational Resources Information Center

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.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

NASA Astrophysics Data System (ADS)

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.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics.

PubMed

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-14

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.

Zero-Point Energy Constraint for Unimolecular Dissociation Reactions. Giving Trajectories Multiple Chances To Dissociate Correctly.

PubMed

Paul, Amit K; Hase, William L

2016-01-28

A zero-point energy (ZPE) constraint model is proposed for classical trajectory simulations of unimolecular decomposition and applied to CH4* → H + CH3 decomposition. With this model trajectories are not allowed to dissociate unless they have ZPE in the CH3 product. If not, they are returned to the CH4* region of phase space and, if necessary, given additional opportunities to dissociate with ZPE. The lifetime for dissociation of an individual trajectory is the time it takes to dissociate with ZPE in CH3, including multiple possible returns to CH4*. With this ZPE constraint the dissociation of CH4* is exponential in time as expected for intrinsic RRKM dynamics and the resulting rate constant is in good agreement with the harmonic quantum value of RRKM theory. In contrast, a model that discards trajectories without ZPE in the reaction products gives a CH4* → H + CH3 rate constant that agrees with the classical and not quantum RRKM value. The rate constant for the purely classical simulation indicates that anharmonicity may be important and the rate constant from the ZPE constrained classical trajectory simulation may not represent the complete anharmonicity of the RRKM quantum dynamics. The ZPE constraint model proposed here is compared with previous models for restricting ZPE flow in intramolecular dynamics, and connecting product and reactant/product quantum energy levels in chemical dynamics simulations.

Quantum dynamical simulations of local field enhancement in metal nanoparticles.

PubMed

Negre, Christian F A; Perassi, Eduardo M; Coronado, Eduardo A; Sánchez, Cristián G

2013-03-27

Field enhancements (Γ) around small Ag nanoparticles (NPs) are calculated using a quantum dynamical simulation formalism and the results are compared with electrodynamic simulations using the discrete dipole approximation (DDA) in order to address the important issue of the intrinsic atomistic structure of NPs. Quite remarkably, in both quantum and classical approaches the highest values of Γ are located in the same regions around single NPs. However, by introducing a complete atomistic description of the metallic NPs in optical simulations, a different pattern of the Γ distribution is obtained. Knowing the correct pattern of the Γ distribution around NPs is crucial for understanding the spectroscopic features of molecules inside hot spots. The enhancement produced by surface plasmon coupling is studied by using both approaches in NP dimers for different inter-particle distances. The results show that the trend of the variation of Γ versus inter-particle distance is different for classical and quantum simulations. This difference is explained in terms of a charge transfer mechanism that cannot be obtained with classical electrodynamics. Finally, time dependent distribution of the enhancement factor is simulated by introducing a time dependent field perturbation into the Hamiltonian, allowing an assessment of the localized surface plasmon resonance quantum dynamics.

Classical molecular dynamics simulations for non-equilibrium correlated plasmas

NASA Astrophysics Data System (ADS)

Ferri, S.; Calisti, A.; Talin, B.

2017-03-01

A classical molecular dynamics model was recently extended to simulate neutral multi-component plasmas where various charge states of the same atom and electrons coexist. It is used to investigate the plasma effects on the ion charge and on the ionization potential in dense plasmas. Different simulated statistical properties will show that the concept of isolated particles is lost in such correlated plasmas. The charge equilibration is discussed for a carbon plasma at solid density and investigation on the charge distribution and on the ionization potential depression (IPD) for aluminum plasmas is discussed with reference to existing experiments.

Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)].

PubMed

Miller, Thomas F; Manolopoulos, David E; Madden, Paul A; Konieczny, Martin; Oberhofer, Harald

2005-02-01

We show that the two phase points considered in the recent simulations of liquid para hydrogen by Hone and Voth lie in the liquid-vapor coexistence region of a purely classical molecular dynamics simulation. By contrast, their phase point for ortho deuterium was in the one-phase liquid region for both classical and quantum simulations. These observations are used to account for their report that quantum mechanical effects enhance the diffusion in liquid para hydrogen and decrease it in ortho deuterium.(c) 2005 American Institute of Physics.

Classical simulation of quantum error correction in a Fibonacci anyon code

NASA Astrophysics Data System (ADS)

Burton, Simon; Brell, Courtney G.; Flammia, Steven T.

2017-02-01

Classically simulating the dynamics of anyonic excitations in two-dimensional quantum systems is likely intractable in general because such dynamics are sufficient to implement universal quantum computation. However, processes of interest for the study of quantum error correction in anyon systems are typically drawn from a restricted class that displays significant structure over a wide range of system parameters. We exploit this structure to classically simulate, and thereby demonstrate the success of, an error-correction protocol for a quantum memory based on the universal Fibonacci anyon model. We numerically simulate a phenomenological model of the system and noise processes on lattice sizes of up to 128 ×128 sites, and find a lower bound on the error-correction threshold of approximately 0.125 errors per edge, which is comparable to those previously known for Abelian and (nonuniversal) non-Abelian anyon models.

Simulation of wave packet tunneling of interacting identical particles

NASA Astrophysics Data System (ADS)

Lozovik, Yu. E.; Filinov, A. V.; Arkhipov, A. S.

2003-02-01

We demonstrate a different method of simulation of nonstationary quantum processes, considering the tunneling of two interacting identical particles, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based on the Wigner representation of quantum mechanics. In the context of this method ensembles of classical trajectories are used to solve quantum Wigner-Liouville equation. These classical trajectories obey Hamiltonian-like equations, where the effective potential consists of the usual classical term and the quantum term, which depends on the Wigner function and its derivatives. The quantum term is calculated using local distribution of trajectories in phase space, therefore, classical trajectories are not independent, contrary to classical molecular dynamics. The developed WMD method takes into account the influence of exchange and interaction between particles. The role of direct and exchange interactions in tunneling is analyzed. The tunneling times for interacting particles are calculated.

Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Costandy, Joseph; Michalis, Vasileios K.; Economou, Ioannis G., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu

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.

Recent Advances and Perspectives on Nonadiabatic Mixed Quantum-Classical Dynamics.

PubMed

Crespo-Otero, Rachel; Barbatti, Mario

2018-05-16

Nonadiabatic mixed quantum-classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods-mean-field Ehrenfest, trajectory surface hopping, and multiple spawning-this review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years. It stresses the relations between approaches and their domains of application. The electronic structure methods most commonly used together with NA-MQC dynamics are reviewed as well. The accuracy and precision of NA-MQC simulations are critically discussed, and general guidelines to choose an adequate method for each application are delivered.

Consider a non-spherical elephant: computational fluid dynamics simulations of heat transfer coefficients and drag verified using wind tunnel experiments.

PubMed

Dudley, Peter N; Bonazza, Riccardo; Porter, Warren P

2013-07-01

Animal momentum and heat transfer analysis has historically used direct animal measurements or approximations to calculate drag and heat transfer coefficients. Research can now use modern 3D rendering and computational fluid dynamics software to simulate animal-fluid interactions. Key questions are the level of agreement between simulations and experiments and how superior they are to classical approximations. In this paper we compared experimental and simulated heat transfer and drag calculations on a scale model solid aluminum African elephant casting. We found good agreement between experimental and simulated data and large differences from classical approximations. We used the simulation results to calculate coefficients for heat transfer and drag of the elephant geometry. Copyright © 2013 Wiley Periodicals, Inc.

Insight into the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corradini, Dario; Vuilleumier, Rodolphe, E-mail: rodolphe.vuilleumier@ens.fr; Sorbonne Universités, UPMC Univ. Paris 06, PASTEUR, 75005 Paris

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} (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, wemore » 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.« less

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

Tamm, A.; Samolyuk, G.; Correa, A. A.; ...

2016-07-14

Here, 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 computermore » 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.« less

Classical-trajectory simulation of accelerating neutral atoms with polarized intense laser pulses

NASA Astrophysics Data System (ADS)

Xia, Q. Z.; Fu, L. B.; Liu, J.

2013-03-01

In the present paper, we perform the classical trajectory Monte Carlo simulation of the complex dynamics of accelerating neutral atoms with linearly or circularly polarized intense laser pulses. Our simulations involve the ion motion as well as the tunneling ionization and the scattering dynamics of valence electron in the combined Coulomb and electromagnetic fields, for both helium (He) and magnesium (Mg). We show that for He atoms, only linearly polarized lasers can effectively accelerate the atoms, while for Mg atoms, we find that both linearly and circularly polarized lasers can successively accelerate the atoms. The underlying mechanism is discussed and the subcycle dynamics of accelerating trajectories is investigated. We have compared our theoretical results with a recent experiment [Eichmann Nature (London)NATUAS0028-083610.1038/nature08481 461, 1261 (2009)].

Efficiency optimization of a fast Poisson solver in beam dynamics simulation

NASA Astrophysics Data System (ADS)

Zheng, Dawei; Pöplau, Gisela; van Rienen, Ursula

2016-01-01

Calculating the solution of Poisson's equation relating to space charge force is still the major time consumption in beam dynamics simulations and calls for further improvement. In this paper, we summarize a classical fast Poisson solver in beam dynamics simulations: the integrated Green's function method. We introduce three optimization steps of the classical Poisson solver routine: using the reduced integrated Green's function instead of the integrated Green's function; using the discrete cosine transform instead of discrete Fourier transform for the Green's function; using a novel fast convolution routine instead of an explicitly zero-padded convolution. The new Poisson solver routine preserves the advantages of fast computation and high accuracy. This provides a fast routine for high performance calculation of the space charge effect in accelerators.

Zero-point energy effects in anion solvation shells.

PubMed

Habershon, Scott

2014-05-21

By comparing classical and quantum-mechanical (path-integral-based) molecular simulations of solvated halide anions X(-) [X = F, Cl, Br and I], we identify an ion-specific quantum contribution to anion-water hydrogen-bond dynamics; this effect has not been identified in previous simulation studies. For anions such as fluoride, which strongly bind water molecules in the first solvation shell, quantum simulations exhibit hydrogen-bond dynamics nearly 40% faster than the corresponding classical results, whereas those anions which form a weakly bound solvation shell, such as iodide, exhibit a quantum effect of around 10%. This observation can be rationalized by considering the different zero-point energy (ZPE) of the water vibrational modes in the first solvation shell; for strongly binding anions, the ZPE of bound water molecules is larger, giving rise to faster dynamics in quantum simulations. These results are consistent with experimental investigations of anion-bound water vibrational and reorientational motion.

High temperature phonon dispersion in graphene using classical molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anees, P., E-mail: anees@igcar.gov.in; Panigrahi, B. K.; Valsakumar, M. C., E-mail: anees@igcar.gov.in

2014-04-24

Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 Kmore » the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.« less

DFT-derived reactive potentials for the simulation of activated processes: the case of CdTe and CdTe:S.

PubMed

Hu, Xiao Liang; Ciaglia, Riccardo; Pietrucci, Fabio; Gallet, Grégoire A; Andreoni, Wanda

2014-06-19

We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfaces) at finite temperature. In particular, we also consider cases with low sulfur concentration (CdTe:S). The analysis of DFT and classical molecular dynamics (MD) simulations performed with the same protocol leads to stringent performance tests and to a detailed comparison of the two schemes. Metadynamics techniques are used to empower both Car-Parrinello and classical molecular dynamics for the simulation of activated processes. For the latter, we consider surface reconstruction and sulfur diffusion in the bulk. The same procedures are applied using previously proposed force fields for CdTe and CdTeS materials, thus allowing for a detailed comparison of the various schemes.

Mapping quantum-classical Liouville equation: projectors and trajectories.

PubMed

Kelly, Aaron; van Zon, Ramses; Schofield, Jeremy; Kapral, Raymond

2012-02-28

The evolution of a mixed quantum-classical system is expressed in the mapping formalism where discrete quantum states are mapped onto oscillator states, resulting in a phase space description of the quantum degrees of freedom. By defining projection operators onto the mapping states corresponding to the physical quantum states, it is shown that the mapping quantum-classical Liouville operator commutes with the projection operator so that the dynamics is confined to the physical space. It is also shown that a trajectory-based solution of this equation can be constructed that requires the simulation of an ensemble of entangled trajectories. An approximation to this evolution equation which retains only the Poisson bracket contribution to the evolution operator does admit a solution in an ensemble of independent trajectories but it is shown that this operator does not commute with the projection operators and the dynamics may take the system outside the physical space. The dynamical instabilities, utility, and domain of validity of this approximate dynamics are discussed. The effects are illustrated by simulations on several quantum systems.

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

NASA Astrophysics Data System (ADS)

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.

Real-time dynamics of matrix quantum mechanics beyond the classical approximation

NASA Astrophysics Data System (ADS)

Buividovich, Pavel; Hanada, Masanori; Schäfer, Andreas

2018-03-01

We describe a numerical method which allows to go beyond the classical approximation for the real-time dynamics of many-body systems by approximating the many-body Wigner function by the most general Gaussian function with time-dependent mean and dispersion. On a simple example of a classically chaotic system with two degrees of freedom we demonstrate that this Gaussian state approximation is accurate for significantly smaller field strengths and longer times than the classical one. Applying this approximation to matrix quantum mechanics, we demonstrate that the quantum Lyapunov exponents are in general smaller than their classical counterparts, and even seem to vanish below some temperature. This behavior resembles the finite-temperature phase transition which was found for this system in Monte-Carlo simulations, and ensures that the system does not violate the Maldacena-Shenker-Stanford bound λL < 2πT, which inevitably happens for classical dynamics at sufficiently small temperatures.

Effects of two-temperature model on cascade evolution in Ni and NiFe

DOE PAGES

Samolyuk, German D.; Xue, Haizhou; Bei, Hongbin; ...

2016-07-05

We perform molecular dynamics simulations of Ni ion cascades in Ni and equiatomic NiFe under the following conditions: (a) classical molecular dynamics (MD) simulations without consideration of electronic energy loss, (b) classical MD simulations with the electronic stopping included, and (c) using the coupled two-temperature MD (2T-MD) model that incorporates both the electronic stopping and the electron-phonon interactions. Our results indicate that the electronic effects are more profound in the higher-energy cascades, and that the 2T-MD model results in a smaller amount of surviving damage and smaller defect clusters, while less damage is produced in NiFe than in Ni.

Classical molecular dynamics simulation of electronically non-adiabatic processes.

PubMed

Miller, William H; Cotton, Stephen J

2016-12-22

Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

Molecular dynamics simulations of collision-induced absorption: Implementation in LAMMPS

NASA Astrophysics Data System (ADS)

Fakhardji, W.; Gustafsson, M.

2017-02-01

We pursue simulations of collision-induced absorption in a mixture of argon and xenon gas at room temperature by means of classical molecular dynamics. The established theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum are well reproduced with the molecular dynamics simulation in comparison with a laboratory measurement. The magnitude of the computed absorption, however, is underestimated in a large part of the spectrum. We suggest some aspects of the simulation that could be improved.

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

Validation of Potential Models for Li2O in Classical Molecular Dynamics Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru

2007-08-01

Four Buckingham-type pairwise potential models for Li2O were assessed by molecular static and dynamics simulations. In the static simulation, all models afforded acceptable agreement with experimental values and ab initio calculation results for the crystalline properties. Moreover, the superionic phase transition was realized in the dynamics simulation. However, the Li diffusivity and the lattice expansion were not adequately reproduced at the same time by any model. When using these models in future radiation simulation, these features should be taken into account, in order to reduce the model dependency of the results.

An analytical derivation of MC-SCF vibrational wave functions for the quantum dynamical simulation of multiple proton transfer reactions: Initial application to protonated water chains

NASA Astrophysics Data System (ADS)

Drukker, Karen; Hammes-Schiffer, Sharon

1997-07-01

This paper presents an analytical derivation of a multiconfigurational self-consistent-field (MC-SCF) solution of the time-independent Schrödinger equation for nuclear motion (i.e. vibrational modes). This variational MC-SCF method is designed for the mixed quantum/classical molecular dynamics simulation of multiple proton transfer reactions, where the transferring protons are treated quantum mechanically while the remaining degrees of freedom are treated classically. This paper presents a proof that the Hellmann-Feynman forces on the classical degrees of freedom are identical to the exact forces (i.e. the Pulay corrections vanish) when this MC-SCF method is used with an appropriate choice of basis functions. This new MC-SCF method is applied to multiple proton transfer in a protonated chain of three hydrogen-bonded water molecules. The ground state and the first three excited state energies and the ground state forces agree well with full configuration interaction calculations. Sample trajectories are obtained using adiabatic molecular dynamics methods, and nonadiabatic effects are found to be insignificant for these sample trajectories. The accuracy of the excited states will enable this MC-SCF method to be used in conjunction with nonadiabatic molecular dynamics methods. This application differs from previous work in that it is a real-time quantum dynamical nonequilibrium simulation of multiple proton transfer in a chain of water molecules.

Simulating Open Quantum Systems with Hamiltonian Ensembles and the Nonclassicality of the Dynamics

NASA Astrophysics Data System (ADS)

Chen, Hong-Bin; Gneiting, Clemens; Lo, Ping-Yuan; Chen, Yueh-Nan; Nori, Franco

2018-01-01

The incoherent dynamical properties of open quantum systems are generically attributed to an ongoing correlation between the system and its environment. Here, we propose a novel way to assess the nature of these system-environment correlations by examining the system dynamics alone. Our approach is based on the possibility or impossibility to simulate open-system dynamics with Hamiltonian ensembles. As we show, such (im)possibility to simulate is closely linked to the system-environment correlations. We thus define the nonclassicality of open-system dynamics in terms of the nonexistence of a Hamiltonian-ensemble simulation. This classifies any nonunital open-system dynamics as nonclassical. We give examples for open-system dynamics that are unital and classical, as well as unital and nonclassical.

Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands

NASA Astrophysics Data System (ADS)

Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe

2013-06-01

Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.

Density-functional theory simulation of large quantum dots

NASA Astrophysics Data System (ADS)

Jiang, Hong; Baranger, Harold U.; Yang, Weitao

2003-10-01

Kohn-Sham spin-density functional theory provides an efficient and accurate model to study electron-electron interaction effects in quantum dots, but its application to large systems is a challenge. Here an efficient method for the simulation of quantum dots using density-function theory is developed; it includes the particle-in-the-box representation of the Kohn-Sham orbitals, an efficient conjugate-gradient method to directly minimize the total energy, a Fourier convolution approach for the calculation of the Hartree potential, and a simplified multigrid technique to accelerate the convergence. We test the methodology in a two-dimensional model system and show that numerical studies of large quantum dots with several hundred electrons become computationally affordable. In the noninteracting limit, the classical dynamics of the system we study can be continuously varied from integrable to fully chaotic. The qualitative difference in the noninteracting classical dynamics has an effect on the quantum properties of the interacting system: integrable classical dynamics leads to higher-spin states and a broader distribution of spacing between Coulomb blockade peaks.

Hybrid annealing: Coupling a quantum simulator to a classical computer

NASA Astrophysics Data System (ADS)

Graß, Tobias; Lewenstein, Maciej

2017-05-01

Finding the global minimum in a rugged potential landscape is a computationally hard task, often equivalent to relevant optimization problems. Annealing strategies, either classical or quantum, explore the configuration space by evolving the system under the influence of thermal or quantum fluctuations. The thermal annealing dynamics can rapidly freeze the system into a low-energy configuration, and it can be simulated well on a classical computer, but it easily gets stuck in local minima. Quantum annealing, on the other hand, can be guaranteed to find the true ground state and can be implemented in modern quantum simulators; however, quantum adiabatic schemes become prohibitively slow in the presence of quasidegeneracies. Here, we propose a strategy which combines ideas from simulated annealing and quantum annealing. In such a hybrid algorithm, the outcome of a quantum simulator is processed on a classical device. While the quantum simulator explores the configuration space by repeatedly applying quantum fluctuations and performing projective measurements, the classical computer evaluates each configuration and enforces a lowering of the energy. We have simulated this algorithm for small instances of the random energy model, showing that it potentially outperforms both simulated thermal annealing and adiabatic quantum annealing. It becomes most efficient for problems involving many quasidegenerate ground states.

Toward simulating complex systems with quantum effects

NASA Astrophysics Data System (ADS)

Kenion-Hanrath, Rachel Lynn

Quantum effects like tunneling, coherence, and zero point energy often play a significant role in phenomena on the scales of atoms and molecules. However, the exact quantum treatment of a system scales exponentially with dimensionality, making it impractical for characterizing reaction rates and mechanisms in complex systems. An ongoing effort in the field of theoretical chemistry and physics is extending scalable, classical trajectory-based simulation methods capable of capturing quantum effects to describe dynamic processes in many-body systems; in the work presented here we explore two such techniques. First, we detail an explicit electron, path integral (PI)-based simulation protocol for predicting the rate of electron transfer in condensed-phase transition metal complex systems. Using a PI representation of the transferring electron and a classical representation of the transition metal complex and solvent atoms, we compute the outer sphere free energy barrier and dynamical recrossing factor of the electron transfer rate while accounting for quantum tunneling and zero point energy effects. We are able to achieve this employing only a single set of force field parameters to describe the system rather than parameterizing along the reaction coordinate. Following our success in describing a simple model system, we discuss our next steps in extending our protocol to technologically relevant materials systems. The latter half focuses on the Mixed Quantum-Classical Initial Value Representation (MQC-IVR) of real-time correlation functions, a semiclassical method which has demonstrated its ability to "tune'' between quantum- and classical-limit correlation functions while maintaining dynamic consistency. Specifically, this is achieved through a parameter that determines the quantumness of individual degrees of freedom. Here, we derive a semiclassical correction term for the MQC-IVR to systematically characterize the error introduced by different choices of simulation parameters, and demonstrate the ability of this approach to optimize MQC-IVR simulations.

Does ℏ play a role in multidimensional spectroscopy? Reduced hierarchy equations of motion approach to molecular vibrations.

PubMed

Sakurai, Atsunori; Tanimura, Yoshitaka

2011-04-28

To investigate the role of quantum effects in vibrational spectroscopies, we have carried out numerically exact calculations of linear and nonlinear response functions for an anharmonic potential system nonlinearly coupled to a harmonic oscillator bath. Although one cannot carry out the quantum calculations of the response functions with full molecular dynamics (MD) simulations for a realistic system which consists of many molecules, it is possible to grasp the essence of the quantum effects on the vibrational spectra by employing a model Hamiltonian that describes an intra- or intermolecular vibrational motion in a condensed phase. The present model fully includes vibrational relaxation, while the stochastic model often used to simulate infrared spectra does not. We have employed the reduced quantum hierarchy equations of motion approach in the Wigner space representation to deal with nonperturbative, non-Markovian, and nonsecular system-bath interactions. Taking the classical limit of the hierarchy equations of motion, we have obtained the classical equations of motion that describe the classical dynamics under the same physical conditions as in the quantum case. By comparing the classical and quantum mechanically calculated linear and multidimensional spectra, we found that the profiles of spectra for a fast modulation case were similar, but different for a slow modulation case. In both the classical and quantum cases, we identified the resonant oscillation peak in the spectra, but the quantum peak shifted to the red compared with the classical one if the potential is anharmonic. The prominent quantum effect is the 1-2 transition peak, which appears only in the quantum mechanically calculated spectra as a result of anharmonicity in the potential or nonlinearity of the system-bath coupling. While the contribution of the 1-2 transition is negligible in the fast modulation case, it becomes important in the slow modulation case as long as the amplitude of the frequency fluctuation is small. Thus, we observed a distinct difference between the classical and quantum mechanically calculated multidimensional spectra in the slow modulation case where spectral diffusion plays a role. This fact indicates that one may not reproduce the experimentally obtained multidimensional spectrum for high-frequency vibrational modes based on classical molecular dynamics simulations if the modulation that arises from surrounding molecules is weak and slow. A practical way to overcome the difference between the classical and quantum simulations was discussed.

The Computer Simulation of Liquids by Molecular Dynamics.

ERIC Educational Resources Information Center

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)

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics

NASA Astrophysics Data System (ADS)

Tao, Xuecheng; Shushkov, Philip; Miller, Thomas F.

2018-03-01

We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation. An advantage of the isomorphic Hamiltonian is that it can easily be combined with existing mixed quantum-classical dynamics methods, such as surface hopping or Ehrenfest dynamics, to enable the simulation of electronically non-adiabatic processes with nuclear quantum effects. We present numerical applications of the isomorphic Hamiltonian to model two- and three-level systems, with encouraging results that include improvement upon a previously reported combination of RPMD with surface hopping in the deep-tunneling regime.

Quantum versus classical dynamics in the optical centrifuge

NASA Astrophysics Data System (ADS)

Armon, Tsafrir; Friedland, Lazar

2017-09-01

The interplay between classical and quantum-mechanical evolution in the optical centrifuge (OC) is discussed. The analysis is based on the quantum-mechanical formalism starting from either the ground state or a thermal ensemble. Two resonant mechanisms are identified, i.e., the classical autoresonance and the quantum-mechanical ladder climbing, yielding different dynamics and rotational excitation efficiencies. The rotating-wave approximation is used to analyze the two resonant regimes in the associated dimensionless two-parameter space and calculate the OC excitation efficiency. The results show good agreement between numerical simulations and theory and are relevant to existing experimental setups.

Dynamical properties of magnetized two-dimensional one-component plasma

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Symmetrical Windowing for Quantum States in Quasi-Classical Trajectory Simulations

NASA Astrophysics Data System (ADS)

Cotton, Stephen Joshua

An approach has been developed for extracting approximate quantum state-to-state information from classical trajectory simulations which "quantizes" symmetrically both the initial and final classical actions associated with the degrees of freedom of interest using quantum number bins (or "window functions") which are significantly narrower than unit-width. This approach thus imposes a more stringent quantization condition on classical trajectory simulations than has been traditionally employed, while doing so in a manner that is time-symmetric and microscopically reversible. To demonstrate this "symmetric quasi-classical" (SQC) approach for a simple real system, collinear H + H2 reactive scattering calculations were performed [S.J. Cotton and W.H. Miller, J. Phys. Chem. A 117, 7190 (2013)] with SQC-quantization applied to the H 2 vibrational degree of freedom (DOF). It was seen that the use of window functions of approximately 1/2-unit width led to calculated reaction probabilities in very good agreement with quantum mechanical results over the threshold energy region, representing a significant improvement over what is obtained using the traditional quasi-classical procedure. The SQC approach was then applied [S.J. Cotton and W.H. Miller, J. Chem. Phys. 139, 234112 (2013)] to the much more interesting and challenging problem of incorporating non-adiabatic effects into what would otherwise be standard classical trajectory simulations. To do this, the classical Meyer-Miller (MM) Hamiltonian was used to model the electronic DOFs, with SQC-quantization applied to the classical "electronic" actions of the MM model---representing the occupations of the electronic states---in order to extract the electronic state population dynamics. It was demonstrated that if one ties the zero-point energy (ZPE) of the electronic DOFs to the SQC windowing function's width parameter this very simple SQC/MM approach is capable of quantitatively reproducing quantum mechanical results for a range of standard benchmark models of electronically non-adiabatic processes, including applications where "quantum" coherence effects are significant. Notably, among these benchmarks was the well-studied "spin-boson" model of condensed phase non-adiabatic dynamics, in both its symmetric and asymmetric forms---the latter of which many classical approaches fail to treat successfully. The SQC/MM approach to the treatment of non-adiabatic dynamics was next applied [S.J. Cotton, K. Igumenshchev, and W.H. Miller, J. Chem. Phys., 141, 084104 (2014)] to several recently proposed models of condensed phase electron transfer (ET) processes. For these problems, a flux-side correlation function framework modified for consistency with the SQC approach was developed for the calculation of thermal ET rate constants, and excellent accuracy was seen over wide ranges of non-adiabatic coupling strength and energetic bias/exothermicity. Significantly, the "inverted regime" in thermal rate constants (with increasing bias) known from Marcus Theory was reproduced quantitatively for these models---representing the successful treatment of another regime that classical approaches generally have difficulty in correctly describing. Relatedly, a model of photoinduced proton coupled electron transfer (PCET) was also addressed, and it was shown that the SQC/MM approach could reasonably model the explicit population dynamics of the photoexcited electron donor and acceptor states over the four parameter regimes considered. The potential utility of the SQC/MM technique lies in its stunning simplicity and the ease by which it may readily be incorporated into "ordinary" molecular dynamics (MD) simulations. In short, a typical MD simulation may be augmented to take non-adiabatic effects into account simply by introducing an auxiliary pair of classical "electronic" action-angle variables for each energetically viable Born-Oppenheimer surface, and time-evolving these auxiliary variables via Hamilton's equations (using the MM electronic Hamiltonian) in the same manner that the other classical variables---i.e., the coordinates of all the nuclei---are evolved forward in time. In a complex molecular system involving many hundreds or thousands of nuclear DOFs, the propagation of these extra "electronic" variables represents a modest increase in computational effort, and yet, the examples presented herein suggest that in many instances the SQC/MM approach will describe the true non-adiabatic quantum dynamics to a reasonable and useful degree of quantitative accuracy.

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

Probability Simulations by Non-Lipschitz Chaos

NASA Technical Reports Server (NTRS)

Zak, Michail

1996-01-01

It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices. Self-organizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed.

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

NASA Astrophysics Data System (ADS)

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.

Structure of water clusters on graphene: A classical molecular dynamics approach

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Yamamoto, Takahiro

2018-03-01

The microscopic structure of surface water adsorbed on graphene is elucidated theoretically by classical molecular dynamics simulation. At a low temperature (100 K), the main polygon consisting of hydrogen bonds in single-layered water on graphene is tetragonal, whereas the dominant polygons in double-layered water are tetragonal, pentagonal, and hexagonal. On the other hand, at room temperature, the tetragonal, pentagonal, and hexagonal water clusters are the main structures in both single- and double-layered water.

A Nonlocal Peridynamic Plasticity Model for the Dynamic Flow and Fracture of Concrete.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogler, Tracy; Lammi, Christopher James

A nonlocal, ordinary peridynamic constitutive model is formulated to numerically simulate the pressure-dependent flow and fracture of heterogeneous, quasi-brittle ma- terials, such as concrete. Classical mechanics and traditional computational modeling methods do not accurately model the distributed fracture observed within this family of materials. The peridynamic horizon, or range of influence, provides a characteristic length to the continuum and limits localization of fracture. Scaling laws are derived to relate the parameters of peridynamic constitutive model to the parameters of the classical Drucker-Prager plasticity model. Thermodynamic analysis of associated and non-associated plastic flow is performed. An implicit integration algorithm is formu-more » lated to calculate the accumulated plastic bond extension and force state. The gov- erning equations are linearized and the simulation of the quasi-static compression of a cylinder is compared to the classical theory. A dissipation-based peridynamic bond failure criteria is implemented to model fracture and the splitting of a concrete cylinder is numerically simulated. Finally, calculation of the impact and spallation of a con- crete structure is performed to assess the suitability of the material and failure models for simulating concrete during dynamic loadings. The peridynamic model is found to accurately simulate the inelastic deformation and fracture behavior of concrete during compression, splitting, and dynamically induced spall. The work expands the types of materials that can be modeled using peridynamics. A multi-scale methodology for simulating concrete to be used in conjunction with the plasticity model is presented. The work was funded by LDRD 158806.« less

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

Mathematical model of the SH-3G helicopter

NASA Technical Reports Server (NTRS)

Phillips, J. D.

1982-01-01

A mathematical model of the Sikorsky SH-3G helicopter based on classical nonlinear, quasi-steady rotor theory was developed. The model was validated statically and dynamically by comparison with Navy flight-test data. The model incorporates ad hoc revisions which address the ideal assumptions of classical rotor theory and improve the static trim characteristics to provide a more realistic simulation, while retaining the simplicity of the classical model.

Simulations of Probabilities for Quantum Computing

NASA Technical Reports Server (NTRS)

Zak, M.

1996-01-01

It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-LIpschitz dynamics, without utilization of any man-made devices (such as random number generators). Self-organizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed.

Use of Direct Dynamics Simulations to Determine Unimolecular Reaction Paths and Arrhenius Parameters for Large Molecules.

PubMed

Yang, Li; Sun, Rui; Hase, William L

2011-11-08

In a previous study (J. Chem. Phys.2008, 129, 094701) it was shown that for a large molecule, with a total energy much greater than its barrier for decomposition and whose vibrational modes are harmonic oscillators, the expressions for the classical Rice-Ramsperger-Kassel-Marcus (RRKM) (i.e., RRK) and classical transition-state theory (TST) rate constants become equivalent. Using this relationship, a molecule's unimolecular rate constants versus temperature may be determined from chemical dynamics simulations of microcanonical ensembles for the molecule at different total energies. The simulation identifies the molecule's unimolecular pathways and their Arrhenius parameters. In the work presented here, this approach is used to study the thermal decomposition of CH3-NH-CH═CH-CH3, an important constituent in the polymer of cross-linked epoxy resins. Direct dynamics simulations, at the MP2/6-31+G* level of theory, were used to investigate the decomposition of microcanonical ensembles for this molecule. The Arrhenius A and Ea parameters determined from the direct dynamics simulation are in very good agreement with the TST Arrhenius parameters for the MP2/6-31+G* potential energy surface. The simulation method applied here may be particularly useful for large molecules with a multitude of decomposition pathways and whose transition states may be difficult to determine and have structures that are not readily obvious.

Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tao E.; Nitzan, Abraham; Sukharev, Maxim

The dynamics of an electronic two-level system coupled to an electromagnetic field are simulated explicitly for one- and three-dimensional systems through semiclassical propagation of the Maxwell-Liouville equations. Here, we consider three flavors of mixed quantum-classical dynamics: (i) the classical path approximation (CPA), (ii) Ehrenfest dynamics, and (iii) symmetrical quasiclassical (SQC) dynamics. Our findings are as follows: (i) The CPA fails to recover a consistent description of spontaneous emission, (ii) a consistent “spontaneous” emission can be obtained from Ehrenfest dynamics, provided that one starts in an electronic superposition state, and (iii) spontaneous emission is always obtained using SQC dynamics. Using themore » SQC and Ehrenfest frameworks, we further calculate the dynamics following an incoming pulse, but here we find very different responses: SQC and Ehrenfest dynamics deviate sometimes strongly in the calculated rate of decay of the transient excited state. Nevertheless, our work confirms the earlier observations by Miller [J. Chem. Phys. 69, 2188 (1978)] that Ehrenfest dynamics can effectively describe some aspects of spontaneous emission and highlights interesting possibilities for studying light-matter interactions with semiclassical mechanics.« less

Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy

NASA Astrophysics Data System (ADS)

Li, Tao E.; Nitzan, Abraham; Sukharev, Maxim; Martinez, Todd; Chen, Hsing-Ta; Subotnik, Joseph E.

2018-03-01

The dynamics of an electronic two-level system coupled to an electromagnetic field are simulated explicitly for one- and three-dimensional systems through semiclassical propagation of the Maxwell-Liouville equations. We consider three flavors of mixed quantum-classical dynamics: (i) the classical path approximation (CPA), (ii) Ehrenfest dynamics, and (iii) symmetrical quasiclassical (SQC) dynamics. Our findings are as follows: (i) The CPA fails to recover a consistent description of spontaneous emission, (ii) a consistent "spontaneous" emission can be obtained from Ehrenfest dynamics, provided that one starts in an electronic superposition state, and (iii) spontaneous emission is always obtained using SQC dynamics. Using the SQC and Ehrenfest frameworks, we further calculate the dynamics following an incoming pulse, but here we find very different responses: SQC and Ehrenfest dynamics deviate sometimes strongly in the calculated rate of decay of the transient excited state. Nevertheless, our work confirms the earlier observations by Miller [J. Chem. Phys. 69, 2188 (1978), 10.1063/1.436793] that Ehrenfest dynamics can effectively describe some aspects of spontaneous emission and highlights interesting possibilities for studying light-matter interactions with semiclassical mechanics.

Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy

DOE PAGES

Li, Tao E.; Nitzan, Abraham; Sukharev, Maxim; ...

2018-03-12

The dynamics of an electronic two-level system coupled to an electromagnetic field are simulated explicitly for one- and three-dimensional systems through semiclassical propagation of the Maxwell-Liouville equations. Here, we consider three flavors of mixed quantum-classical dynamics: (i) the classical path approximation (CPA), (ii) Ehrenfest dynamics, and (iii) symmetrical quasiclassical (SQC) dynamics. Our findings are as follows: (i) The CPA fails to recover a consistent description of spontaneous emission, (ii) a consistent “spontaneous” emission can be obtained from Ehrenfest dynamics, provided that one starts in an electronic superposition state, and (iii) spontaneous emission is always obtained using SQC dynamics. Using themore » SQC and Ehrenfest frameworks, we further calculate the dynamics following an incoming pulse, but here we find very different responses: SQC and Ehrenfest dynamics deviate sometimes strongly in the calculated rate of decay of the transient excited state. Nevertheless, our work confirms the earlier observations by Miller [J. Chem. Phys. 69, 2188 (1978)] that Ehrenfest dynamics can effectively describe some aspects of spontaneous emission and highlights interesting possibilities for studying light-matter interactions with semiclassical mechanics.« less

Molecular dynamic simulations of N2-broadened methane line shapes and comparison with experiments

NASA Astrophysics Data System (ADS)

Le, Tuong; Doménech, José-Luis; Lepère, Muriel; Tran, Ha

2017-03-01

Absorption spectra of methane transitions broadened by nitrogen have been calculated for the first time using classical molecular dynamic simulations. For that, the time evolution of the auto-correlation function of the dipole moment vector, assumed along a C-H axis, was computed using an accurate site-site intermolecular potential for CH4-N2. Quaternion coordinates were used to treat the rotation of the molecules. A requantization procedure was applied to the classical rotation and spectra were then derived as the Fourier-Laplace transform of the auto-correlation function. These computed spectra were compared with experimental ones recorded with a tunable diode laser and a difference-frequency laser spectrometer. Specifically, nine isolated methane lines broadened by nitrogen, belonging to various vibrational bands and having rotational quantum numbers J from 0 to 9, were measured at room temperature and at several pressures from 20 to 945 mbar. Comparisons between measured and calculated spectra were made through their fits using the Voigt profile. The results show that ab initio calculated spectra reproduce with very high fidelity non-Voigt effects on the measurements and that classical molecular dynamic simulations can be used to predict spectral shapes of isolated lines of methane perturbed by nitrogen.

Parametric models to compute tryptophan fluorescence wavelengths from classical protein simulations.

PubMed

Lopez, Alvaro J; Martínez, Leandro

2018-02-26

Fluorescence spectroscopy is an important method to study protein conformational dynamics and solvation structures. Tryptophan (Trp) residues are the most important and practical intrinsic probes for protein fluorescence due to the variability of their fluorescence wavelengths: Trp residues emit in wavelengths ranging from 308 to 360 nm depending on the local molecular environment. Fluorescence involves electronic transitions, thus its computational modeling is a challenging task. We show that it is possible to predict the wavelength of emission of a Trp residue from classical molecular dynamics simulations by computing the solvent-accessible surface area or the electrostatic interaction between the indole group and the rest of the system. Linear parametric models are obtained to predict the maximum emission wavelengths with standard errors of the order 5 nm. In a set of 19 proteins with emission wavelengths ranging from 308 to 352 nm, the best model predicts the maximum wavelength of emission with a standard error of 4.89 nm and a quadratic Pearson correlation coefficient of 0.81. These models can be used for the interpretation of fluorescence spectra of proteins with multiple Trp residues, or for which local Trp environmental variability exists and can be probed by classical molecular dynamics simulations. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Anomalous dynamics of interstitial dopants in soft crystals

PubMed Central

Tauber, Justin; Higler, Ruben; Sprakel, Joris

2016-01-01

The dynamics of interstitial dopants govern the properties of a wide variety of doped crystalline materials. To describe the hopping dynamics of such interstitial impurities, classical approaches often assume that dopant particles do not interact and travel through a static potential energy landscape. Here we show, using computer simulations, how these assumptions and the resulting predictions from classical Eyring-type theories break down in entropically stabilized body-centered cubic (BCC) crystals due to the thermal excitations of the crystalline matrix. Deviations are particularly severe close to melting where the lattice becomes weak and dopant dynamics exhibit strongly localized and heterogeneous dynamics. We attribute these anomalies to the failure of both assumptions underlying the classical description: (i) The instantaneous potential field experienced by dopants becomes largely disordered due to thermal fluctuations and (ii) elastic interactions cause strong dopant–dopant interactions even at low doping fractions. These results illustrate how describing nonclassical dopant dynamics requires taking the effective disordered potential energy landscape of strongly excited crystals and dopant–dopant interactions into account. PMID:27856751

Development and application of a local linearization algorithm for the integration of quaternion rate equations in real-time flight simulation problems

NASA Technical Reports Server (NTRS)

Barker, L. E., Jr.; Bowles, R. L.; Williams, L. H.

1973-01-01

High angular rates encountered in real-time flight simulation problems may require a more stable and accurate integration method than the classical methods normally used. A study was made to develop a general local linearization procedure of integrating dynamic system equations when using a digital computer in real-time. The procedure is specifically applied to the integration of the quaternion rate equations. For this application, results are compared to a classical second-order method. The local linearization approach is shown to have desirable stability characteristics and gives significant improvement in accuracy over the classical second-order integration methods.

Symmetrical windowing for quantum states in quasi-classical trajectory simulations: Application to electronically non-adiabatic processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cotton, Stephen J.; Miller, William H., E-mail: millerwh@berkeley.edu

A recently described symmetrical windowing methodology [S. J. Cotton and W. H. Miller, J. Phys. Chem. A 117, 7190 (2013)] for quasi-classical trajectory simulations is applied here to the Meyer-Miller [H.-D. Meyer and W. H. Miller, J. Chem. Phys. 70, 3214 (1979)] model for the electronic degrees of freedom in electronically non-adiabatic dynamics. Results generated using this classical approach are observed to be in very good agreement with accurate quantum mechanical results for a variety of test applications, including problems where coherence effects are significant such as the challenging asymmetric spin-boson system.

A Study on Fast Gates for Large-Scale Quantum Simulation with Trapped Ions

PubMed Central

Taylor, Richard L.; Bentley, Christopher D. B.; Pedernales, Julen S.; Lamata, Lucas; Solano, Enrique; Carvalho, André R. R.; Hope, Joseph J.

2017-01-01

Large-scale digital quantum simulations require thousands of fundamental entangling gates to construct the simulated dynamics. Despite success in a variety of small-scale simulations, quantum information processing platforms have hitherto failed to demonstrate the combination of precise control and scalability required to systematically outmatch classical simulators. We analyse how fast gates could enable trapped-ion quantum processors to achieve the requisite scalability to outperform classical computers without error correction. We analyze the performance of a large-scale digital simulator, and find that fidelity of around 70% is realizable for π-pulse infidelities below 10−5 in traps subject to realistic rates of heating and dephasing. This scalability relies on fast gates: entangling gates faster than the trap period. PMID:28401945

A Study on Fast Gates for Large-Scale Quantum Simulation with Trapped Ions.

PubMed

Taylor, Richard L; Bentley, Christopher D B; Pedernales, Julen S; Lamata, Lucas; Solano, Enrique; Carvalho, André R R; Hope, Joseph J

2017-04-12

Large-scale digital quantum simulations require thousands of fundamental entangling gates to construct the simulated dynamics. Despite success in a variety of small-scale simulations, quantum information processing platforms have hitherto failed to demonstrate the combination of precise control and scalability required to systematically outmatch classical simulators. We analyse how fast gates could enable trapped-ion quantum processors to achieve the requisite scalability to outperform classical computers without error correction. We analyze the performance of a large-scale digital simulator, and find that fidelity of around 70% is realizable for π-pulse infidelities below 10 -5 in traps subject to realistic rates of heating and dephasing. This scalability relies on fast gates: entangling gates faster than the trap period.

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

PubMed

Komeiji, Y; Yokoyama, H; Uebayasi, M; Taiji, M; Fukushige, T; Sugimoto, D; Takata, R; Shimizu, A; Itsukashi, K

1996-01-01

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

PubMed Central

2016-01-01

The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

PubMed

Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

2016-06-22

The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.

Car and Parrinello meet Green and Kubo: simulating atomic heat transport from equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Baroni, Stefano

Modern simulation methods based on electronic-structure theory have long been deemed unfit to compute heat transport coefficients within the Green-Kubo formalism. This is so because the quantum-mechanical energy density from which the heat flux is derived is inherently ill defined, thus allegedly hampering the use of the Green-Kubo formula. While this objection would actually apply to classical systems as well, I will demonstrate that the thermal conductivity is indeed independent of the specific microscopic expression for the energy density and current from which it is derived. This fact results from a kind of gauge invariance stemming from energy conservation and extensivity, which I will illustrate numerically for a classical Lennard-Jones fluid. I will then introduce an expression for the adiabatic energy flux, derived within density-functional theory, that allows simulating atomic heat transport using equilibrium ab initio molecular dynamics. The resulting methodology is demonstrated by comparing results from ab-initio and classical molecular-dynamics simulations of a model liquid-Argon system, for which accurate inter-atomic potentials are derived by the force-matching method, and applied to compute the thermal conductivity of heavy water at ambient conditions. The problem of evaluating transport coefficients along with their accuracy from relatively short trajectories is finally addressed and discussed with a few representative examples. Partially funded by the European Union through the MaX Centre of Excellence (Grant No. 676598).

Molecular simulation of disjoining-pressure isotherms for free liquid , Lennard-Jones thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhatt, Divesh; Newman, John; Radke, C.J.

2001-10-01

We present canonical-ensemble molecular-dynamics simulations of disjoining-pressure isotherms in Lennard-Jones free liquid films. Thermodynamics demands that the disjoining pressure is determined uniquely as a function of the chemical potential purely from the phase diagram of the fluid. Our results from molecular dynamics validate this argument. The inverse-sixth-power distance term in the Lennard-Jones intermolecular potential represents van der Waals dispersion forces. Hence, we compare our results with classical Hamaker theory that is based on dispersion forces but assumes a slab geometry for the density profile and completely neglects fluid structure and entropy. We find that the Hamaker constant obtained from ourmore » simulations is about an order of magnitude larger than that from classical theory. To investigate the origin of this discrepancy, we calculate the disjoining-pressure isotherm using a density-functional theory relaxing the inherent assumptions in the Hamaker theory and imparting to the fluid an approximate structure. For disjoining pressure as a function of chemical potential, the results of density-functional theory and molecular dynamics are very close. Even for disjoining-pressure isotherms, and the subsequently calculated Hamaker constant, results of the density-functional theory are closer to the molecular-dynamics simulations by about a factor of 4 compared to Hamaker theory. [References: 44]« less

Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

NASA Technical Reports Server (NTRS)

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.

Modeling light-induced charge transfer dynamics across a metal-molecule-metal junction: Bridging classical electrodynamics and quantum dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Zixuan; Ratner, Mark A.; Seideman, Tamar, E-mail: t-seideman@northwestern.edu

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 ourmore » 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.« less

Including Memory Friction in Single- and Two-State Quantum Dynamics Simulations.

PubMed

Brown, Paul A; Messina, Michael

2016-03-03

We present a simple computational algorithm that allows for the inclusion of memory friction in a quantum dynamics simulation of a small, quantum, primary system coupled to many atoms in the surroundings. We show how including a memory friction operator, F̂, in the primary quantum system's Hamiltonian operator builds memory friction into the dynamics of the primary quantum system. We show that, in the harmonic, semi-classical limit, this friction operator causes the classical phase-space centers of a wavepacket to evolve exactly as if it were a classical particle experiencing memory friction. We also show that this friction operator can be used to include memory friction in the quantum dynamics of an anharmonic primary system. We then generalize the algorithm so that it can be used to treat a primary quantum system that is evolving, non-adiabatically on two coupled potential energy surfaces, i.e., a model that can be used to model H atom transfer, for example. We demonstrate this approach's computational ease and flexibility by showing numerical results for both harmonic and anharmonic primary quantum systems in the single surface case. Finally, we present numerical results for a model of non-adiabatic H atom transfer between a reactant and product state that includes memory friction on one or both of the non-adiabatic potential energy surfaces and uncover some interesting dynamical effects of non-memory friction on the H atom transfer process.

Dynamic Simulation of Human Gait Model With Predictive Capability.

PubMed

Sun, Jinming; Wu, Shaoli; Voglewede, Philip A

2018-03-01

In this paper, it is proposed that the central nervous system (CNS) controls human gait using a predictive control approach in conjunction with classical feedback control instead of exclusive classical feedback control theory that controls based on past error. To validate this proposition, a dynamic model of human gait is developed using a novel predictive approach to investigate the principles of the CNS. The model developed includes two parts: a plant model that represents the dynamics of human gait and a controller that represents the CNS. The plant model is a seven-segment, six-joint model that has nine degrees-of-freedom (DOF). The plant model is validated using data collected from able-bodied human subjects. The proposed controller utilizes model predictive control (MPC). MPC uses an internal model to predict the output in advance, compare the predicted output to the reference, and optimize the control input so that the predicted error is minimal. To decrease the complexity of the model, two joints are controlled using a proportional-derivative (PD) controller. The developed predictive human gait model is validated by simulating able-bodied human gait. The simulation results show that the developed model is able to simulate the kinematic output close to experimental data.

Quantum chemistry simulation on quantum computers: theories and experiments.

PubMed

Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

2012-07-14

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

Selectivity trend of gas separation through nanoporous graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hongjun; Chen, Zhongfang; Dai, Sheng

2015-04-15

By means of molecular dynamics (MD) simulations, we demonstrate that porous graphene can efficiently separate gases according to their molecular sizes. The flux sequence from the classical MD simulation is H{sub 2}>CO{sub 2}≫N{sub 2}>Ar>CH{sub 4}, which generally follows the trend in the kinetic diameters. This trend is also confirmed from the fluxes based on the computed free energy barriers for gas permeation using the umbrella sampling method and kinetic theory of gases. Both brute-force MD simulations and free-energy calcualtions lead to the flux trend consistent with experiments. Case studies of two compositions of CO{sub 2}/N{sub 2} mixtures further demonstrate themore » separation capability of nanoporous graphene. - Graphical abstract: Classical molecular dynamics simulations show the flux trend of H{sub 2}>CO{sub 2}≫N{sub 2}>Ar>CH{sub 4} for their permeation through a porous graphene, in excellent agreement with a recent experiment. - Highlights: • Classical MD simulations show the flux trend of H{sub 2}>CO{sub 2}≫N{sub 2}>Ar>CH{sub 4} for their permeation through a porous graphene. • Free energy calculations yield permeation barriers for those gases. • Selectivities for several gas pairs are estimated from the free-energy barriers and the kinetic theory of gases. • The selectivity trend is in excellent agreement with a recent experiment.« less

Mixed quantum-classical simulation of the hydride transfer reaction catalyzed by dihydrofolate reductase based on a mapped system-harmonic bath model

NASA Astrophysics Data System (ADS)

Xu, Yang; Song, Kai; Shi, Qiang

2018-03-01

The hydride transfer reaction catalyzed by dihydrofolate reductase is studied using a recently developed mixed quantum-classical method to investigate the nuclear quantum effects on the reaction. Molecular dynamics simulation is first performed based on a two-state empirical valence bond potential to map the atomistic model to an effective double-well potential coupled to a harmonic bath. In the mixed quantum-classical simulation, the hydride degree of freedom is quantized, and the effective harmonic oscillator modes are treated classically. It is shown that the hydride transfer reaction rate using the mapped effective double-well/harmonic-bath model is dominated by the contribution from the ground vibrational state. Further comparison with the adiabatic reaction rate constant based on the Kramers theory confirms that the reaction is primarily vibrationally adiabatic, which agrees well with the high transmission coefficients found in previous theoretical studies. The calculated kinetic isotope effect is also consistent with the experimental and recent theoretical results.

Transferability of polarizable models for ion-water electrostatic interaction

NASA Astrophysics Data System (ADS)

Masia, Marco

2009-06-01

Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li+- water and Cl--water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

Molecular dynamics studies of thermal dissipation during shock induced spalling

NASA Astrophysics Data System (ADS)

Xiang, Meizhen; Hu, Haibo; Chen, Jun; Liao, Yi

2013-09-01

Under shock loadings, the temperature of materials may vary dramatically during deformation and fracture processes. Thus, thermal effect is important for constructing dynamical failure models. Existing works on thermal dissipation effects are mostly from meso- to macro-scale levels based on phenomenological assumptions. The main purpose of the present work is to provide several atomistic scale perspectives about thermal dissipation during spall fracture by nonequilibrium molecular dynamics simulations on single-crystalline and nanocrystalline Pb. The simulations show that temperature arising starts from the vicinity of voids during spalling. The thermal dissipation rate in void nucleation stage is much higher than that in the later growth and coalescence stages. Both classical spallation and micro-spallation are taken into account. Classical spallation is corresponding to spallation phenomenon where materials keep in solid state during shock compression and release stages, while micro-spallation is corresponding to spallation phenomenon where melting occurs during shock compression and release stages. In classical spallation, whether residuary dislocations are produced in pre-spall stages has significant influences on thermal dissipation rate during void growth and coalescence. The thermal dissipation rates decrease as shock intensity increases. When the shock intensity exceeds the threshold of micro-spallation, the thermal dissipation rate in void nucleation stage drops precipitously. It is found that grain boundaries mainly influence the thermal dissipation rate in void nucleation stage in classical spallation. In micro-spallation, the grain boundary effects are insignificant.

Functionality limit of classical simulated annealing

NASA Astrophysics Data System (ADS)

Hasegawa, M.

2015-09-01

By analyzing the system dynamics in the landscape paradigm, optimization function of classical simulated annealing is reviewed on the random traveling salesman problems. The properly functioning region of the algorithm is experimentally determined in the size-time plane and the influence of its boundary on the scalability test is examined in the standard framework of this method. From both results, an empirical choice of temperature length is plausibly explained as a minimum requirement that the algorithm maintains its scalability within its functionality limit. The study exemplifies the applicability of computational physics analysis to the optimization algorithm research.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Quasi-classical approaches to vibronic spectra revisited

NASA Astrophysics Data System (ADS)

Karsten, Sven; Ivanov, Sergei D.; Bokarev, Sergey I.; Kühn, Oliver

2018-03-01

The framework to approach quasi-classical dynamics in the electronic ground state is well established and is based on the Kubo-transformed time correlation function (TCF), being the most classical-like quantum TCF. Here we discuss whether the choice of the Kubo-transformed TCF as a starting point for simulating vibronic spectra is as unambiguous as it is for vibrational ones. Employing imaginary-time path integral techniques in combination with the interaction representation allowed us to formulate a method for simulating vibronic spectra in the adiabatic regime that takes nuclear quantum effects and dynamics on multiple potential energy surfaces into account. Further, a generalized quantum TCF is proposed that contains many well-established TCFs, including the Kubo one, as particular cases. Importantly, it also provides a framework to construct new quantum TCFs. Applying the developed methodology to the generalized TCF leads to a plethora of simulation protocols, which are based on the well-known TCFs as well as on new ones. Their performance is investigated on 1D anharmonic model systems at finite temperatures. It is shown that the protocols based on the new TCFs may lead to superior results with respect to those based on the common ones. The strategies to find the optimal approach are discussed.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

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

First-Principle Simulations of Water

NASA Astrophysics Data System (ADS)

Schwegler, Eric

2004-03-01

The structural and dynamical properties of water are investigated with a series of first-principle and classical molecular dynamics simulations. A number of effects that can influence the simulated properties of water will be discussed including temperature, intramolecular flexibility [1], and the quantum nature of protons. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48. [1] M. Allesch, E. Schwegler, G. Galli, F. Gygi, J. Chem. Phys. in press 2004.

The Development of Rigorously Correct, Dynamical Pseudopotentials for Use in Mixed Quantum/Classical Molecular Dynamics Simulations in the Condensed Phase

NASA Astrophysics Data System (ADS)

Kahros, Argyris

Incorporating quantum mechanics into an atomistic simulation necessarily involves solving the Schrodinger equation. Unfortunately, the computational expense associated with solving this equation scales miserably with the number of included quantum degrees of freedom (DOF). The situation is so dire, in fact, that a molecular dynamics (MD) simulation cannot include more than a small number of quantum DOFs before it becomes computationally intractable. Thus, if one were to simulate a relatively large system, such as one containing several hundred atoms or molecules, it would be unreasonable to attempt to include the effects of all of the electrons associated with all of the components of the system. The mixed quantum/classical (MQC) approach provides a way to circumvent this issue. It involves treating the vast majority of the system classically, which incurs minimal computational expense, and reserves the consideration of quantum mechanical effects for only the few degrees of freedom more directly involved in the chemical phenomenon being studied. For example, if one were to study the bonding of a single diatomic molecule in the gas phase, one could employ a MQC approach by treating the nuclei of the molecule's two atoms classically---including the deeply bound, low-energy electrons that change relatively little---and solving the Schrodinger equation only for the high energy electron(s) directly involved in the bonding of the classical cores. In such a way, one could study the bonding of this molecule in a rigorous fashion while treating only the directly related degrees of freedom quantum mechanically. Pseudopotentials are then responsible for dictating the interactions between the quantum and classical degrees of freedom. As these potentials are the sole link between the quantum and classical DOFs, their proper development is of the utmost importance. This Thesis is concerned primarily with my work on the development of novel, rigorous and dynamical pseudopotentials for use in mixed quantum/ classical simulations in the condensed phase. The pseudopotentials discussed within are constructed in an ab initio fashion, without the introduction of any empiricism, and are able to exactly reproduce the results of higher level, fully quantum mechanical Hartree-Fock calculations. A recurring theme in the following pages is overcoming the so-called frozen core approximation (FCA). This essentially comes down to creating pseudopotentials that are able to respond in some way to the local molecular environment in a rigorous fashion. The various methods and discussions that are part of this document are presented in the context of two particular systems. The first is the sodium dimer cation molecule, which serves as a proof of concept for the development of coordinate-dependent pseudopotentials and is the subject of Chapters 2 and 3. Next, the hydrated electron---the excess electron in liquid water---is tackled in an effort to address the recent controversy concerning its true structure and is the subject of Chapters 4 and 5. In essence, the work in this Dissertation is concerned with finding new ways to overcome the problem of a lack of infinite computer processing power.

CABS-flex: Server for fast simulation of protein structure fluctuations.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

Computer Simulations and Theoretical Studies of Complex Systems: from complex fluids to frustrated magnets

NASA Astrophysics Data System (ADS)

Choi, Eunsong

Computer simulations are an integral part of research in modern condensed matter physics; they serve as a direct bridge between theory and experiment by systemactically applying a microscopic model to a collection of particles that effectively imitate a macroscopic system. In this thesis, we study two very differnt condensed systems, namely complex fluids and frustrated magnets, primarily by simulating classical dynamics of each system. In the first part of the thesis, we focus on ionic liquids (ILs) and polymers--the two complementary classes of materials that can be combined to provide various unique properties. The properties of polymers/ILs systems, such as conductivity, viscosity, and miscibility, can be fine tuned by choosing an appropriate combination of cations, anions, and polymers. However, designing a system that meets a specific need requires a concrete understanding of physics and chemistry that dictates a complex interplay between polymers and ionic liquids. In this regard, molecular dynamics (MD) simulation is an efficient tool that provides a molecular level picture of such complex systems. We study the behavior of Poly (ethylene oxide) (PEO) and the imidazolium based ionic liquids, using MD simulations and statistical mechanics. We also discuss our efforts to develop reliable and efficient classical force-fields for PEO and the ionic liquids. The second part is devoted to studies on geometrically frustrated magnets. In particular, a microscopic model, which gives rise to an incommensurate spiral magnetic ordering observed in a pyrochlore antiferromagnet is investigated. The validation of the model is made via a comparison of the spin-wave spectra with the neutron scattering data. Since the standard Holstein-Primakoff method is difficult to employ in such a complex ground state structure with a large unit cell, we carry out classical spin dynamics simulations to compute spin-wave spectra directly from the Fourier transform of spin trajectories. We conclude the study by showing an excellent agreement between the simulation and the experiment.

Molecular dynamics simulations of bubble nucleation in dark matter detectors.

PubMed

Denzel, Philipp; Diemand, Jürg; Angélil, Raymond

2016-01-01

Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.

Dynamically biased statistical model for the ortho/para conversion in the H2 + H3+ → H3+ + H2 reaction.

PubMed

Gómez-Carrasco, Susana; González-Sánchez, Lola; Aguado, Alfredo; Sanz-Sanz, Cristina; Zanchet, Alexandre; Roncero, Octavio

2012-09-07

In this work we present a dynamically biased statistical model to describe the evolution of the title reaction from statistical to a more direct mechanism, using quasi-classical trajectories (QCT). The method is based on the one previously proposed by Park and Light [J. Chem. Phys. 126, 044305 (2007)]. A recent global potential energy surface is used here to calculate the capture probabilities, instead of the long-range ion-induced dipole interactions. The dynamical constraints are introduced by considering a scrambling matrix which depends on energy and determine the probability of the identity/hop/exchange mechanisms. These probabilities are calculated using QCT. It is found that the high zero-point energy of the fragments is transferred to the rest of the degrees of freedom, what shortens the lifetime of H(5)(+) complexes and, as a consequence, the exchange mechanism is produced with lower proportion. The zero-point energy (ZPE) is not properly described in quasi-classical trajectory calculations and an approximation is done in which the initial ZPE of the reactants is reduced in QCT calculations to obtain a new ZPE-biased scrambling matrix. This reduction of the ZPE is explained by the need of correcting the pure classical level number of the H(5)(+) complex, as done in classical simulations of unimolecular processes and to get equivalent quantum and classical rate constants using Rice-Ramsperger-Kassel-Marcus theory. This matrix allows to obtain a ratio of hop/exchange mechanisms, α(T), in rather good agreement with recent experimental results by Crabtree et al. [J. Chem. Phys. 134, 194311 (2011)] at room temperature. At lower temperatures, however, the present simulations predict too high ratios because the biased scrambling matrix is not statistical enough. This demonstrates the importance of applying quantum methods to simulate this reaction at the low temperatures of astrophysical interest.

Dynamically biased statistical model for the ortho/para conversion in the H2+H3+ --> H3++ H2 reaction

NASA Astrophysics Data System (ADS)

Gómez-Carrasco, Susana; González-Sánchez, Lola; Aguado, Alfredo; Sanz-Sanz, Cristina; Zanchet, Alexandre; Roncero, Octavio

2012-09-01

In this work we present a dynamically biased statistical model to describe the evolution of the title reaction from statistical to a more direct mechanism, using quasi-classical trajectories (QCT). The method is based on the one previously proposed by Park and Light [J. Chem. Phys. 126, 044305 (2007), 10.1063/1.2430711]. A recent global potential energy surface is used here to calculate the capture probabilities, instead of the long-range ion-induced dipole interactions. The dynamical constraints are introduced by considering a scrambling matrix which depends on energy and determine the probability of the identity/hop/exchange mechanisms. These probabilities are calculated using QCT. It is found that the high zero-point energy of the fragments is transferred to the rest of the degrees of freedom, what shortens the lifetime of H_5^+ complexes and, as a consequence, the exchange mechanism is produced with lower proportion. The zero-point energy (ZPE) is not properly described in quasi-classical trajectory calculations and an approximation is done in which the initial ZPE of the reactants is reduced in QCT calculations to obtain a new ZPE-biased scrambling matrix. This reduction of the ZPE is explained by the need of correcting the pure classical level number of the H_5^+ complex, as done in classical simulations of unimolecular processes and to get equivalent quantum and classical rate constants using Rice-Ramsperger-Kassel-Marcus theory. This matrix allows to obtain a ratio of hop/exchange mechanisms, α(T), in rather good agreement with recent experimental results by Crabtree et al. [J. Chem. Phys. 134, 194311 (2011), 10.1063/1.3587246] at room temperature. At lower temperatures, however, the present simulations predict too high ratios because the biased scrambling matrix is not statistical enough. This demonstrates the importance of applying quantum methods to simulate this reaction at the low temperatures of astrophysical interest.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Application of the GRC Stirling Convertor System Dynamic Model

NASA Technical Reports Server (NTRS)

Regan, Timothy F.; Lewandowski, Edward J.; Schreiber, Jeffrey G. (Technical Monitor)

2004-01-01

The GRC Stirling Convertor System Dynamic Model (SDM) has been developed to simulate dynamic performance of power systems incorporating free-piston Stirling convertors. This paper discusses its use in evaluating system dynamics and other systems concerns. Detailed examples are provided showing the use of the model in evaluation of off-nominal operating conditions. The many degrees of freedom in both the mechanical and electrical domains inherent in the Stirling convertor and the nonlinear dynamics make simulation an attractive analysis tool in conjunction with classical analysis. Application of SDM in studying the relationship of the size of the resonant circuit quality factor (commonly referred to as Q) in the various resonant mechanical and electrical sub-systems is discussed.

Thermal conductance at atomically clean and disordered silicon/aluminum interfaces: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Ih Choi, Woon; Kim, Kwiseon; Narumanchi, Sreekant

2012-09-01

Thermal resistance between layers impedes effective heat dissipation in electronics packaging applications. Thermal conductance for clean and disordered interfaces between silicon (Si) and aluminum (Al) was computed using realistic Si/Al interfaces and classical molecular dynamics with the modified embedded atom method potential. These realistic interfaces, which include atomically clean as well as disordered interfaces, were obtained using density functional theory. At 300 K, the magnitude of interfacial conductance due to phonon-phonon scattering obtained from the classical molecular dynamics simulations was approximately five times higher than the conductance obtained using analytical elastic diffuse mismatch models. Interfacial disorder reduced the thermal conductance due to increased phonon scattering with respect to the atomically clean interface. Also, the interfacial conductance, due to electron-phonon scattering at the interface, was greater than the conductance due to phonon-phonon scattering. This indicates that phonon-phonon scattering is the bottleneck for interfacial transport at the semiconductor/metal interfaces. The molecular dynamics modeling predictions for interfacial thermal conductance for a 5-nm disordered interface between Si/Al were in-line with recent experimental data in the literature.

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

PubMed

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

Scaling analysis and instantons for thermally assisted tunneling and quantum Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Jiang, Zhang; Smelyanskiy, Vadim N.; Isakov, Sergei V.; Boixo, Sergio; Mazzola, Guglielmo; Troyer, Matthias; Neven, Hartmut

2017-01-01

We develop an instantonic calculus to derive an analytical expression for the thermally assisted tunneling decay rate of a metastable state in a fully connected quantum spin model. The tunneling decay problem can be mapped onto the Kramers escape problem of a classical random dynamical field. This dynamical field is simulated efficiently by path-integral quantum Monte Carlo (QMC). We show analytically that the exponential scaling with the number of spins of the thermally assisted quantum tunneling rate and the escape rate of the QMC process are identical. We relate this effect to the existence of a dominant instantonic tunneling path. The instanton trajectory is described by nonlinear dynamical mean-field theory equations for a single-site magnetization vector, which we solve exactly. Finally, we derive scaling relations for the "spiky" barrier shape when the spin tunneling and QMC rates scale polynomially with the number of spins N while a purely classical over-the-barrier activation rate scales exponentially with N .

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

PubMed

Riniker, Sereina

2018-03-26

In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

Time Domain Stability Margin Assessment Method

NASA Technical Reports Server (NTRS)

Clements, Keith

2017-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

Time-Domain Stability Margin Assessment

NASA Technical Reports Server (NTRS)

Clements, Keith

2016-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

Non-Gaussian statistics and nanosecond dynamics of electrostatic fluctuations affecting optical transitions in proteins.

PubMed

Martin, Daniel R; Matyushov, Dmitry V

2012-08-30

We show that electrostatic fluctuations of the protein-water interface are globally non-Gaussian. The electrostatic component of the optical transition energy (energy gap) in a hydrated green fluorescent protein is studied here by classical molecular dynamics simulations. The distribution of the energy gap displays a high excess in the breadth of electrostatic fluctuations over the prediction of the Gaussian statistics. The energy gap dynamics include a nanosecond component. When simulations are repeated with frozen protein motions, the statistics shifts to the expectations of linear response and the slow dynamics disappear. We therefore suggest that both the non-Gaussian statistics and the nanosecond dynamics originate largely from global, low-frequency motions of the protein coupled to the interfacial water. The non-Gaussian statistics can be experimentally verified from the temperature dependence of the first two spectral moments measured at constant-volume conditions. Simulations at different temperatures are consistent with other indicators of the non-Gaussian statistics. In particular, the high-temperature part of the energy gap variance (second spectral moment) scales linearly with temperature and extrapolates to zero at a temperature characteristic of the protein glass transition. This result, violating the classical limit of the fluctuation-dissipation theorem, leads to a non-Boltzmann statistics of the energy gap and corresponding non-Arrhenius kinetics of radiationless electronic transitions, empirically described by the Vogel-Fulcher-Tammann law.

The ReaxFF reactive force-field: Development, applications, and future directions

DOE PAGES

Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...

2016-03-04

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less

Simulation of quantum dynamics based on the quantum stochastic differential equation.

PubMed

Li, Ming

2013-01-01

The quantum stochastic differential equation derived from the Lindblad form quantum master equation is investigated. The general formulation in terms of environment operators representing the quantum state diffusion is given. The numerical simulation algorithm of stochastic process of direct photodetection of a driven two-level system for the predictions of the dynamical behavior is proposed. The effectiveness and superiority of the algorithm are verified by the performance analysis of the accuracy and the computational cost in comparison with the classical Runge-Kutta algorithm.

Numerical simulation of the geodynamo reaches Earth's core dynamical regime

NASA Astrophysics Data System (ADS)

Aubert, J.; Gastine, T.; Fournier, A.

2016-12-01

Numerical simulations of the geodynamo have been successful at reproducing a number of static (field morphology) and kinematic (secular variation patterns, core surface flows and westward drift) features of Earth's magnetic field, making them a tool of choice for the analysis and retrieval of geophysical information on Earth's core. However, classical numerical models have been run in a parameter regime far from that of the real system, prompting the question of whether we do get "the right answers for the wrong reasons", i.e. whether the agreement between models and nature simply occurs by chance and without physical relevance in the dynamics. In this presentation, we show that classical models succeed in describing the geodynamo because their large-scale spatial structure is essentially invariant as one progresses along a well-chosen path in parameter space to Earth's core conditions. This path is constrained by the need to enforce the relevant force balance (MAC or Magneto-Archimedes-Coriolis) and preserve the ratio of the convective overturn and magnetic diffusion times. Numerical simulations performed along this path are shown to be spatially invariant at scales larger than that where the magnetic energy is ohmically dissipated. This property enables the definition of large-eddy simulations that show good agreement with direct numerical simulations in the range where both are feasible, and that can be computed at unprecedented values of the control parameters, such as an Ekman number E=10-8. Combining direct and large-eddy simulations, large-scale invariance is observed over half the logarithmic distance in parameter space between classical models and Earth. The conditions reached at this mid-point of the path are furthermore shown to be representative of the rapidly-rotating, asymptotic dynamical regime in which Earth's core resides, with a MAC force balance undisturbed by viscosity or inertia, the enforcement of a Taylor state and strong-field dynamo action. We conclude that numerical modelling has advanced to a stage where it is possible to use models correctly representing the statics, kinematics and now the dynamics of the geodynamo. This opens the way to a better analysis of the geomagnetic field in the time and space domains.

Appearance of metastable B2 phase during solidification of Ni 50 Zr 50 alloy: electrostatic levitation and molecular dynamics simulation studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quirinale, D. G.; Rustan, G. E.; Wilson, S. R.

2015-02-04

High-energy x-ray diffraction measurements of undercooled, electrostatically levitated Ni 50Zr 50 liquid droplets were performed. The observed solidification pathway proceeded through the nucleation and growth of the metastable B2 phase, which persisted for several seconds before the rapid appearance of the stable B33 phase. This sequence is shown to be consistent with predictions from classical nucleation theory using data obtained from molecular dynamics (MD) simulations. A plausible mechanism for the B2–B33 transformation is proposed and investigated through further MD simulations.

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

Communication: On the consistency of approximate quantum dynamics simulation methods for vibrational spectra in the condensed phase.

PubMed

Rossi, Mariana; Liu, Hanchao; Paesani, Francesco; Bowman, Joel; Ceriotti, Michele

2014-11-14

Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these limitations can be traced down to two approaches: methods that treat a small subset of the degrees of freedom with rigorous quantum mechanics, considering the rest of the system as a static or classical environment, and methods that treat the whole system quantum mechanically, but using approximate dynamics. Here, we perform a systematic comparison between these two philosophies for the description of quantum effects in vibrational spectroscopy, taking the Embedded Local Monomer model and a mixed quantum-classical model as representatives of the first family of methods, and centroid molecular dynamics and thermostatted ring polymer molecular dynamics as examples of the latter. We use as benchmarks D2O doped with HOD and pure H2O at three distinct thermodynamic state points (ice Ih at 150 K, and the liquid at 300 K and 600 K), modeled with the simple q-TIP4P/F potential energy and dipole moment surfaces. With few exceptions the different techniques yield IR absorption frequencies that are consistent with one another within a few tens of cm(-1). Comparison with classical molecular dynamics demonstrates the importance of nuclear quantum effects up to the highest temperature, and a detailed discussion of the discrepancies between the various methods let us draw some (circumstantial) conclusions about the impact of the very different approximations that underlie them. Such cross validation between radically different approaches could indicate a way forward to further improve the state of the art in simulations of condensed-phase quantum dynamics.

Computational Nanomechanics of Carbon Nanotubes and Composites

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Wei, Chenyu; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2002-01-01

Nanomechanics of individual carbon and boron-nitride nanotubes and their application as reinforcing fibers in polymer composites has been reviewed with interplay of theoretical modeling, computer simulations and experimental observations. The emphasis in this work is on elucidating the multi-length scales of the problems involved, and of different simulation techniques that are needed to address specific characteristics of individual nanotubes and nanotube polymer-matrix interfaces. Classical molecular dynamics simulations are shown to be sufficient to describe the generic behavior such as strength and stiffness modulus but are inadequate to describe elastic limit and nature of plastic buckling at large strength. Quantum molecular dynamics simulations are shown to bring out explicit atomic nature dependent behavior of these nanoscale materials objects that are not accessible either via continuum mechanics based descriptions or through classical molecular dynamics based simulations. As examples, we discus local plastic collapse of carbon nanotubes under axial compression and anisotropic plastic buckling of boron-nitride nanotubes. Dependence of the yield strain on the strain rate is addressed through temperature dependent simulations, a transition-state-theory based model of the strain as a function of strain rate and simulation temperature is presented, and in all cases extensive comparisons are made with experimental observations. Mechanical properties of nanotube-polymer composite materials are simulated with diverse nanotube-polymer interface structures (with van der Waals interaction). The atomistic mechanisms of the interface toughening for optimal load transfer through recycling, high-thermal expansion and diffusion coefficient composite formation above glass transition temperature, and enhancement of Young's modulus on addition of nanotubes to polymer are discussed and compared with experimental observations.

Quantum and quasi-classical collisional dynamics of O{sub 2}–Ar at high temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulusoy, Inga S.; Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400; Andrienko, Daniil A.

A hypersonic vehicle traveling at a high speed disrupts the distribution of internal states in the ambient flow and introduces a nonequilibrium distribution in the post-shock conditions. We investigate the vibrational relaxation in diatom-atom collisions in the range of temperatures between 1000 and 10 000 K by comparing results of extensive fully quantum-mechanical and quasi-classical simulations with available experimental data. The present paper simulates the interaction of molecular oxygen with argon as the first step in developing the aerothermodynamics models based on first principles. We devise a routine to standardize such calculations also for other scattering systems. Our results demonstrate verymore » good agreement of vibrational relaxation time, derived from quantum-mechanical calculations with the experimental measurements conducted in shock tube facilities. At the same time, the quasi-classical simulations fail to accurately predict rates of vibrationally inelastic transitions at temperatures lower than 3000 K. This observation and the computational cost of adopted methods suggest that the next generation of high fidelity thermochemical models should be a combination of quantum and quasi-classical approaches.« less

Quantum and quasi-classical collisional dynamics of O2-Ar at high temperatures

NASA Astrophysics Data System (ADS)

Ulusoy, Inga S.; Andrienko, Daniil A.; Boyd, Iain D.; Hernandez, Rigoberto

2016-06-01

A hypersonic vehicle traveling at a high speed disrupts the distribution of internal states in the ambient flow and introduces a nonequilibrium distribution in the post-shock conditions. We investigate the vibrational relaxation in diatom-atom collisions in the range of temperatures between 1000 and 10 000 K by comparing results of extensive fully quantum-mechanical and quasi-classical simulations with available experimental data. The present paper simulates the interaction of molecular oxygen with argon as the first step in developing the aerothermodynamics models based on first principles. We devise a routine to standardize such calculations also for other scattering systems. Our results demonstrate very good agreement of vibrational relaxation time, derived from quantum-mechanical calculations with the experimental measurements conducted in shock tube facilities. At the same time, the quasi-classical simulations fail to accurately predict rates of vibrationally inelastic transitions at temperatures lower than 3000 K. This observation and the computational cost of adopted methods suggest that the next generation of high fidelity thermochemical models should be a combination of quantum and quasi-classical approaches.

Experimental and numerical study of premixed hydrogen/air flame propagating in a combustion chamber.

PubMed

Xiao, Huahua; Sun, Jinhua; Chen, Peng

2014-03-15

An experimental and numerical study of dynamics of premixed hydrogen/air flame in a closed explosion vessel is described. High-speed shlieren cinematography and pressure recording are used to elucidate the dynamics of the combustion process in the experiment. A dynamically thickened flame model associated with a detailed reaction mechanism is employed in the numerical simulation to examine the flame-flow interaction and effect of wall friction on the flame dynamics. The shlieren photographs show that the flame develops into a distorted tulip shape after a well-pronounced classical tulip front has been formed. The experimental results reveal that the distorted tulip flame disappears with the primary tulip cusp and the distortions merging into each other, and then a classical tulip is repeated. The combustion dynamics is reasonably reproduced in the numerical simulations, including the variations in flame shape and position, pressure build-up and periodically oscillating behavior. It is found that both the tulip and distorted tulip flames can be created in the simulation with free-slip boundary condition at the walls of the vessel and behave in a manner quite close to that in the experiments. This means that the wall friction could be unimportant for the tulip and distorted tulip formation although the boundary layer formed along the sidewalls has an influence to a certain extent on the flame behavior near the sidewalls. The distorted tulip flame is also observed to be produced in the absence of vortex flow in the numerical simulations. The TF model with a detailed chemical scheme is reliable for investigating the dynamics of distorted tulip flame propagation and its underlying mechanism. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Quantum decision-maker theory and simulation

NASA Astrophysics Data System (ADS)

Zak, Michail; Meyers, Ronald E.; Deacon, Keith S.

2000-07-01

A quantum device simulating the human decision making process is introduced. It consists of quantum recurrent nets generating stochastic processes which represent the motor dynamics, and of classical neural nets describing the evolution of probabilities of these processes which represent the mental dynamics. The autonomy of the decision making process is achieved by a feedback from the mental to motor dynamics which changes the stochastic matrix based upon the probability distribution. This feedback replaces unavailable external information by an internal knowledge- base stored in the mental model in the form of probability distributions. As a result, the coupled motor-mental dynamics is described by a nonlinear version of Markov chains which can decrease entropy without an external source of information. Applications to common sense based decisions as well as to evolutionary games are discussed. An example exhibiting self-organization is computed using quantum computer simulation. Force on force and mutual aircraft engagements using the quantum decision maker dynamics are considered.

Driven topological systems in the classical limit

NASA Astrophysics Data System (ADS)

Duncan, Callum W.; Öhberg, Patrik; Valiente, Manuel

2017-03-01

Periodically driven quantum systems can exhibit topologically nontrivial behavior, even when their quasienergy bands have zero Chern numbers. Much work has been conducted on noninteracting quantum-mechanical models where this kind of behavior is present. However, the inclusion of interactions in out-of-equilibrium quantum systems can prove to be quite challenging. On the other hand, the classical counterpart of hard-core interactions can be simulated efficiently via constrained random walks. The noninteracting model, proposed by Rudner et al. [Phys. Rev. X 3, 031005 (2013), 10.1103/PhysRevX.3.031005], has a special point for which the system is equivalent to a classical random walk. We consider the classical counterpart of this model, which is exact at a special point even when hard-core interactions are present, and show how these quantitatively affect the edge currents in a strip geometry. We find that the interacting classical system is well described by a mean-field theory. Using this we simulate the dynamics of the classical system, which show that the interactions play the role of Markovian, or time-dependent disorder. By comparing the evolution of classical and quantum edge currents in small lattices, we find regimes where the classical limit considered gives good insight into the quantum problem.

Time Domain Stability Margin Assessment of the NASA Space Launch System GN&C Design for Exploration Mission One

NASA Technical Reports Server (NTRS)

Clements, Keith; Wall, John

2017-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

Time Domain Stability Margin Assessment of the NS Space Launch System GN&C Design for Exploration Mission One

NASA Technical Reports Server (NTRS)

Clements, Keith; Wall, John

2017-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Jincheng; Rimsza, Jessica

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Diffusion Dynamics and Creative Destruction in a Simple Classical Model

PubMed Central

2015-01-01

ABSTRACT The article explores the impact of the diffusion of new methods of production on output and employment growth and income distribution within a Classical one‐sector framework. Disequilibrium paths are studied analytically and in terms of simulations. Diffusion by differential growth affects aggregate dynamics through several channels. The analysis reveals the non‐steady nature of economic change and shows that the adaptation pattern depends both on the innovation's factor‐saving bias and on the extent of the bias, which determines the strength of the selection pressure on non‐innovators. The typology of different cases developed shows various aspects of Schumpeter's concept of creative destruction. PMID:27642192

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu, E-mail: okazaki@apchem.nagoya-u.ac.jp

2014-08-28

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 transfermore » 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{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −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.« less

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Classical continuum theory limits to determine the size-dependency of mechanical properties of GaN NWs

NASA Astrophysics Data System (ADS)

Zamani Kouhpanji, Mohammad Reza; Behzadirad, Mahmoud; Busani, Tito

2017-12-01

We used the stable strain gradient theory including acceleration gradients to investigate the classical and nonclassical mechanical properties of gallium nitride (GaN) nanowires (NWs). We predicted the static length scales, Young's modulus, and shear modulus of the GaN NWs from the experimental data. Combining these results with atomic simulations, we also found the dynamic length scale of the GaN NWs. Young's modulus, shear modulus, static, and dynamic length scales were found to be 318 GPa, 131 GPa, 8 nm, and 8.9 nm, respectively, usable for demonstrating the static and dynamic behaviors of GaN NWs having diameters from a few nm to bulk dimensions. Furthermore, the experimental data were analyzed with classical continuum theory (CCT) and compared with the available literature to illustrate the size-dependency of the mechanical properties of GaN NWs. This practice resolves the previous published discrepancies that happened due to the limitations of CCT used for determining the mechanical properties of GaN NWs and their size-dependency.

Classical Molecular Dynamics with Mobile Protons.

PubMed

Lazaridis, Themis; Hummer, Gerhard

2017-11-27

An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.

Classical Coset Hamiltonian for the Electronic Motion and its Application to Anderson Localization and Hammett Equation

NASA Astrophysics Data System (ADS)

Xing, Guan; Wu, Guo-Zhen

2001-02-01

A classical coset Hamiltonian is introduced for the system of one electron in multi-sites. By this Hamiltonian, the dynamical behaviour of the electronic motion can be readily simulated. The simulation reproduces the retardation of the electron density decay in a lattice with site energies randomly distributed - an analogy with Anderson localization. This algorithm is also applied to reproduce the Hammett equation which relates the reaction rate with the property of the substitutions in the organic chemical reactions. The advantages and shortcomings of this algorithm, as contrasted with traditional quantum methods such as the molecular orbital theory, are also discussed.

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

Chemical reactivity and spectroscopy explored from QM/MM molecular dynamics simulations using the LIO code

NASA Astrophysics Data System (ADS)

Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Dario A.; González Lebrero, Mariano C.; Scherlis, Damián A.

2018-03-01

In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Consequences of nonclassical measurement for the algorithmic description of continuous dynamical systems

NASA Technical Reports Server (NTRS)

Fields, Chris

1989-01-01

Continuous dynamical systems intuitively seem capable of more complex behavior than discrete systems. If analyzed in the framework of the traditional theory of computation, a continuous dynamical system with countably many quasistable states has at least the computational power of a universal Turing machine. Such an analysis assumes, however, the classical notion of measurement. If measurement is viewed nonclassically, a continuous dynamical system cannot, even in principle, exhibit behavior that cannot be simulated by a universal Turing machine.

Consequences of nonclassical measurement for the algorithmic description of continuous dynamical systems

NASA Technical Reports Server (NTRS)

Fields, Chris

1989-01-01

Continuous dynamical systems intuitively seem capable of more complex behavior than discrete systems. If analyzed in the framework of the traditional theory of computation, a continuous dynamical system with countablely many quasistable states has at least the computational power of a universal Turing machine. Such an analyses assumes, however, the classical notion of measurement. If measurement is viewed nonclassically, a continuous dynamical system cannot, even in principle, exhibit behavior that cannot be simulated by a universal Turing machine.

Classical and quantum simulations of warm dense carbon

NASA Astrophysics Data System (ADS)

Whitley, Heather; Sanchez, David; Hamel, Sebastien; Correa, Alfredo; Benedict, Lorin

We have applied classical and DFT-based molecular dynamics (MD) simulations to study the equation of state of carbon in the warm dense matter regime (ρ = 3.7 g/cc, 0.86 eV

Magnetization dynamics driven by spin-polarized current in nanomagnets

NASA Astrophysics Data System (ADS)

Carpentieri, M.; Torres, L.; Azzerboni, B.; Finocchio, G.; Consolo, G.; Lopez-Diaz, L.

2007-09-01

In this report, micromagnetic simulations of magnetization dynamics driven by spin-polarized currents (SPCs) on magnetic nanopillars of permalloy/Cu/permalloy with different rectangular cross-sections are presented. Complete dynamical stability diagrams from initial parallel and antiparallel states have been computed for 100 ns. The effects of a space-dependent polarization function together with the presence of magnetostatic coupling from the fixed layer and classical Ampere field have been taken into account.

Fully compressible solutions for early stage Richtmyer–Meshkov instability

DOE PAGES

Margolin, Len G.; Reisner, Jon Michael

2016-10-27

Here, we will consider the effects of compressibility and viscosity on the early dynamics of the Richtmyer–Meshkov instability (RMI). In particular, we will combine theory, scaling, and high resolution simulation of RMI to probe the details of the initial compression and the subsequent viscous damping as a shock interacts with a density discontinuity. We will propose a refinement of the classic 1D model for the linear regime of RMI that, for small initial perturbation wavelengths, more accurately reproduces the 2D dynamics of a fully resolved numerical simulation.

Dynamical Casimir Effect for Gaussian Boson Sampling.

PubMed

Peropadre, Borja; Huh, Joonsuk; Sabín, Carlos

2018-02-28

We show that the Dynamical Casimir Effect (DCE), realized on two multimode coplanar waveg-uide resonators, implements a gaussian boson sampler (GBS). The appropriate choice of the mirror acceleration that couples both resonators translates into the desired initial gaussian state and many-boson interference in a boson sampling network. In particular, we show that the proposed quantum simulator naturally performs a classically hard task, known as scattershot boson sampling. Our result unveils an unprecedented computational power of DCE, and paves the way for using DCE as a resource for quantum simulation.

Molecular dynamics simulations of dense plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, L.A.; Kress, J.D.; Kwon, I.

1993-12-31

We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.

Hidden Statistics Approach to Quantum Simulations

NASA Technical Reports Server (NTRS)

Zak, Michail

2010-01-01

Recent advances in quantum information theory have inspired an explosion of interest in new quantum algorithms for solving hard computational (quantum and non-quantum) problems. The basic principle of quantum computation is that the quantum properties can be used to represent structure data, and that quantum mechanisms can be devised and built to perform operations with this data. Three basic non-classical properties of quantum mechanics superposition, entanglement, and direct-product decomposability were main reasons for optimism about capabilities of quantum computers that promised simultaneous processing of large massifs of highly correlated data. Unfortunately, these advantages of quantum mechanics came with a high price. One major problem is keeping the components of the computer in a coherent state, as the slightest interaction with the external world would cause the system to decohere. That is why the hardware implementation of a quantum computer is still unsolved. The basic idea of this work is to create a new kind of dynamical system that would preserve the main three properties of quantum physics superposition, entanglement, and direct-product decomposability while allowing one to measure its state variables using classical methods. In other words, such a system would reinforce the advantages and minimize limitations of both quantum and classical aspects. Based upon a concept of hidden statistics, a new kind of dynamical system for simulation of Schroedinger equation is proposed. The system represents a modified Madelung version of Schroedinger equation. It preserves superposition, entanglement, and direct-product decomposability while allowing one to measure its state variables using classical methods. Such an optimal combination of characteristics is a perfect match for simulating quantum systems. The model includes a transitional component of quantum potential (that has been overlooked in previous treatment of the Madelung equation). The role of the transitional potential is to provide a jump from a deterministic state to a random state with prescribed probability density. This jump is triggered by blowup instability due to violation of Lipschitz condition generated by the quantum potential. As a result, the dynamics attains quantum properties on a classical scale. The model can be implemented physically as an analog VLSI-based (very-large-scale integration-based) computer, or numerically on a digital computer. This work opens a way of developing fundamentally new algorithms for quantum simulations of exponentially complex problems that expand NASA capabilities in conducting space activities. It has been illustrated that the complexity of simulations of particle interaction can be reduced from an exponential one to a polynomial one.

Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations.

PubMed

Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando

2016-12-07

Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

Mechanism of Urea Crystal Dissolution in Water from Molecular Dynamics Simulation.

PubMed

Anand, Abhinav; Patey, G N

2018-01-25

Molecular dynamics simulations are used to determine the mechanism of urea crystal dissolution in water under sink conditions. Crystals of cubic and tablet shapes are considered, and results are reported for four commonly used water models. The dissolution rates for different water models can differ considerably, but the overall dissolution mechanism remains the same. Urea dissolution occurs in three stages: a relatively fast initial stage, a slower intermediate stage, and a final stage. We show that the long intermediate stage is well described by classical rate laws, which assume that the dissolution rate is proportional to the active surface area. By carrying out simulations at different temperatures, we show that urea dissolution is an activated process, with an activation energy of ∼32 kJ mol -1 . Our simulations give no indication of a significant diffusion layer, and we conclude that the detachment of molecules from the crystal is the rate-determining step for dissolution. The results we report for urea are consistent with earlier observations for the dissolution of NaCl crystals. This suggests that the three-stage mechanism and classical rate laws might apply to the dissolution of other ionic and molecular crystals.

Application of classical simulations for the computation of vibrational properties of free molecules.

PubMed

Tikhonov, Denis S; Sharapa, Dmitry I; Schwabedissen, Jan; Rybkin, Vladimir V

2016-10-12

In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS 2 , benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I 2 -1,2-closo-C 2 B 10 H 10 . The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.

Convergence acceleration of molecular dynamics methods for shocked materials using velocity scaling

NASA Astrophysics Data System (ADS)

Taylor, DeCarlos E.

2017-03-01

In this work, a convergence acceleration method applicable to extended system molecular dynamics techniques for shock simulations of materials is presented. The method uses velocity scaling to reduce the instantaneous value of the Rankine-Hugoniot conservation of energy constraint used in extended system molecular dynamics methods to more rapidly drive the system towards a converged Hugoniot state. When used in conjunction with the constant stress Hugoniostat method, the velocity scaled trajectories show faster convergence to the final Hugoniot state with little difference observed in the converged Hugoniot energy, pressure, volume and temperature. A derivation of the scale factor is presented and the performance of the technique is demonstrated using the boron carbide armour ceramic as a test material. It is shown that simulation of boron carbide Hugoniot states, from 5 to 20 GPa, using both a classical Tersoff potential and an ab initio density functional, are more rapidly convergent when the velocity scaling algorithm is applied. The accelerated convergence afforded by the current algorithm enables more rapid determination of Hugoniot states thus reducing the computational demand of such studies when using expensive ab initio or classical potentials.

Statistical benchmark for BosonSampling

NASA Astrophysics Data System (ADS)

Walschaers, Mattia; Kuipers, Jack; Urbina, Juan-Diego; Mayer, Klaus; Tichy, Malte Christopher; Richter, Klaus; Buchleitner, Andreas

2016-03-01

Boson samplers—set-ups that generate complex many-particle output states through the transmission of elementary many-particle input states across a multitude of mutually coupled modes—promise the efficient quantum simulation of a classically intractable computational task, and challenge the extended Church-Turing thesis, one of the fundamental dogmas of computer science. However, as in all experimental quantum simulations of truly complex systems, one crucial problem remains: how to certify that a given experimental measurement record unambiguously results from enforcing the claimed dynamics, on bosons, fermions or distinguishable particles? Here we offer a statistical solution to the certification problem, identifying an unambiguous statistical signature of many-body quantum interference upon transmission across a multimode, random scattering device. We show that statistical analysis of only partial information on the output state allows to characterise the imparted dynamics through particle type-specific features of the emerging interference patterns. The relevant statistical quantifiers are classically computable, define a falsifiable benchmark for BosonSampling, and reveal distinctive features of many-particle quantum dynamics, which go much beyond mere bunching or anti-bunching effects.

Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

PubMed

Gao, J

2016-01-01

Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects. © 2016 Elsevier Inc. All rights reserved.

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

Nuclear quantum effects in water exchange around lithium and fluoride ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, David M.; Manolopoulos, David E.; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.« less

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

PubMed Central

Zhan, Cheng; Lian, Cheng; Zhang, Yu; Thompson, Matthew W.; Xie, Yu; Wu, Jianzhong; Kent, Paul R. C.; Cummings, Peter T.; Wesolowski, David J.

2017-01-01

Supercapacitors such as electric double‐layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double‐layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte‐Carlo (MC) methods. In recent years, combining first‐principles and classical simulations to investigate the carbon‐based EDLCs has shed light on the importance of quantum capacitance in graphene‐like 2D systems. More recently, the development of joint density functional theory (JDFT) enables self‐consistent electronic‐structure calculation for an electrode being solvated by an electrolyte. In contrast with the large amount of theoretical and computational effort on EDLCs, theoretical understanding of pseudocapacitance is very limited. In this review, we first introduce popular modeling methods and then focus on several important aspects of EDLCs including nanoconfinement, quantum capacitance, dielectric screening, and novel 2D electrode design; we also briefly touch upon pseudocapactive mechanism in RuO2. We summarize and conclude with an outlook for the future of materials simulation and design for capacitive energy storage. PMID:28725531

Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3.

PubMed

Schie, Marcel; Marchewka, Astrid; Müller, Thomas; De Souza, Roger A; Waser, Rainer

2012-12-05

A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO(3)). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO(3) was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.

Using Molecular Dynamics to quantify the electrical double layer and examine the potential for its direct observation in the in-situ TEM

DOE PAGES

Welch, David A.; Mehdi, Beata L.; Hatchell, Hanna J.; ...

2015-03-25

Understanding the fundamental processes taking place at the electrode-electrolyte interface in batteries will play a key role in the development of next generation energy storage technologies. One of the most fundamental aspects of the electrode-electrolyte interface is the electrical double layer (EDL). Given the recent development of high spatial resolution in-situ electrochemical cells for scanning transmission electron microscopy (STEM), there now exists the possibility that we can directly observe the formation and dynamics of the EDL. In this paper we predict electrolyte structure within the EDL using classical models and atomistic Molecular Dynamics (MD) simulations. The MD simulations show thatmore » the classical models fail to accurately reproduce concentration profiles that exist within the electrolyte. It is thus suggested that MD must be used in order to accurately predict STEM images of the electrode-electrolyte interface. Using MD and image simulations together for a high contrast electrolyte (the high atomic number CsCl electrolyte), it is determined that, for a smooth interface, concentration profiles within the EDL should be visible experimentally. When normal experimental parameters such as rough interfaces and low-Z electrolytes (like those used in Li-ion batteries) are considered, observation of the EDL appears to be more difficult.« less

Detailed Balance of Thermalization Dynamics in Rydberg-Atom Quantum Simulators.

PubMed

Kim, Hyosub; Park, YeJe; Kim, Kyungtae; Sim, H-S; Ahn, Jaewook

2018-05-04

Dynamics of large complex systems, such as relaxation towards equilibrium in classical statistical mechanics, often obeys a master equation that captures essential information from the complexities. Here, we find that thermalization of an isolated many-body quantum state can be described by a master equation. We observe sudden quench dynamics of quantum Ising-like models implemented in our quantum simulator, defect-free single-atom tweezers in conjunction with Rydberg-atom interaction. Saturation of their local observables, a thermalization signature, obeys a master equation experimentally constructed by monitoring the occupation probabilities of prequench states and imposing the principle of the detailed balance. Our experiment agrees with theories and demonstrates the detailed balance in a thermalization dynamics that does not require coupling to baths or postulated randomness.

Detailed Balance of Thermalization Dynamics in Rydberg-Atom Quantum Simulators

NASA Astrophysics Data System (ADS)

Kim, Hyosub; Park, YeJe; Kim, Kyungtae; Sim, H.-S.; Ahn, Jaewook

2018-05-01

Dynamics of large complex systems, such as relaxation towards equilibrium in classical statistical mechanics, often obeys a master equation that captures essential information from the complexities. Here, we find that thermalization of an isolated many-body quantum state can be described by a master equation. We observe sudden quench dynamics of quantum Ising-like models implemented in our quantum simulator, defect-free single-atom tweezers in conjunction with Rydberg-atom interaction. Saturation of their local observables, a thermalization signature, obeys a master equation experimentally constructed by monitoring the occupation probabilities of prequench states and imposing the principle of the detailed balance. Our experiment agrees with theories and demonstrates the detailed balance in a thermalization dynamics that does not require coupling to baths or postulated randomness.

GPU accelerated Discrete Element Method (DEM) molecular dynamics for conservative, faceted particle simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spellings, Matthew; Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109; Marson, Ryan L.

Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks–Chandler–Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method ismore » a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.« less

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

CABS-flex: server for fast simulation of protein structure fluctuations

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model–based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics—a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions. PMID:23658222

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Distribution and Dynamic Properties of Xenon Dissolved in the Ionic Smectic Phase of [C16mim][NO3]: MD Simulation and Theoretical Model.

PubMed

Frezzato, Diego; Saielli, Giacomo

2016-03-10

We have investigated the structural and dynamic properties of Xe dissolved in the ionic liquid crystal (ILC) phase of 1-hexadecyl-3-methylimidazolium nitrate using classical molecular dynamics (MD) simulations. Xe is found to be preferentially dissolved within the hydrophobic environment of the alkyl chains rather than in the ionic layers of the smectic phase. The structural parameters and the estimated local diffusion coefficients concerning the short-time motion of Xe are used to parametrize a theoretical model based on the Smoluchowski equation for the macroscopic dynamics across the smectic layers, a feature which cannot be directly obtained from the relatively short MD simulations. This protocol represents an efficient combination of computational and theoretical tools to obtain information on slow processes concerning the permeability and diffusivity of the xenon in smectic ILCs.

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Continuous variable quantum optical simulation for time evolution of quantum harmonic oscillators

PubMed Central

Deng, Xiaowei; Hao, Shuhong; Guo, Hong; Xie, Changde; Su, Xiaolong

2016-01-01

Quantum simulation enables one to mimic the evolution of other quantum systems using a controllable quantum system. Quantum harmonic oscillator (QHO) is one of the most important model systems in quantum physics. To observe the transient dynamics of a QHO with high oscillation frequency directly is difficult. We experimentally simulate the transient behaviors of QHO in an open system during time evolution with an optical mode and a logical operation system of continuous variable quantum computation. The time evolution of an atomic ensemble in the collective spontaneous emission is analytically simulated by mapping the atomic ensemble onto a QHO. The measured fidelity, which is used for quantifying the quality of the simulation, is higher than its classical limit. The presented simulation scheme provides a new tool for studying the dynamic behaviors of QHO. PMID:26961962

Realistic finite temperature simulations of magnetic systems using quantum statistics

NASA Astrophysics Data System (ADS)

Bergqvist, Lars; Bergman, Anders

2018-01-01

We have performed realistic atomistic simulations at finite temperatures using Monte Carlo and atomistic spin dynamics simulations incorporating quantum (Bose-Einstein) statistics. The description is much improved at low temperatures compared to classical (Boltzmann) statistics normally used in these kind of simulations, while at higher temperatures the classical statistics are recovered. This corrected low-temperature description is reflected in both magnetization and the magnetic specific heat, the latter allowing for improved modeling of the magnetic contribution to free energies. A central property in the method is the magnon density of states at finite temperatures, and we have compared several different implementations for obtaining it. The method has no restrictions regarding chemical and magnetic order of the considered materials. This is demonstrated by applying the method to elemental ferromagnetic systems, including Fe and Ni, as well as Fe-Co random alloys and the ferrimagnetic system GdFe3.

High-density amorphous ice: A path-integral simulation

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.; Ramírez, Rafael

2012-09-01

Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Quantum nuclear motion is found to affect several observable properties of the amorphous solid. At low temperature (T = 50 K) the molar volume of HDA ice is found to increase by 6%, and the intramolecular O-H distance rises by 1.4% due to quantum motion. Peaks in the radial distribution function of HDA ice are broadened with respect to their classical expectancy. The bulk modulus, B, is found to rise linearly with the pressure, with a slope ∂B/∂P = 7.1. Our results are compared with those derived earlier from classical and path-integral simulations of HDA ice. We discuss similarities and discrepancies with those earlier simulations.

Issues of Dynamic Coalition Formation Among Rational Agents

DTIC Science & Technology

2002-04-01

approaches of forming stable coalitions among rational agents. Issues and problems of dynamic coalition environments are discussed in section 3 while...2.2. 2.1.2 Coalition Algorithm, Coalition Formation Environment and Model Rational agents which are involved in a co-operative game (A,v) are...publicly available simulation environment for coalition formation among rational information agents based on selected classic coalition theories is, for

Removing the barrier to the calculation of activation energies

DOE PAGES

Mesele, Oluwaseun O.; Thompson, Ward H.

2016-10-06

Approaches for directly calculating the activation energy for a chemical reaction from a simulation at a single temperature are explored with applications to both classical and quantum systems. The activation energy is obtained from a time correlation function that can be evaluated from the same molecular dynamics trajectories or quantum dynamics used to evaluate the rate constant itself and thus requires essentially no extra computational work.

On the emission of radiation by an isolated vibrating metallic mirror

NASA Astrophysics Data System (ADS)

Arkhipov, M. V.; Babushkin, I.; Pul'kin, N. S.; Arkhipov, R. M.; Rosanov, N. N.

2017-04-01

Quantum electrodynamics predicts the appearance of radiation in an empty cavity in which one of the mirrors is vibrating. It also predicts the appearance of radiation from an isolated vibrating mirror. Such effects can be described within the framework of classical electrodynamics. We present the qualitative explanation of the effect, along with the results of numerical simulation of the emission of radiation by an isolated vibrating metallic mirror, which can be induced by mirror illumination by an ultrashort pulse of light. The dynamics of conduction electrons in the metallic mirror is described by the classical Drude model. Simulation was performed for the cases of mirror illumination by either a bipolar or a unipolar pulse.

Nonmonotonic Classical Magnetoconductivity of a Two-Dimensional Electron Gas in a Disordered Array of Obstacles

NASA Astrophysics Data System (ADS)

Siboni, N. H.; Schluck, J.; Pierz, K.; Schumacher, H. W.; Kazazis, D.; Horbach, J.; Heinzel, T.

2018-02-01

Magnetotransport measurements in combination with molecular dynamics simulations on two-dimensional disordered Lorentz gases in the classical regime are reported. In quantitative agreement between experiment and simulation, the magnetoconductivity displays a pronounced peak as a function of the perpendicular magnetic field B which cannot be explained by existing kinetic theories. This peak is linked to the onset of a directed motion of the electrons along the contour of the disordered obstacle matrix when the cyclotron radius becomes smaller than the size of the obstacles. This directed motion leads to transient superdiffusive motion and strong scaling corrections in the vicinity of the insulator-to-conductor transitions of the Lorentz gas.

Evolutionary dynamics of a smoothed war of attrition game.

PubMed

Iyer, Swami; Killingback, Timothy

2016-05-07

In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game assumes that no errors are made in the implementation of an animal׳s strategy. However, it is inevitable in reality that such errors must sometimes occur. Here we introduce an extension of the classical War of Attrition game which includes the effect of errors in the implementation of an individual׳s strategy. This extension of the classical game has the important feature that the payoff is continuous, and as a consequence admits evolutionary behavior that is fundamentally different from that possible in the original game. We study the evolutionary dynamics of this new game in well-mixed populations both analytically using adaptive dynamics and through individual-based simulations, and show that there are a variety of possible outcomes, including simple monomorphic or dimorphic configurations which are evolutionarily stable and cannot occur in the classical War of Attrition game. In addition, we study the evolutionary dynamics of this extended game in a variety of spatially and socially structured populations, as represented by different complex network topologies, and show that similar outcomes can also occur in these situations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Adsorption of Aqueous Crude Oil Components on the Basal Surfaces of Clay Minerals: Molecular Simulations Including Salinity and Temperature Effects

DOE PAGES

Greathouse, J. A.; Cygan, R. T.; Fredrich, J. T.; ...

2017-09-28

Molecular simulations of the adsorption of representative organic molecules onto the basal surfaces of various clay minerals were used to assess the mechanisms of enhanced oil recovery associated with salinity changes and water flooding. Simulations at the density functional theory (DFT) and classical levels provide insights into the molecular structure, binding energy, and interfacial behavior of saturate, aromatic, and resin molecules near clay mineral surfaces. Periodic DFT calculations reveal binding geometries and ion pairing mechanisms at mineral surfaces while also providing a basis for validating the classical force field approach. Through classical molecular dynamics simulations, the influence of aqueous cationsmore » at the interface and the role of water solvation are examined to better evaluate the dynamical nature of cation-organic complexes and their co-adsorption onto the clay surfaces. The extent of adsorption is controlled by the hydrophilic nature and layer charge of the clay mineral. All organic species studied showed preferential adsorption on hydrophobic mineral surfaces. However, the anionic form of the resin (decahydro-2-naphthoic acid)—expected to be prevalent at near-neutral pH conditions in petroleum reservoirs—readily adsorbs to the hydrophilic kaolinite surface through a combination of cation pairing and hydrogen bonding with surface hydroxyl groups. Analysis of cation-organic pairing in both the adsorbed and desorbed states reveals a strong preference for organic anions to coordinate with divalent calcium ions rather than monovalent sodium ions, lending support to current theories regarding low-salinity water flooding.« less

Adsorption of Aqueous Crude Oil Components on the Basal Surfaces of Clay Minerals: Molecular Simulations Including Salinity and Temperature Effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greathouse, J. A.; Cygan, R. T.; Fredrich, J. T.

Molecular simulations of the adsorption of representative organic molecules onto the basal surfaces of various clay minerals were used to assess the mechanisms of enhanced oil recovery associated with salinity changes and water flooding. Simulations at the density functional theory (DFT) and classical levels provide insights into the molecular structure, binding energy, and interfacial behavior of saturate, aromatic, and resin molecules near clay mineral surfaces. Periodic DFT calculations reveal binding geometries and ion pairing mechanisms at mineral surfaces while also providing a basis for validating the classical force field approach. Through classical molecular dynamics simulations, the influence of aqueous cationsmore » at the interface and the role of water solvation are examined to better evaluate the dynamical nature of cation-organic complexes and their co-adsorption onto the clay surfaces. The extent of adsorption is controlled by the hydrophilic nature and layer charge of the clay mineral. All organic species studied showed preferential adsorption on hydrophobic mineral surfaces. However, the anionic form of the resin (decahydro-2-naphthoic acid)—expected to be prevalent at near-neutral pH conditions in petroleum reservoirs—readily adsorbs to the hydrophilic kaolinite surface through a combination of cation pairing and hydrogen bonding with surface hydroxyl groups. Analysis of cation-organic pairing in both the adsorbed and desorbed states reveals a strong preference for organic anions to coordinate with divalent calcium ions rather than monovalent sodium ions, lending support to current theories regarding low-salinity water flooding.« less

Time evolution of linearized gauge field fluctuations on a real-time lattice

NASA Astrophysics Data System (ADS)

Kurkela, A.; Lappi, T.; Peuron, J.

2016-12-01

Classical real-time lattice simulations play an important role in understanding non-equilibrium phenomena in gauge theories and are used in particular to model the prethermal evolution of heavy-ion collisions. Due to instabilities, small quantum fluctuations on top of the classical background may significantly affect the dynamics of the system. In this paper we argue for the need for a numerical calculation of a system of classical gauge fields and small linearized fluctuations in a way that keeps the separation between the two manifest. We derive and test an explicit algorithm to solve these equations on the lattice, maintaining gauge invariance and Gauss' law.

Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Laskin, A.

2017-12-01

Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

Two-temperature model in molecular dynamics simulations of cascades in Ni-based alloys

DOE PAGES

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2017-01-03

In high-energy irradiation events, energy from the fast moving ion is transferred to the system via nuclear and electronic energy loss mechanisms. The nuclear energy loss results in the creation of point defects and clusters, while the energy transferred to the electrons results in the creation of high electronic temperatures, which can affect the damage evolution. In this paper, we perform molecular dynamics simulations of 30 keV and 50 keV Ni ion cascades in nickel-based alloys without and with the electronic effects taken into account. We compare the results of classical molecular dynamics (MD) simulations, where the electronic effects aremore » ignored, with results from simulations that include the electronic stopping only, as well as simulations where both the electronic stopping and the electron-phonon coupling are incorporated, as described by the two temperature model (2T-MD). Finally, our results indicate that the 2T-MD leads to a smaller amount of damage, more isolated defects and smaller defect clusters.« less

Molecular Simulations of The Formation of Gold-Molecule-Gold Junctions

NASA Astrophysics Data System (ADS)

Wang, Huachuan

2013-03-01

We perform classical molecular simulations by combining grand canonical Monte Carlo (GCMC) sampling with molecular dynamics (MD) simulation to explore the dynamic gold nanojunctions in a Alkenedithiol (ADT) solvent. With the aid of a simple driving-spring model, which can reasonably represent the long-range elasticity of the gold electrode, the spring forces are obtained during the dynamic stretching procedure. A specific multi-time-scale double reversible reference system propagator (double-RESPA) algorithm has been designed for the metal-organic complex in MD simulations to identify the detailed metal-molecule bonding geometry at metal-molecule-metal interface. We investigate the variations of bonding sites of ADT molecules on gold nanojunctions at Au (111) surface at a constant chemical potential. Simulation results show that an Au-ADT-Au interface is formed on Au nanojunctions, bond-breaking intersection is at 1-1 bond of the monatomic chain of the cross-section, instead of at the Au-S bond. Breaking force is around 1.5 nN. These are consistent with the experimental measurements.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

NASA Astrophysics Data System (ADS)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; Huy Pham, C.; Riera, Marc; Moberg, Daniel R.; Morales, Miguel A.; Knight, Chris; Götz, Andreas W.; Paesani, Francesco

2016-11-01

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulations as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.

Thrust vector control algorithm design for the Cassini spacecraft

NASA Technical Reports Server (NTRS)

Enright, Paul J.

1993-01-01

This paper describes a preliminary design of the thrust vector control algorithm for the interplanetary spacecraft, Cassini. Topics of discussion include flight software architecture, modeling of sensors, actuators, and vehicle dynamics, and controller design and analysis via classical methods. Special attention is paid to potential interactions with structural flexibilities and propellant dynamics. Controller performance is evaluated in a simulation environment built around a multi-body dynamics model, which contains nonlinear models of the relevant hardware and preliminary versions of supporting attitude determination and control functions.

In vitro dynamic model simulating the digestive tract of 6-month-old infants.

PubMed

Passannanti, Francesca; Nigro, Federica; Gallo, Marianna; Tornatore, Fabio; Frasso, Annalisa; Saccone, Giulia; Budelli, Andrea; Barone, Maria V; Nigro, Roberto

2017-01-01

In vivo assays cannot always be conducted because of ethical reasons, technical constraints or costs, but a better understanding of the digestive process, especially in infants, could be of great help in preventing food-related pathologies and in developing new formulas with health benefits. In this context, in vitro dynamic systems to simulate human digestion and, in particular, infant digestion could become increasingly valuable. To simulate the digestive process through the use of a dynamic model of the infant gastroenteric apparatus to study the digestibility of starch-based infant foods. Using M.I.D.A (Model of an Infant Digestive Apparatus), the oral, gastric and intestinal digestibility of two starch-based products were measured: 1) rice starch mixed with distilled water and treated using two different sterilization methods (the classical method with a holding temperature of 121°C for 37 min and the HTST method with a holding temperature of 137°C for 70 sec) and 2) a rice cream with (premium product) or without (basic product) an aliquot of rice flour fermented by Lactobacillus paracasei CBA L74. After the digestion the foods were analyzed for the starch concentration, the amount of D-glucose released and the percentage of hydrolyzed starch. An in vitro dynamic system, which was referred to as M.I.D.A., was obtained. Using this system, the starch digestion occurred only during the oral and intestinal phase, as expected. The D-glucose released during the intestinal phase was different between the classical and HTST methods (0.795 grams for the HTST versus 0.512 for the classical product). The same analysis was performed for the basic and premium products. In this case, the premium product had a significant difference in terms of the starch hydrolysis percentage during the entire process. The M.I.D.A. system was able to digest simple starches and a more complex food in the correct compartments. In this study, better digestibility of the premium product was revealed.

Ion-ion dynamic structure factor of warm dense mixtures

DOE PAGES

Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; ...

2015-06-25

In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ionmore » dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.« less

Dynamics of Topological Excitations in a Model Quantum Spin Ice

NASA Astrophysics Data System (ADS)

Huang, Chun-Jiong; Deng, Youjin; Wan, Yuan; Meng, Zi Yang

2018-04-01

We study the quantum spin dynamics of a frustrated X X Z model on a pyrochlore lattice by using large-scale quantum Monte Carlo simulation and stochastic analytic continuation. In the low-temperature quantum spin ice regime, we observe signatures of coherent photon and spinon excitations in the dynamic spin structure factor. As the temperature rises to the classical spin ice regime, the photon disappears from the dynamic spin structure factor, whereas the dynamics of the spinon remain coherent in a broad temperature window. Our results provide experimentally relevant, quantitative information for the ongoing pursuit of quantum spin ice materials.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Qiang

The rational design of materials, the development of accurate and efficient material simulation algorithms, and the determination of the response of materials to environments and loads occurring in practice all require an understanding of mechanics at disparate spatial and temporal scales. The project addresses mathematical and numerical analyses for material problems for which relevant scales range from those usually treated by molecular dynamics all the way up to those most often treated by classical elasticity. The prevalent approach towards developing a multiscale material model couples two or more well known models, e.g., molecular dynamics and classical elasticity, each of whichmore » is useful at a different scale, creating a multiscale multi-model. However, the challenges behind such a coupling are formidable and largely arise because the atomistic and continuum models employ nonlocal and local models of force, respectively. The project focuses on a multiscale analysis of the peridynamics materials model. Peridynamics can be used as a transition between molecular dynamics and classical elasticity so that the difficulties encountered when directly coupling those two models are mitigated. In addition, in some situations, peridynamics can be used all by itself as a material model that accurately and efficiently captures the behavior of materials over a wide range of spatial and temporal scales. Peridynamics is well suited to these purposes because it employs a nonlocal model of force, analogous to that of molecular dynamics; furthermore, at sufficiently large length scales and assuming smooth deformation, peridynamics can be approximated by classical elasticity. The project will extend the emerging mathematical and numerical analysis of peridynamics. One goal is to develop a peridynamics-enabled multiscale multi-model that potentially provides a new and more extensive mathematical basis for coupling classical elasticity and molecular dynamics, thus enabling next generation atomistic-to-continuum multiscale simulations. In addition, a rigorous studyof nite element discretizations of peridynamics will be considered. Using the fact that peridynamics is spatially derivative free, we will also characterize the space of admissible peridynamic solutions and carry out systematic analyses of the models, in particular rigorously showing how peridynamics encompasses fracture and other failure phenomena. Additional aspects of the project include the mathematical and numerical analysis of peridynamics applied to stochastic peridynamics models. In summary, the project will make feasible mathematically consistent multiscale models for the analysis and design of advanced materials.« less

Quantum Spin Glasses, Annealing and Computation

NASA Astrophysics Data System (ADS)

Chakrabarti, Bikas K.; Inoue, Jun-ichi; Tamura, Ryo; Tanaka, Shu

2017-05-01

List of tables; List of figures, Preface; 1. Introduction; Part I. Quantum Spin Glass, Annealing and Computation: 2. Classical spin models from ferromagnetic spin systems to spin glasses; 3. Simulated annealing; 4. Quantum spin glass; 5. Quantum dynamics; 6. Quantum annealing; Part II. Additional Notes: 7. Notes on adiabatic quantum computers; 8. Quantum information and quenching dynamics; 9. A brief historical note on the studies of quantum glass, annealing and computation.

Homogeneous nucleation in supersaturated vapors of methane, ethane, and carbon dioxide predicted by brute force molecular dynamics.

PubMed

Horsch, Martin; Vrabec, Jadran; Bernreuther, Martin; Grottel, Sebastian; Reina, Guido; Wix, Andrea; Schaber, Karlheinz; Hasse, Hans

2008-04-28

Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a 10(6) particles were conducted with a massively parallel MD program. This leads to reliable statistics and makes nucleation rates down to the order of 10(30) m(-3) s(-1) accessible to the direct simulation approach. Simulation results are compared to the classical nucleation theory (CNT) as well as the modification of Laaksonen, Ford, and Kulmala (LFK) which introduces a size dependence of the specific surface energy. CNT describes the nucleation of ethane and carbon dioxide excellently over the entire studied temperature range, whereas LFK provides a better approach to methane at low temperatures.

PyRETIS: A well-done, medium-sized python library for rare events.

PubMed

Lervik, Anders; Riccardi, Enrico; van Erp, Titus S

2017-10-30

Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Method for construction of a biased potential for hyperdynamic simulation of atomic systems

NASA Astrophysics Data System (ADS)

Duda, E. V.; Kornich, G. V.

2017-10-01

An approach to constructing a biased potential for hyperdynamic simulation of atomic systems is considered. Using this approach, the diffusion of an atom adsorbed on the surface of a two-dimensional crystal and a vacancy in the bulk of the crystal are simulated. The influence of the variation in the potential barriers due to thermal vibrations of atoms on the results of calculations is discussed. It is shown that the bias of the potential in the hyperdynamic simulation makes it possible to obtain statistical samples of transitions of atomic systems between states, similar to those given by classical molecular dynamics. However, hyperdynamics significantly accelerates computations in comparison with molecular dynamics in the case of temperature-activated transitions and the associated processes in atomic systems.

First-principles simulations of heat transport

NASA Astrophysics Data System (ADS)

Puligheddu, Marcello; Gygi, Francois; Galli, Giulia

2017-11-01

Advances in understanding heat transport in solids were recently reported by both experiment and theory. However an efficient and predictive quantum simulation framework to investigate thermal properties of solids, with the same complexity as classical simulations, has not yet been developed. Here we present a method to compute the thermal conductivity of solids by performing ab initio molecular dynamics at close to equilibrium conditions, which only requires calculations of first-principles trajectories and atomic forces, thus avoiding direct computation of heat currents and energy densities. In addition the method requires much shorter sequential simulation times than ordinary molecular dynamics techniques, making it applicable within density functional theory. We discuss results for a representative oxide, MgO, at different temperatures and for ordered and nanostructured morphologies, showing the performance of the method in different conditions.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics.

PubMed

de Buyl, Pierre; Nies, Erik

2015-04-07

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics

NASA Astrophysics Data System (ADS)

de Buyl, Pierre; Nies, Erik

2015-04-01

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

DOE PAGES

Gordiz, Kiarash; Singh, David J.; Henry, Asegun

2015-01-29

In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

Transient chaos - a resolution of breakdown of quantum-classical correspondence in optomechanics.

PubMed

Wang, Guanglei; Lai, Ying-Cheng; Grebogi, Celso

2016-10-17

Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories. The transient behavior is consistent with chaos in the classical limit, while the long term evolution of the quantum system is regular. Transient chaos thus serves as a bridge for the quantum-classical transition (QCT). Strikingly, as the system transitions from the quantum to the classical regime, the average chaotic transient lifetime increases dramatically (faster than the Ehrenfest time characterizing the QCT for isolated quantum systems). We develop a physical theory to explain the scaling law.

Transient chaos - a resolution of breakdown of quantum-classical correspondence in optomechanics

PubMed Central

Wang, Guanglei; Lai, Ying-Cheng; Grebogi, Celso

2016-01-01

Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories. The transient behavior is consistent with chaos in the classical limit, while the long term evolution of the quantum system is regular. Transient chaos thus serves as a bridge for the quantum-classical transition (QCT). Strikingly, as the system transitions from the quantum to the classical regime, the average chaotic transient lifetime increases dramatically (faster than the Ehrenfest time characterizing the QCT for isolated quantum systems). We develop a physical theory to explain the scaling law. PMID:27748418

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

DOE PAGES

Zhan, Cheng; Lian, Cheng; Zhang, Yu; ...

2017-04-24

Supercapacitors such as electric double-layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double-layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte-Carlo (MC) methods. In recent years, combining first-principles and classical simulations to investigate the carbon-based EDLCs has shed light on the importance of quantum capacitance in graphene-like 2D systems. More recently, the development of joint density functional theorymore » (JDFT) enables self-consistent electronic-structure calculation for an electrode being solvated by an electrolyte. In contrast with the large amount of theoretical and computational effort on EDLCs, theoretical understanding of pseudocapacitance is very limited. In this review, we first introduce popular modeling methods and then focus on several important aspects of EDLCs including nanoconfinement, quantum capacitance, dielectric screening, and novel 2D electrode design; we also briefly touch upon pseudocapactive mechanism in RuO 2. We summarize and conclude with an outlook for the future of materials simulation and design for capacitive energy storage.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao Xiaoqiang; Wang Hongfu; Zhang Shou

We present an approach for implementation of a 1->3 orbital state quantum cloning machine based on the quantum Zeno dynamics via manipulating three rf superconducting quantum interference device (SQUID) qubits to resonantly interact with a superconducting cavity assisted by classical fields. Through appropriate modulation of the coupling constants between rf SQUIDs and classical fields, the quantum cloning machine can be realized within one step. We also discuss the effects of decoherence such as spontaneous emission and the loss of cavity in virtue of master equation. The numerical simulation result reveals that the quantum cloning machine is especially robust against themore » cavity decay, since all qubits evolve in the decoherence-free subspace with respect to cavity decay due to the quantum Zeno dynamics.« less

A classical phase r-centroid approach to molecular wave packet dynamics illustrating the danger of using an incomplete set of initial states for thermal averaging

NASA Astrophysics Data System (ADS)

Hansson, Tony

1999-08-01

An inexpensive semiclassical method to simulate time-resolved pump-probe spectroscopy on molecular wave packets is applied to NaK molecules at high temperature. The method builds on the introduction of classical phase factors related to the r-centroids for vibronic transitions and assumes instantaneous laser-molecule interaction. All observed quantum mechanical features are reproduced - for short times where experimental data are available even quantitatively. Furthermore, it is shown that fully quantum dynamical molecular wave packet calculations on molecules at elevated temperatures, which do not include all rovibrational states, must be regarded with caution, as they easily might yield even qualitatively incorrect results.

Simple improvements to classical bubble nucleation models.

PubMed

Tanaka, Kyoko K; Tanaka, Hidekazu; Angélil, Raymond; Diemand, Jürg

2015-08-01

We revisit classical nucleation theory (CNT) for the homogeneous bubble nucleation rate and improve the classical formula using a correct prefactor in the nucleation rate. Most of the previous theoretical studies have used the constant prefactor determined by the bubble growth due to the evaporation process from the bubble surface. However, the growth of bubbles is also regulated by the thermal conduction, the viscosity, and the inertia of liquid motion. These effects can decrease the prefactor significantly, especially when the liquid pressure is much smaller than the equilibrium one. The deviation in the nucleation rate between the improved formula and the CNT can be as large as several orders of magnitude. Our improved, accurate prefactor and recent advances in molecular dynamics simulations and laboratory experiments for argon bubble nucleation enable us to precisely constrain the free energy barrier for bubble nucleation. Assuming the correction to the CNT free energy is of the functional form suggested by Tolman, the precise evaluations of the free energy barriers suggest the Tolman length is ≃0.3σ independently of the temperature for argon bubble nucleation, where σ is the unit length of the Lennard-Jones potential. With this Tolman correction and our prefactor one gets accurate bubble nucleation rate predictions in the parameter range probed by current experiments and molecular dynamics simulations.

Molecular dynamics simulations of disjoining pressure effects in ultra-thin water films on a metal surface

NASA Astrophysics Data System (ADS)

Hu, Han; Sun, Ying

2013-11-01

Disjoining pressure, the excess pressure in an ultra-thin liquid film as a result of van der Waals interactions, is important in lubrication, wetting, flow boiling, and thin film evaporation. The classic theory of disjoining pressure is developed for simple monoatomic liquids. However, real world applications often utilize water, a polar liquid, for which fundamental understanding of disjoining pressure is lacking. In the present study, molecular dynamics (MD) simulations are used to gain insights into the effect of disjoining pressure in a water thin film. Our MD models were firstly validated against Derjaguin's experiments on gold-gold interactions across a water film and then verified against disjoining pressure in an argon thin film using the Lennard-Jones potential. Next, a water thin film adsorbed on a gold surface was simulated to examine the change of vapor pressure with film thickness. The results agree well with the classic theory of disjoining pressure, which implies that the polar nature of water molecules does not play an important role. Finally, the effects of disjoining pressure on thin film evaporation in nanoporous membrane and on bubble nucleation are discussed.

Rayleigh instability at small length scales.

PubMed

Gopan, Nandu; Sathian, Sarith P

2014-09-01

The Rayleigh instability (also called the Plateau-Rayleigh instability) of a nanosized liquid propane thread is investigated using molecular dynamics (MD). The validity of classical predictions at small length scales is verified by comparing the temporal evolution of liquid thread simulated by MD against classical predictions. Previous works have shown that thermal fluctuations become dominant at small length scales. The role and influence of the stochastic nature of thermal fluctuations in determining the instability at small length scale is also investigated. Thermal fluctuations are seen to dominate and accelerate the breakup process only during the last stages of breakup. The simulations also reveal that the breakup profile of nanoscale threads undergo modification due to reorganization of molecules by the evaporation-condensation process.

Hybrid molecular dynamics simulation for plasma induced damage analysis

NASA Astrophysics Data System (ADS)

Matsukuma, Masaaki

2016-09-01

In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam experiments. This observed damage profile dependence on species and substrate cannot be reproduced using classical MD simulations. While the Moliere potential is convenient to describe the interactions between halogens and other atoms, more accurate interatomic modeling such as DFTB method which takes the molecular orbitals into account should be utilized to make the simulations more realistic. Based on the simulations results, the damage formation scenario will be discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Torii, Hajime, E-mail: torii.hajime@shizuoka.ac.jp

The intensity of the band at ∼200 cm{sup −1} (∼6 THz) in the Terahertz spectrum of liquid water mainly arises from the modulations of the extent of intermolecular charge transfer through hydrogen bonds, called intermolecular charge fluxes, occurring upon molecular translations along the O…H hydrogen bonds. To obtain reasonable spectral profiles from simulations, it is necessary to effectively incorporate the effects of those intermolecular charge fluxes, but apparently it is not possible by simple classical molecular dynamics simulations with fixed atomic partial charges even if they are amended by molecular induced dipoles due to intermolecular electrostatic interactions. The present paper showsmore » how we can do reasonably correct spectral simulations, without resorting to fully ab initio molecular dynamics.« less

Molecular Dynamics Simulations of the Interfacial Region between Boehmite and Gibbsite Basal Surfaces and High Ionic Strength Aqueous Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Zhizhang; Ilton, Eugene S.; Prange, Micah P.

Classical molecular dynamics (MD) simulations were used to study the interactions of up to 2 M NaCl and NaNO3 aqueous solutions with the presumed inert boehmite (010) and gibbsite (001) surfaces. The force field parameters used in these simulations were validated against density functional theory calculations of Na+ and Cl- hydrated complexes adsorbed at the boehmite (010) surface. In all the classical MD simulations and regardless of the ionic strength or the nature of the anion, Na+ ions were found to preferably form inner-sphere complexes over outer-sphere complexes at the aluminum (oxy)hydroxide surfaces, adsorbing closer to the surface than bothmore » water molecules and anions. In contrast, Cl- ions were distributed almost equally between inner- and outer-sphere positions. The resulting asymmetry in adsorption strengths offers molecular-scale evidence for the observed isoelectric point (IEP) shift to higher pH at high ionic strength for aluminum (oxy)hydroxides. As such, the MD simulations also provided clear evidence against the assumption that the basal surfaces of boehmite and gibbsite are inert to background electrolytes. Finally, the MD simulations indicated that, although the adsorption behavior of Na+ in NaNO3 and NaCl solutions was similar, the different affinities of NO3- and Cl- for the aluminum (oxy)hydroxide surfaces might have macroscopic consequences, such as difference in the sensitivity of the IEP to the electrolyte concentration.« less

Chandrasekhar's dynamical friction and non-extensive statistics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silva, J.M.; Lima, J.A.S.; De Souza, R.E.

2016-05-01

The motion of a point like object of mass M passing through the background potential of massive collisionless particles ( m || M ) suffers a steady deceleration named dynamical friction. In his classical work, Chandrasekhar assumed a Maxwellian velocity distribution in the halo and neglected the self gravity of the wake induced by the gravitational focusing of the mass M . In this paper, by relaxing the validity of the Maxwellian distribution due to the presence of long range forces, we derive an analytical formula for the dynamical friction in the context of the q -nonextensive kinetic theory. Inmore » the extensive limiting case ( q = 1), the classical Gaussian Chandrasekhar result is recovered. As an application, the dynamical friction timescale for Globular Clusters spiraling to the galactic center is explicitly obtained. Our results suggest that the problem concerning the large timescale as derived by numerical N -body simulations or semi-analytical models can be understood as a departure from the standard extensive Maxwellian regime as measured by the Tsallis nonextensive q -parameter.« less

Many-body kinetics of dynamic nuclear polarization by the cross effect

NASA Astrophysics Data System (ADS)

Karabanov, A.; Wiśniewski, D.; Raimondi, F.; Lesanovsky, I.; Köckenberger, W.

2018-03-01

Dynamic nuclear polarization (DNP) is an out-of-equilibrium method for generating nonthermal spin polarization which provides large signal enhancements in modern diagnostic methods based on nuclear magnetic resonance. A particular instance is cross-effect DNP, which involves the interaction of two coupled electrons with the nuclear spin ensemble. Here we develop a theory for this important DNP mechanism and show that the nonequilibrium nuclear polarization buildup is effectively driven by three-body incoherent Markovian dissipative processes involving simultaneous state changes of two electrons and one nucleus. We identify different parameter regimes for effective polarization transfer and discuss under which conditions the polarization dynamics can be simulated by classical kinetic Monte Carlo methods. Our theoretical approach allows simulations of the polarization dynamics on an individual spin level for ensembles consisting of hundreds of nuclear spins. The insight obtained by these simulations can be used to find optimal experimental conditions for cross-effect DNP and to design tailored radical systems that provide optimal DNP efficiency.

Membrane surface engineering for protein separations: experiments and simulations.

PubMed

Liu, Zizhao; Du, Hongbo; Wickramasinghe, S Ranil; Qian, Xianghong

2014-09-09

A bisphosphonate derived ligand was successfully synthesized and grafted from the surface of regenerated cellulose membrane using atom transfer radical polymerization (ATRP) for protein separations. This ligand has a remarkable affinity for arginine (Arg) residues on protein surface. Hydrophilic residues N-(2-hydroxypropyl) methacrylamide (HPMA) was copolymerized to enhance the flexibility of the copolymer ligand and further improve specific protein adsorption. The polymerization of bisphosphonate derivatives was successful for the first time using ATRP. Static and dynamic binding capacities were determined for binding and elution of Arg rich lysozyme. The interaction mechanism between the copolymer ligand and lysozyme was elucidated using classical molecular dynamics (MD) simulations.

Subtle Monte Carlo Updates in Dense Molecular Systems.

PubMed

Bottaro, Sandro; Boomsma, Wouter; E Johansson, Kristoffer; Andreetta, Christian; Hamelryck, Thomas; Ferkinghoff-Borg, Jesper

2012-02-14

Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.

A plasma source driven predator-prey like mechanism as a potential cause of spiraling intermittencies in linear plasma devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reiser, D.; Ohno, N.; Tanaka, H.

2014-03-15

Three-dimensional global drift fluid simulations are carried out to analyze coherent plasma structures appearing in the NAGDIS-II linear device (nagoya divertor plasma Simulator-II). The numerical simulations reproduce several features of the intermittent spiraling structures observed, for instance, statistical properties, rotation frequency, and the frequency of plasma expulsion. The detailed inspection of the three-dimensional plasma dynamics allows to identify the key mechanism behind the formation of these intermittent events. The resistive coupling between electron pressure and parallel electric field in the plasma source region gives rise to a quasilinear predator-prey like dynamics where the axisymmetric mode represents the prey and themore » spiraling structure with low azimuthal mode number represents the predator. This interpretation is confirmed by a reduced one-dimensional quasilinear model derived on the basis of the findings in the full three-dimensional simulations. The dominant dynamics reveals certain similarities to the classical Lotka-Volterra cycle.« less

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory

NASA Astrophysics Data System (ADS)

Langenbach, K.; Heilig, M.; Horsch, M.; Hasse, H.

2018-03-01

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO2). The molecular model of CO2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory.

PubMed

Langenbach, K; Heilig, M; Horsch, M; Hasse, H

2018-03-28

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO 2 ). The molecular model of CO 2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.

PubMed

Zheng, Mo; Li, Xiaoxia; Guo, Li

2013-04-01

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

Transfer of training for aerospace operations: How to measure, validate, and improve it

NASA Technical Reports Server (NTRS)

Cohen, Malcolm M.

1993-01-01

It has been a commonly accepted practice to train pilots and astronauts in expensive, extremely sophisticated, high fidelity simulators, with as much of the real-world feel and response as possible. High fidelity and high validity have often been assumed to be inextricably interwoven, although this assumption may not be warranted. The Project Mercury rate-damping task on the Naval Air Warfare Center's Human Centrifuge Dynamic Flight Simulator, the shuttle landing task on the NASA-ARC Vertical Motion Simulator, and the almost complete acceptance by the airline industry of full-up Boeing 767 flight simulators, are just a few examples of this approach. For obvious reasons, the classical models of transfer of training have never been adequately evaluated in aerospace operations, and there have been few, if any, scientifically valid replacements for the classical models. This paper reviews some of the earlier work involving transfer of training in aerospace operations, and discusses some of the methods by which appropriate criteria for assessing the validity of training may be established.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

DOE PAGES

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; ...

2016-11-17

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

Atomic quantum simulation of dynamical gauge fields coupled to fermionic matter: from string breaking to evolution after a quench.

PubMed

Banerjee, D; Dalmonte, M; Müller, M; Rico, E; Stebler, P; Wiese, U-J; Zoller, P

2012-10-26

Using a Fermi-Bose mixture of ultracold atoms in an optical lattice, we construct a quantum simulator for a U(1) gauge theory coupled to fermionic matter. The construction is based on quantum links which realize continuous gauge symmetry with discrete quantum variables. At low energies, quantum link models with staggered fermions emerge from a Hubbard-type model which can be quantum simulated. This allows us to investigate string breaking as well as the real-time evolution after a quench in gauge theories, which are inaccessible to classical simulation methods.

A Simulation Tool for Dynamic Contrast Enhanced MRI

PubMed Central

Mauconduit, Franck; Christen, Thomas; Barbier, Emmanuel Luc

2013-01-01

The quantification of bolus-tracking MRI techniques remains challenging. The acquisition usually relies on one contrast and the analysis on a simplified model of the various phenomena that arise within a voxel, leading to inaccurate perfusion estimates. To evaluate how simplifications in the interstitial model impact perfusion estimates, we propose a numerical tool to simulate the MR signal provided by a dynamic contrast enhanced (DCE) MRI experiment. Our model encompasses the intrinsic and relaxations, the magnetic field perturbations induced by susceptibility interfaces (vessels and cells), the diffusion of the water protons, the blood flow, the permeability of the vessel wall to the the contrast agent (CA) and the constrained diffusion of the CA within the voxel. The blood compartment is modeled as a uniform compartment. The different blocks of the simulation are validated and compared to classical models. The impact of the CA diffusivity on the permeability and blood volume estimates is evaluated. Simulations demonstrate that the CA diffusivity slightly impacts the permeability estimates ( for classical blood flow and CA diffusion). The effect of long echo times is investigated. Simulations show that DCE-MRI performed with an echo time may already lead to significant underestimation of the blood volume (up to 30% lower for brain tumor permeability values). The potential and the versatility of the proposed implementation are evaluated by running the simulation with realistic vascular geometry obtained from two photons microscopy and with impermeable cells in the extravascular environment. In conclusion, the proposed simulation tool describes DCE-MRI experiments and may be used to evaluate and optimize acquisition and processing strategies. PMID:23516414

Neuromorphic Implementation of Attractor Dynamics in a Two-Variable Winner-Take-All Circuit with NMDARs: A Simulation Study

PubMed Central

You, Hongzhi; Wang, Da-Hui

2017-01-01

Neural networks configured with winner-take-all (WTA) competition and N-methyl-D-aspartate receptor (NMDAR)-mediated synaptic dynamics are endowed with various dynamic characteristics of attractors underlying many cognitive functions. This paper presents a novel method for neuromorphic implementation of a two-variable WTA circuit with NMDARs aimed at implementing decision-making, working memory and hysteresis in visual perceptions. The method proposed is a dynamical system approach of circuit synthesis based on a biophysically plausible WTA model. Notably, slow and non-linear temporal dynamics of NMDAR-mediated synapses was generated. Circuit simulations in Cadence reproduced ramping neural activities observed in electrophysiological recordings in experiments of decision-making, the sustained activities observed in the prefrontal cortex during working memory, and classical hysteresis behavior during visual discrimination tasks. Furthermore, theoretical analysis of the dynamical system approach illuminated the underlying mechanisms of decision-making, memory capacity and hysteresis loops. The consistence between the circuit simulations and theoretical analysis demonstrated that the WTA circuit with NMDARs was able to capture the attractor dynamics underlying these cognitive functions. Their physical implementations as elementary modules are promising for assembly into integrated neuromorphic cognitive systems. PMID:28223913

Neuromorphic Implementation of Attractor Dynamics in a Two-Variable Winner-Take-All Circuit with NMDARs: A Simulation Study.

PubMed

You, Hongzhi; Wang, Da-Hui

2017-01-01

Neural networks configured with winner-take-all (WTA) competition and N-methyl-D-aspartate receptor (NMDAR)-mediated synaptic dynamics are endowed with various dynamic characteristics of attractors underlying many cognitive functions. This paper presents a novel method for neuromorphic implementation of a two-variable WTA circuit with NMDARs aimed at implementing decision-making, working memory and hysteresis in visual perceptions. The method proposed is a dynamical system approach of circuit synthesis based on a biophysically plausible WTA model. Notably, slow and non-linear temporal dynamics of NMDAR-mediated synapses was generated. Circuit simulations in Cadence reproduced ramping neural activities observed in electrophysiological recordings in experiments of decision-making, the sustained activities observed in the prefrontal cortex during working memory, and classical hysteresis behavior during visual discrimination tasks. Furthermore, theoretical analysis of the dynamical system approach illuminated the underlying mechanisms of decision-making, memory capacity and hysteresis loops. The consistence between the circuit simulations and theoretical analysis demonstrated that the WTA circuit with NMDARs was able to capture the attractor dynamics underlying these cognitive functions. Their physical implementations as elementary modules are promising for assembly into integrated neuromorphic cognitive systems.

The effect of host relaxation and dynamics on guest molecule dynamics in H2/tetrahydrofuranhydrate.

PubMed

Peterson, Vanessa K; Shoko, Elvis; Kearley, Gordon J

2011-01-01

We use ab initio molecular dynamics simulations to obtain classically the effects of H2O cage motions on the potential-energy surface (PES) of encapsulated H2 in the H2/tetrahydrofuran-hydrate system. The significant differences between the PES for the H2 in rigid and flexible cages that we find will influence calculation of the quantum dynamics of the H2. Part of these differences arises from the relaxation of the H2O cage around the classical H2, with a second part arising from the coupling of both translational and rotational motions of H2 with the H20 cage. We find that isotopic substitution of 2H for 1H of the H2O cage affects the coupling, which has implications for experiments that require the use of 2H2O, including inelastic neutron scattering that uses 2H2O cages in order to focus on the H2 guest dynamics. Overall, this work emphasizes the importance of taking into account cage dynamics in any approach used to understand the dynamics of H2 guests in porous framework materials.

Dynamics of open quantum systems by interpolation of von Neumann and classical master equations, and its application to quantum annealing

NASA Astrophysics Data System (ADS)

Kadowaki, Tadashi

2018-02-01

We propose a method to interpolate dynamics of von Neumann and classical master equations with an arbitrary mixing parameter to investigate the thermal effects in quantum dynamics. The two dynamics are mixed by intervening to continuously modify their solutions, thus coupling them indirectly instead of directly introducing a coupling term. This maintains the quantum system in a pure state even after the introduction of thermal effects and obtains not only a density matrix but also a state vector representation. Further, we demonstrate that the dynamics of a two-level system can be rewritten as a set of standard differential equations, resulting in quantum dynamics that includes thermal relaxation. These equations are equivalent to the optical Bloch equations at the weak coupling and asymptotic limits, implying that the dynamics cause thermal effects naturally. Numerical simulations of ferromagnetic and frustrated systems support this idea. Finally, we use this method to study thermal effects in quantum annealing, revealing nontrivial performance improvements for a spin glass model over a certain range of annealing time. This result may enable us to optimize the annealing time of real annealing machines.

Investigation of the Dynamic Contact Angle Using a Direct Numerical Simulation Method.

PubMed

Zhu, Guangpu; Yao, Jun; Zhang, Lei; Sun, Hai; Li, Aifen; Shams, Bilal

2016-11-15

A large amount of residual oil, which exists as isolated oil slugs, remains trapped in reservoirs after water flooding. Numerous numerical studies are performed to investigate the fundamental flow mechanism of oil slugs to improve flooding efficiency. Dynamic contact angle models are usually introduced to simulate an accurate contact angle and meniscus displacement of oil slugs under a high capillary number. Nevertheless, in the oil slug flow simulation process, it is unnecessary to introduce the dynamic contact angle model because of a negligible change in the meniscus displacement after using the dynamic contact angle model when the capillary number is small. Therefore, a critical capillary number should be introduced to judge whether the dynamic contact model should be incorporated into simulations. In this study, a direct numerical simulation method is employed to simulate the oil slug flow in a capillary tube at the pore scale. The position of the interface between water and the oil slug is determined using the phase-field method. The capacity and accuracy of the model are validated using a classical benchmark: a dynamic capillary filling process. Then, different dynamic contact angle models and the factors that affect the dynamic contact angle are analyzed. The meniscus displacements of oil slugs with a dynamic contact angle and a static contact angle (SCA) are obtained during simulations, and the relative error between them is calculated automatically. The relative error limit has been defined to be 5%, beyond which the dynamic contact angle model needs to be incorporated into the simulation to approach the realistic displacement. Thus, the desired critical capillary number can be determined. A three-dimensional universal chart of critical capillary number, which functions as static contact angle and viscosity ratio, is given to provide a guideline for oil slug simulation. Also, a fitting formula is presented for ease of use.

Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium

DOE PAGES

Smith, Kyle K.G.; Poulsen, Jens Aage; Nyman, Gunnar; ...

2015-06-30

Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm -3) and (T = 23.0 K, n = 24.61 nm -3), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this showsmore » that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Kyle K.G.; Poulsen, Jens Aage; Nyman, Gunnar

Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm -3) and (T = 23.0 K, n = 24.61 nm -3), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this showsmore » that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Application of a new ensemble conserving quantum dynamics simulation algorithm to liquid para-hydrogen and ortho-deuterium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Kyle K. G., E-mail: kylesmith@utexas.edu; Poulsen, Jens Aage, E-mail: jens72@chem.gu.se; Nyman, Gunnar, E-mail: nyman@chem.gu.se

We apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −3}), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. This shows that FK-QCWmore » provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Application of a new ensemble conserving quantum dynamics simulation algorithm to liquid para-hydrogen and ortho-deuterium.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Nyman, Gunnar; Cunsolo, Alessandro; Rossky, Peter J

2015-06-28

We apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm(-3)) and (T = 23.0 K, n = 24.61 nm(-3)), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. This shows that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

Dislocation Dissociation Strongly Influences on Frank—Read Source Nucleation and Microplasticy of Materials with Low Stacking Fault Energy

NASA Astrophysics Data System (ADS)

Huang, Min-Sheng; Zhu, Ya-Xin; Li, Zhen-Huan

2014-04-01

The influence of dislocation dissociation on the evolution of Frank—Read (F-R) sources is studied using a three-dimensional discrete dislocation dynamics simulation (3D-DDD). The classical Orowan nucleation stress and recently proposed Benzerga nucleation time models for F-R sources are improved. This work shows that it is necessary to introduce the dislocation dissociation scheme into 3D-DDD simulation, especially for simulations on micro-plasticity of small sized materials with low stacking fault energy.

Porting LAMMPS to GPUs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, William Michael; Plimpton, Steven James; Wang, Peng

2010-03-01

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalewski, Markus, E-mail: mkowalew@uci.edu; Mukamel, Shaul, E-mail: smukamel@uci.edu

2015-07-28

Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.

Classical plasma dynamics of Mie-oscillations in atomic clusters

NASA Astrophysics Data System (ADS)

Kull, H.-J.; El-Khawaldeh, A.

2018-04-01

Mie plasmons are of basic importance for the absorption of laser light by atomic clusters. In this work we first review the classical Rayleigh-theory of a dielectric sphere in an external electric field and Thomson’s plum-pudding model applied to atomic clusters. Both approaches allow for elementary discussions of Mie oscillations, however, they also indicate deficiencies in describing the damping mechanisms by electrons crossing the cluster surface. Nonlinear oscillator models have been widely studied to gain an understanding of damping and absorption by outer ionization of the cluster. In the present work, we attempt to address the issue of plasmon relaxation in atomic clusters in more detail based on classical particle simulations. In particular, we wish to study the role of thermal motion on plasmon relaxation, thereby extending nonlinear models of collective single-electron motion. Our simulations are particularly adopted to the regime of classical kinetics in weakly coupled plasmas and to cluster sizes extending the Debye-screening length. It will be illustrated how surface scattering leads to the relaxation of Mie oscillations in the presence of thermal motion and of electron spill-out at the cluster surface. This work is intended to give, from a classical perspective, further insight into recent work on plasmon relaxation in quantum plasmas [1].

Absolute comparison of simulated and experimental protein-folding dynamics

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Nguyen, Houbi; Pande, Vijay S.; Gruebele, Martin

2002-11-01

Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as α-helices and β-hairpins can form in 0.1-10µs (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds. The longest folding simulation to date is a single 1-µs simulation of the villin headpiece; however, such single runs may miss many features of the folding process as it is a heterogeneous reaction involving an ensemble of transition states. Here, we have used a distributed computing implementation to produce tens of thousands of 5-20-ns trajectories (700µs) to simulate mutants of the designed mini-protein BBA5. The fast relaxation dynamics these predict were compared with the results of laser temperature-jump experiments. Our computational predictions are in excellent agreement with the experimentally determined mean folding times and equilibrium constants. The rapid folding of BBA5 is due to the swift formation of secondary structure. The convergence of experimentally and computationally accessible timescales will allow the comparison of absolute quantities characterizing in vitro and in silico (computed) protein folding.

Molecular dynamics-driven drug discovery: leaping forward with confidence.

PubMed

Ganesan, Aravindhan; Coote, Michelle L; Barakat, Khaled

2017-02-01

Given the significant time and financial costs of developing a commercial drug, it remains important to constantly reform the drug discovery pipeline with novel technologies that can narrow the candidates down to the most promising lead compounds for clinical testing. The past decade has witnessed tremendous growth in computational capabilities that enable in silico approaches to expedite drug discovery processes. Molecular dynamics (MD) has become a particularly important tool in drug design and discovery. From classical MD methods to more sophisticated hybrid classical/quantum mechanical (QM) approaches, MD simulations are now able to offer extraordinary insights into ligand-receptor interactions. In this review, we discuss how the applications of MD approaches are significantly transforming current drug discovery and development efforts. Copyright © 2016 Elsevier Ltd. All rights reserved.

Symmetric solitonic excitations of the (1 + 1)-dimensional Abelian-Higgs classical vacuum.

PubMed

Diakonos, F K; Katsimiga, G C; Maintas, X N; Tsagkarakis, C E

2015-02-01

We study the classical dynamics of the Abelian-Higgs model in (1 + 1) space-time dimensions for the case of strongly broken gauge symmetry. In this limit the wells of the potential are almost harmonic and sufficiently deep, presenting a scenario far from the associated critical point. Using a multiscale perturbation expansion, the equations of motion for the fields are reduced to a system of coupled nonlinear Schrödinger equations. Exact solutions of the latter are used to obtain approximate analytical solutions for the full dynamics of both the gauge and Higgs field in the form of oscillons and oscillating kinks. Numerical simulations of the exact dynamics verify the validity of these solutions. We explore their persistence for a wide range of the model's single parameter, which is the ratio of the Higgs mass (m(H)) to the gauge-field mass (m(A)). We show that only oscillons oscillating symmetrically with respect to the "classical vacuum," for both the gauge and the Higgs field, are long lived. Furthermore, plane waves and oscillating kinks are shown to decay into oscillon-like patterns, due to the modulation instability mechanism.

Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

PubMed

Cendagorta, Joseph R; Powers, Anna; Hele, Timothy J H; Marsalek, Ondrej; Bačić, Zlatko; Tuckerman, Mark E

2016-11-30

Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H 2 and D 2 diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H 2 and D 2 as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H 2 and D 2 diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are strongly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as a result the quantum rate is greater than the classical rate.

Quantifying non-linear dynamics of mass-springs in series oscillators via asymptotic approach

NASA Astrophysics Data System (ADS)

Starosta, Roman; Sypniewska-Kamińska, Grażyna; Awrejcewicz, Jan

2017-05-01

Dynamical regular response of an oscillator with two serially connected springs with nonlinear characteristics of cubic type and governed by a set of differential-algebraic equations (DAEs) is studied. The classical approach of the multiple scales method (MSM) in time domain has been employed and appropriately modified to solve the governing DAEs of two systems, i.e. with one- and two degrees-of-freedom. The approximate analytical solutions have been verified by numerical simulations.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE PAGES

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

2018-03-22

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

PubMed

Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

2016-05-12

An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

NASA Astrophysics Data System (ADS)

Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

2018-05-01

One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

A physical-based gas-surface interaction model for rarefied gas flow simulation

NASA Astrophysics Data System (ADS)

Liang, Tengfei; Li, Qi; Ye, Wenjing

2018-01-01

Empirical gas-surface interaction models, such as the Maxwell model and the Cercignani-Lampis model, are widely used as the boundary condition in rarefied gas flow simulations. The accuracy of these models in the prediction of macroscopic behavior of rarefied gas flows is less satisfactory in some cases especially the highly non-equilibrium ones. Molecular dynamics simulation can accurately resolve the gas-surface interaction process at atomic scale, and hence can predict accurate macroscopic behavior. They are however too computationally expensive to be applied in real problems. In this work, a statistical physical-based gas-surface interaction model, which complies with the basic relations of boundary condition, is developed based on the framework of the washboard model. In virtue of its physical basis, this new model is capable of capturing some important relations/trends for which the classic empirical models fail to model correctly. As such, the new model is much more accurate than the classic models, and in the meantime is more efficient than MD simulations. Therefore, it can serve as a more accurate and efficient boundary condition for rarefied gas flow simulations.

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Nuclear quantum effects in water exchange around lithium and fluoride ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, David M.; Manolopoulos, David; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the water exchange reactions are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium, and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium. LXD was supported by US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

ATK-ForceField: a new generation molecular dynamics software package

NASA Astrophysics Data System (ADS)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution.

PubMed

Silva, Daniel L; Murugan, N Arul; Kongsted, Jacob; Rinkevicius, Zilvinas; Canuto, Sylvio; Ågren, Hans

2012-07-19

Solvent effects on the one- and two-photon absorption (1PA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations.

PubMed

Oleinikovas, Vladimiras; Saladino, Giorgio; Cossins, Benjamin P; Gervasio, Francesco L

2016-11-02

Cryptic pockets, that is, sites on protein targets that only become apparent when drugs bind, provide a promising alternative to classical binding sites for drug development. Here, we investigate the nature and dynamical properties of cryptic sites in four pharmacologically relevant targets, while comparing the efficacy of various simulation-based approaches in discovering them. We find that the studied cryptic sites do not correspond to local minima in the computed conformational free energy landscape of the unliganded proteins. They thus promptly close in all of the molecular dynamics simulations performed, irrespective of the force-field used. Temperature-based enhanced sampling approaches, such as Parallel Tempering, do not improve the situation, as the entropic term does not help in the opening of the sites. The use of fragment probes helps, as in long simulations occasionally it leads to the opening and binding to the cryptic sites. Our observed mechanism of cryptic site formation is suggestive of an interplay between two classical mechanisms: induced-fit and conformational selection. Employing this insight, we developed a novel Hamiltonian Replica Exchange-based method "SWISH" (Sampling Water Interfaces through Scaled Hamiltonians), which combined with probes resulted in a promising general approach for cryptic site discovery. We also addressed the issue of "false-positives" and propose a simple approach to distinguish them from druggable cryptic pockets. Our simulations, whose cumulative sampling time was more than 200 μs, help in clarifying the molecular mechanism of pocket formation, providing a solid basis for the choice of an efficient computational method.

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

PubMed

Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

2018-01-01

Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

Quantum-Inspired Maximizer

NASA Technical Reports Server (NTRS)

Zak, Michail

2008-01-01

A report discusses an algorithm for a new kind of dynamics based on a quantum- classical hybrid-quantum-inspired maximizer. The model is represented by a modified Madelung equation in which the quantum potential is replaced by different, specially chosen 'computational' potential. As a result, the dynamics attains both quantum and classical properties: it preserves superposition and entanglement of random solutions, while allowing one to measure its state variables, using classical methods. Such optimal combination of characteristics is a perfect match for quantum-inspired computing. As an application, an algorithm for global maximum of an arbitrary integrable function is proposed. The idea of the proposed algorithm is very simple: based upon the Quantum-inspired Maximizer (QIM), introduce a positive function to be maximized as the probability density to which the solution is attracted. Then the larger value of this function will have the higher probability to appear. Special attention is paid to simulation of integer programming and NP-complete problems. It is demonstrated that the problem of global maximum of an integrable function can be found in polynomial time by using the proposed quantum- classical hybrid. The result is extended to a constrained maximum with applications to integer programming and TSP (Traveling Salesman Problem).

CO{sub 2} isolated line shapes by classical molecular dynamics simulations: Influence of the intermolecular potential and comparison with new measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larcher, G.; Tran, H., E-mail: ha.tran@lisa.u-pec.fr; Schwell, M.

2014-02-28

Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 μm and 0.8 μm regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both themore » Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.« less

A simulator for discrete quantum walks on lattices

NASA Astrophysics Data System (ADS)

Rodrigues, J.; Paunković, N.; Mateus, P.

In this paper, we present a simulator for two-particle quantum walks on the line and one-particle on a two-dimensional squared lattice. It can be used to investigate the equivalence between the two cases (one- and two-particle walks) for various boundary conditions (open, circular, reflecting, absorbing and their combinations). For the case of a single walker on a two-dimensional lattice, the simulator can also implement the Möbius strip. Furthermore, other topologies for the walker are also simulated by the proposed tool, like certain types of planar graphs with degree up to 4, by considering missing links over the lattice. The main purpose of the simulator is to study the genuinely quantum effects on the global properties of the two-particle joint probability distribution on the entanglement between the walkers/axis. For that purpose, the simulator is designed to compute various quantities such as: the entanglement and classical correlations, (classical and quantum) mutual information, the average distance between the two walkers, different hitting times and quantum discord. These quantities are of vital importance in designing possible algorithmic applications of quantum walks, namely in search, 3-SAT problems, etc. The simulator can also implement the static partial measurements of particle(s) positions and dynamic breaking of the links between certain nodes, both of which can be used to investigate the effects of decoherence on the walker(s). Finally, the simulator can be used to investigate the dynamic Anderson-like particle localization by varying the coin operators of certain nodes on the line/lattice. We also present some illustrative and relevant examples of one- and two-particle quantum walks in various scenarios. The tool was implemented in C and is available on-line at http://qwsim.weebly.com/.

Structure and dynamics of propylammonium nitrate-acetonitrile mixtures: An intricate multi-scale system probed with experimental and theoretical techniques.

PubMed

Campetella, Marco; Mariani, Alessandro; Sadun, Claudia; Wu, Boning; Castner, Edward W; Gontrani, Lorenzo

2018-04-07

In this article, we report the study of structural and dynamical properties for a series of acetonitrile/propylammonium nitrate mixtures as a function of their composition. These systems display an unusual increase in intensity in their X-ray diffraction patterns in the low-q regime, and their 1 H-NMR diffusion-ordered NMR spectroscopy (DOSY) spectra display unusual diffusivities. However, the magnitude of both phenomena for mixtures of propylammonium nitrate is smaller than those observed for ethylammonium nitrate mixtures with the same cosolvent, suggesting that the cation alkyl tail plays an important role in these observations. The experimental X-ray scattering data are compared with the results of molecular dynamics simulations, including both ab initio studies used to interpret short-range interactions and classical simulations to describe longer range interactions. The higher level calculations highlight the presence of a strong hydrogen bond network within the ionic liquid, only slightly perturbed even at high acetonitrile concentration. These strong interactions lead to the symmetry breaking of the NO 3 - vibrations, with a splitting of about 88 cm -1 in the ν 3 antisymmetric stretch. The classical force field simulations use a greater number of ion pairs, but are not capable of fully describing the longest range interactions, although they do successfully account for the observed concentration trend, and the analysis of the models confirms the nano-inhomogeneity of these kinds of samples.

Structure and dynamics of propylammonium nitrate-acetonitrile mixtures: An intricate multi-scale system probed with experimental and theoretical techniques

NASA Astrophysics Data System (ADS)

Campetella, Marco; Mariani, Alessandro; Sadun, Claudia; Wu, Boning; Castner, Edward W.; Gontrani, Lorenzo

2018-04-01

In this article, we report the study of structural and dynamical properties for a series of acetonitrile/propylammonium nitrate mixtures as a function of their composition. These systems display an unusual increase in intensity in their X-ray diffraction patterns in the low-q regime, and their 1H-NMR diffusion-ordered NMR spectroscopy (DOSY) spectra display unusual diffusivities. However, the magnitude of both phenomena for mixtures of propylammonium nitrate is smaller than those observed for ethylammonium nitrate mixtures with the same cosolvent, suggesting that the cation alkyl tail plays an important role in these observations. The experimental X-ray scattering data are compared with the results of molecular dynamics simulations, including both ab initio studies used to interpret short-range interactions and classical simulations to describe longer range interactions. The higher level calculations highlight the presence of a strong hydrogen bond network within the ionic liquid, only slightly perturbed even at high acetonitrile concentration. These strong interactions lead to the symmetry breaking of the NO3 - vibrations, with a splitting of about 88 cm-1 in the ν3 antisymmetric stretch. The classical force field simulations use a greater number of ion pairs, but are not capable of fully describing the longest range interactions, although they do successfully account for the observed concentration trend, and the analysis of the models confirms the nano-inhomogeneity of these kinds of samples.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, La Tonya Nicole; Malczynski, Leonard A.

DYNAMO is a computer program for building and running 'continuous' simulation models. It was developed by the Industrial Dynamics Group at the Massachusetts Institute of Technology for simulating dynamic feedback models of business, economic, and social systems. The history of the system dynamics method since 1957 includes many classic models built in DYANMO. It was not until the late 1980s that software was built to take advantage of the rise of personal computers and graphical user interfaces that DYNAMO was supplanted. There is much learning and insight to be gained from examining the DYANMO models and their accompanying research papers.more » We believe that it is a worthwhile exercise to convert DYNAMO models to more recent software packages. We have made an attempt to make it easier to turn these models into a more current system dynamics software language, Powersim © Studio produced by Powersim AS 2 of Bergen, Norway. This guide shows how to convert DYNAMO syntax into Studio syntax.« less

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

PubMed Central

Craveur, Pierrick; Joseph, Agnel Praveen; Jallu, Vincent

2017-01-01

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license. PMID:29177113

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

PubMed Central

Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

2015-01-01

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. PMID:26156459

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Quantum spin chains with multiple dynamics

NASA Astrophysics Data System (ADS)

Chen, Xiao; Fradkin, Eduardo; Witczak-Krempa, William

2017-11-01

Many-body systems with multiple emergent time scales arise in various contexts, including classical critical systems, correlated quantum materials, and ultracold atoms. We investigate such nontrivial quantum dynamics in a different setting: a spin-1 bilinear-biquadratic chain. It has a solvable entangled ground state, but a gapless excitation spectrum that is poorly understood. By using large-scale density matrix renormalization group simulations, we find that the lowest excitations have a dynamical exponent z that varies from 2 to 3.2 as we vary a coupling in the Hamiltonian. We find an additional gapless mode with a continuously varying exponent 2 ≤z <2.7 , which establishes the presence of multiple dynamics. In order to explain these striking properties, we construct a continuum wave function for the ground state, which correctly describes the correlations and entanglement properties. We also give a continuum parent Hamiltonian, but show that additional ingredients are needed to capture the excitations of the chain. By using an exact mapping to the nonequilibrium dynamics of a classical spin chain, we find that the large dynamical exponent is due to subdiffusive spin motion. Finally, we discuss the connections to other spin chains and to a family of quantum critical models in two dimensions.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

Nuclear quantum dynamics in dense hydrogen

PubMed Central

Kang, Dongdong; Sun, Huayang; Dai, Jiayu; Chen, Wenbo; Zhao, Zengxiu; Hou, Yong; Zeng, Jiaolong; Yuan, Jianmin

2014-01-01

Nuclear dynamics in dense hydrogen, which is determined by the key physics of large-angle scattering or many-body collisions between particles, is crucial for the dynamics of planet's evolution and hydrodynamical processes in inertial confinement confusion. Here, using improved ab initio path-integral molecular dynamics simulations, we investigated the nuclear quantum dynamics regarding transport behaviors of dense hydrogen up to the temperatures of 1 eV. With the inclusion of nuclear quantum effects (NQEs), the ionic diffusions are largely higher than the classical treatment by the magnitude from 20% to 146% as the temperature is decreased from 1 eV to 0.3 eV at 10 g/cm3, meanwhile, electrical and thermal conductivities are significantly lowered. In particular, the ionic diffusion is found much larger than that without NQEs even when both the ionic distributions are the same at 1 eV. The significant quantum delocalization of ions introduces remarkably different scattering cross section between protons compared with classical particle treatments, which explains the large difference of transport properties induced by NQEs. The Stokes-Einstein relation, Wiedemann-Franz law, and isotope effects are re-examined, showing different behaviors in nuclear quantum dynamics. PMID:24968754

NEPTUNE'S WILD DAYS: CONSTRAINTS FROM THE ECCENTRICITY DISTRIBUTION OF THE CLASSICAL KUIPER BELT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dawson, Rebekah I.; Murray-Clay, Ruth, E-mail: rdawson@cfa.harvard.edu

2012-05-01

Neptune's dynamical history shaped the current orbits of Kuiper Belt objects (KBOs), leaving clues to the planet's orbital evolution. In the 'classical' region, a population of dynamically 'hot' high-inclination KBOs overlies a flat 'cold' population with distinct physical properties. Simulations of qualitatively different histories for Neptune, including smooth migration on a circular orbit or scattering by other planets to a high eccentricity, have not simultaneously produced both populations. We explore a general Kuiper Belt assembly model that forms hot classical KBOs interior to Neptune and delivers them to the classical region, where the cold population forms in situ. First, wemore » present evidence that the cold population is confined to eccentricities well below the limit dictated by long-term survival. Therefore, Neptune must deliver hot KBOs into the long-term survival region without excessively exciting the eccentricities of the cold population. Imposing this constraint, we explore the parameter space of Neptune's eccentricity and eccentricity damping, migration, and apsidal precession. We rule out much of parameter space, except where Neptune is scattered to a moderately eccentric orbit (e > 0.15) and subsequently migrates a distance {Delta}a{sub N} = 1-6 AU. Neptune's moderate eccentricity must either damp quickly or be accompanied by fast apsidal precession. We find that Neptune's high eccentricity alone does not generate a chaotic sea in the classical region. Chaos can result from Neptune's interactions with Uranus, exciting the cold KBOs and placing additional constraints. Finally, we discuss how to interpret our constraints in the context of the full, complex dynamical history of the solar system.« less

Spontaneous cavitation in a Lennard-Jones liquid: Molecular dynamics simulation and the van der Waals-Cahn-Hilliard gradient theory

NASA Astrophysics Data System (ADS)

Baidakov, Vladimir G.

2016-02-01

The process of bubble nucleation in a Lennard-Jones (LJ) liquid is studied by molecular dynamics (MD) simulation. The bubble nucleation rate J is determined by the mean life-time method at temperatures above that of the triple point in the region of negative pressures. The results of simulation are compared with classical nucleation theory (CNT) and modified classical nucleation theory (MCNT), in which the work of formation of a critical bubble is determined in the framework of the van der Waals-Cahn-Hilliard gradient theory (GT). It has been found that the values of J obtained in MD simulation systematically exceed the data of CNT, and this excess in the nucleation rate reaches 8-10 orders of magnitude close to the triple point temperature. The results of MCNT are in satisfactory agreement with the data of MD simulation. To describe the properties of vapor-phase nuclei in the framework of GT, an equation of state has been built up which describes stable, metastable and labile regions of LJ fluids. The surface tension of critical bubbles γ has been found from CNT and data of MD simulation as a function of the radius of curvature of the surface of tension R*. The dependence γ(R*) has also been calculated from GT. The Tolman length has been determined, which is negative and in modulus equal to ≈(0.1 - 0.2) σ. The paper discusses the applicability of the Tolman formula to the description of the properties of critical nuclei in nucleation.

Structure and Dynamics of Hydroxyl-Functionalized Protic Ammonium Carboxylate Ionic Liquids.

PubMed

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

We performed classical molecular dynamics simulations to investigate the structure and dynamics of protic ionic liquids, 2-hydroxy ethylammonium acetate, ethylammonium hydroxyacetate, and 2-hydroxyethylammonium hydroxyacetate at ambient conditions. Structural properties such as density, radial distribution functions, spatial distribution functions, and structure factors have been calculated. Dynamic properties such as mean square displacements, as well as residence and hydrogen bond dynamics have also been calculated. Hydrogen bond lifetimes and residence times change with the addition of hydroxyl groups. We observe that when a hydroxyl group is present on the cation, dynamics become very slow and it forms a strong hydrogen bond with carboxylate oxygen atoms of the anion. The hydroxyl functionalized ILs show more dynamic diversity than structurally similar ILs.

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter.

PubMed

Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D

2015-01-01

Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis.

Thermophysical properties of liquid Ni around the melting temperature from molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rozas, R. E.; Department of Physics, University of Bío-Bío, Av. Collao 1202, P.O. Box 5C, Concepción; Demiraǧ, A. D.

Thermophysical properties of liquid nickel (Ni) around the melting temperature are investigated by means of classical molecular dynamics (MD) simulation, using three different embedded atom method potentials to model the interactions between the Ni atoms. Melting temperature, enthalpy, static structure factor, self-diffusion coefficient, shear viscosity, and thermal diffusivity are compared to recent experimental results. Using ab initio MD simulation, we also determine the static structure factor and the mean-squared displacement at the experimental melting point. For most of the properties, excellent agreement is found between experiment and simulation, provided the comparison relative to the corresponding melting temperature. We discuss themore » validity of the Hansen-Verlet criterion for the static structure factor as well as the Stokes-Einstein relation between self-diffusion coefficient and shear viscosity. The thermal diffusivity is extracted from the autocorrelation function of a wavenumber-dependent temperature fluctuation variable.« less

Classical Molecular Dynamics Simulation of Nuclear Fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

2015-10-10

Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a varietymore » of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.« less

Development of interatomic potential of Ge(1- x - y )Si x Sn y ternary alloy semiconductors for classical lattice dynamics simulation

NASA Astrophysics Data System (ADS)

Tomita, Motohiro; Ogasawara, Masataka; Terada, Takuya; Watanabe, Takanobu

2018-04-01

We provide the parameters of Stillinger-Weber potentials for GeSiSn ternary mixed systems. These parameters can be used in molecular dynamics (MD) simulations to reproduce phonon properties and thermal conductivities. The phonon dispersion relation is derived from the dynamical structure factor, which is calculated by the space-time Fourier transform of atomic trajectories in an MD simulation. The phonon properties and thermal conductivities of GeSiSn ternary crystals calculated using these parameters mostly reproduced both the findings of previous experiments and earlier calculations made using MD simulations. The atomic composition dependence of these properties in GeSiSn ternary crystals obtained by previous studies (both experimental and theoretical) and the calculated data were almost exactly reproduced by our proposed parameters. Moreover, the results of the MD simulation agree with the previous calculations made using a time-independent phonon Boltzmann transport equation with complicated scattering mechanisms. These scattering mechanisms are very important in complicated nanostructures, as they allow the heat-transfer properties to be more accurately calculated by MD simulations. This work enables us to predict the phonon- and heat-related properties of bulk group IV alloys, especially ternary alloys.

In vitro dynamic model simulating the digestive tract of 6-month-old infants

PubMed Central

Gallo, Marianna; Tornatore, Fabio; Frasso, Annalisa; Saccone, Giulia; Budelli, Andrea; Barone, Maria V.

2017-01-01

Background In vivo assays cannot always be conducted because of ethical reasons, technical constraints or costs, but a better understanding of the digestive process, especially in infants, could be of great help in preventing food-related pathologies and in developing new formulas with health benefits. In this context, in vitro dynamic systems to simulate human digestion and, in particular, infant digestion could become increasingly valuable. Objective To simulate the digestive process through the use of a dynamic model of the infant gastroenteric apparatus to study the digestibility of starch-based infant foods. Design Using M.I.D.A (Model of an Infant Digestive Apparatus), the oral, gastric and intestinal digestibility of two starch-based products were measured: 1) rice starch mixed with distilled water and treated using two different sterilization methods (the classical method with a holding temperature of 121°C for 37 min and the HTST method with a holding temperature of 137°C for 70 sec) and 2) a rice cream with (premium product) or without (basic product) an aliquot of rice flour fermented by Lactobacillus paracasei CBA L74. After the digestion the foods were analyzed for the starch concentration, the amount of D-glucose released and the percentage of hydrolyzed starch. Results An in vitro dynamic system, which was referred to as M.I.D.A., was obtained. Using this system, the starch digestion occurred only during the oral and intestinal phase, as expected. The D-glucose released during the intestinal phase was different between the classical and HTST methods (0.795 grams for the HTST versus 0.512 for the classical product). The same analysis was performed for the basic and premium products. In this case, the premium product had a significant difference in terms of the starch hydrolysis percentage during the entire process. Conclusions The M.I.D.A. system was able to digest simple starches and a more complex food in the correct compartments. In this study, better digestibility of the premium product was revealed. PMID:29261742

Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.

2015-07-07

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPDmore » simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.« less

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

Short- and medium-range structure of multicomponent bioactive glasses and melts: An assessment of the performances of shell-model and rigid-ion potentials.

PubMed

Tilocca, Antonio

2008-08-28

Classical and ab initio molecular dynamics (MD) simulations have been carried out to investigate the effect of a different treatment of interatomic forces in modeling the structural properties of multicomponent glasses and melts. The simulated system is a soda-lime phosphosilicate composition with bioactive properties. Because the bioactivity of these materials depends on their medium-range structural features, such as the network connectivity and the Q(n) distribution (where Q(n) is a tetrahedral species bonded to n bridging oxygens) of silicon and phosphorus network formers, it is essential to assess whether, and up to what extent, classical potentials can reproduce these properties. The results indicate that the inclusion of the oxide ion polarization through a shell-model (SM) approach provides a more accurate representation of the medium-range structure compared to rigid-ion (RI) potentials. Insight into the causes of these improvements has been obtained by comparing the melt-and-quench transformation of a small sample of the same system, modeled using Car-Parrinello MD (CPMD), to the classical MD runs with SM and RI potentials. Both classical potentials show some limitations in reproducing the highly distorted structure of the melt denoted by the CPMD runs; however, the inclusion of polarization in the SM potential results in a better and qualitatively correct dynamical balance between the interconversion of Q(n) species during the cooling of the melt. This effect seems to reflect the slower decay of the fraction of structural defects during the cooling with the SM potential. Because these transient defects have a central role in mediating the Q(n) transformations, as previously proposed and confirmed by the current simulations, their presence in the melt is essential to produce an accurate final distribution of Q(n) species in the glass.

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

PubMed

Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

2015-12-15

Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to emulate one ATP cycle of a molecular motor, kinesin. Second, nonspecific protein-DNA binding was studied by a combination of elaborate protein and DNA models. Third, a transcription factor, p53, that contains highly fluctuating regions was simulated on two perpendicularly arranged DNA segments, addressing intersegmental transfer of p53. Fourth, we simulated structural dynamics of dinucleosomes connected by a linker DNA finding distinct types of internucleosome docking and salt-concentration-dependent compaction. Finally, we discuss many of limitations in the current approaches and future directions. Especially, more accurate electrostatic treatment and a phospholipid model that matches our CG resolutions are of immediate importance.

A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Pierre, Sadrach; Duke, Jessica R.; Hele, Timothy J. H.; Ananth, Nandini

2017-12-01

We investigate the mechanisms of condensed phase proton-coupled electron transfer (PCET) using Mapping-Variable Ring Polymer Molecular Dynamics (MV-RPMD), a recently developed method that employs an ensemble of classical trajectories to simulate nonadiabatic excited state dynamics. Here, we construct a series of system-bath model Hamiltonians for the PCET, where four localized electron-proton states are coupled to a thermal bath via a single solvent mode, and we employ MV-RPMD to simulate state population dynamics. Specifically, for each model, we identify the dominant PCET mechanism, and by comparing against rate theory calculations, we verify that our simulations correctly distinguish between concerted PCET, where the electron and proton transfer together, and sequential PCET, where either the electron or the proton transfers first. This work represents a first application of MV-RPMD to multi-level condensed phase systems; we introduce a modified MV-RPMD expression that is derived using a symmetric rather than asymmetric Trotter discretization scheme and an initialization protocol that uses a recently derived population estimator to constrain trajectories to a dividing surface. We also demonstrate that, as expected, the PCET mechanisms predicted by our simulations are robust to an arbitrary choice of the initial dividing surface.

Supersonic N-Crowdions in a Two-Dimensional Morse Crystal

NASA Astrophysics Data System (ADS)

Dmitriev, S. V.; Korznikova, E. A.; Chetverikov, A. P.

2018-03-01

An interstitial atom placed in a close-packed atomic row of a crystal is called crowdion. Such defects are highly mobile; they can move along the row, transferring mass and energy. We generalize the concept of a classical supersonic crowdion to an N-crowdion in which not one but N atoms move simultaneously with a high velocity. Using molecular dynamics simulations for a close-packed two-dimensional Morse crystal, we show that N-crowdions transfer mass much more efficiently, because they are capable of covering large distances while having a lower total energy than that of a classical 1-crowdion.

Stochastic solution to quantum dynamics

NASA Technical Reports Server (NTRS)

John, Sarah; Wilson, John W.

1994-01-01

The quantum Liouville equation in the Wigner representation is solved numerically by using Monte Carlo methods. For incremental time steps, the propagation is implemented as a classical evolution in phase space modified by a quantum correction. The correction, which is a momentum jump function, is simulated in the quasi-classical approximation via a stochastic process. The technique, which is developed and validated in two- and three- dimensional momentum space, extends an earlier one-dimensional work. Also, by developing a new algorithm, the application to bound state motion in an anharmonic quartic potential shows better agreement with exact solutions in two-dimensional phase space.

Classical problems in computational aero-acoustics

NASA Technical Reports Server (NTRS)

Hardin, Jay C.

1996-01-01

In relation to the expected problems in the development of computational aeroacoustics (CAA), the preliminary applications were to classical problems where the known analytical solutions could be used to validate the numerical results. Such comparisons were used to overcome the numerical problems inherent in these calculations. Comparisons were made between the various numerical approaches to the problems such as direct simulations, acoustic analogies and acoustic/viscous splitting techniques. The aim was to demonstrate the applicability of CAA as a tool in the same class as computational fluid dynamics. The scattering problems that occur are considered and simple sources are discussed.

A method for data handling numerical results in parallel OpenFOAM simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anton, Alin; Muntean, Sebastian

Parallel computational fluid dynamics simulations produce vast amount of numerical result data. This paper introduces a method for reducing the size of the data by replaying the interprocessor traffic. The results are recovered only in certain regions of interest configured by the user. A known test case is used for several mesh partitioning scenarios using the OpenFOAM toolkit{sup ®}[1]. The space savings obtained with classic algorithms remain constant for more than 60 Gb of floating point data. Our method is most efficient on large simulation meshes and is much better suited for compressing large scale simulation results than the regular algorithms.

A molecular dynamics study of lithium-containing aprotic heterocyclic ionic liquid electrolytes

NASA Astrophysics Data System (ADS)

Lourenço, Tuanan C.; Zhang, Yong; Costa, Luciano T.; Maginn, Edward J.

2018-05-01

Classical molecular dynamics simulations were performed on twelve different ionic liquids containing aprotic heterocyclic anions doped with Li+. These ionic liquids have been shown to be promising electrolytes for lithium ion batteries. Self-diffusivities, lithium transference numbers, densities, and free volumes were computed as a function of lithium concentration. The dynamics and free volume decreased with increasing lithium concentration, and the trends were rationalized by examining the changes to the liquid structure. Of those examined in the present work, it was found that (methyloxymethyl)triethylphosphonium triazolide ionic liquids have the overall best performance.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

NASA Astrophysics Data System (ADS)

Petrov, Yu V.; Inogamov, N. A.; Mokshin, A. V.; Galimzyanov, B. N.

2018-01-01

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman-Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo-Greenwood with the quantum molecular dynamics calculations.

Predictor-Based Model Reference Adaptive Control

NASA Technical Reports Server (NTRS)

Lavretsky, Eugene; Gadient, Ross; Gregory, Irene M.

2009-01-01

This paper is devoted to robust, Predictor-based Model Reference Adaptive Control (PMRAC) design. The proposed adaptive system is compared with the now-classical Model Reference Adaptive Control (MRAC) architecture. Simulation examples are presented. Numerical evidence indicates that the proposed PMRAC tracking architecture has better than MRAC transient characteristics. In this paper, we presented a state-predictor based direct adaptive tracking design methodology for multi-input dynamical systems, with partially known dynamics. Efficiency of the design was demonstrated using short period dynamics of an aircraft. Formal proof of the reported PMRAC benefits constitute future research and will be reported elsewhere.

Computational quantum-classical boundary of noisy commuting quantum circuits

PubMed Central

Fujii, Keisuke; Tamate, Shuhei

2016-01-01

It is often said that the transition from quantum to classical worlds is caused by decoherence originated from an interaction between a system of interest and its surrounding environment. Here we establish a computational quantum-classical boundary from the viewpoint of classical simulatability of a quantum system under decoherence. Specifically, we consider commuting quantum circuits being subject to decoherence. Or equivalently, we can regard them as measurement-based quantum computation on decohered weighted graph states. To show intractability of classical simulation in the quantum side, we utilize the postselection argument and crucially strengthen it by taking noise effect into account. Classical simulatability in the classical side is also shown constructively by using both separable criteria in a projected-entangled-pair-state picture and the Gottesman-Knill theorem for mixed state Clifford circuits. We found that when each qubit is subject to a single-qubit complete-positive-trace-preserving noise, the computational quantum-classical boundary is sharply given by the noise rate required for the distillability of a magic state. The obtained quantum-classical boundary of noisy quantum dynamics reveals a complexity landscape of controlled quantum systems. This paves a way to an experimentally feasible verification of quantum mechanics in a high complexity limit beyond classically simulatable region. PMID:27189039

Computational quantum-classical boundary of noisy commuting quantum circuits.

PubMed

Fujii, Keisuke; Tamate, Shuhei

2016-05-18

It is often said that the transition from quantum to classical worlds is caused by decoherence originated from an interaction between a system of interest and its surrounding environment. Here we establish a computational quantum-classical boundary from the viewpoint of classical simulatability of a quantum system under decoherence. Specifically, we consider commuting quantum circuits being subject to decoherence. Or equivalently, we can regard them as measurement-based quantum computation on decohered weighted graph states. To show intractability of classical simulation in the quantum side, we utilize the postselection argument and crucially strengthen it by taking noise effect into account. Classical simulatability in the classical side is also shown constructively by using both separable criteria in a projected-entangled-pair-state picture and the Gottesman-Knill theorem for mixed state Clifford circuits. We found that when each qubit is subject to a single-qubit complete-positive-trace-preserving noise, the computational quantum-classical boundary is sharply given by the noise rate required for the distillability of a magic state. The obtained quantum-classical boundary of noisy quantum dynamics reveals a complexity landscape of controlled quantum systems. This paves a way to an experimentally feasible verification of quantum mechanics in a high complexity limit beyond classically simulatable region.

Computational quantum-classical boundary of noisy commuting quantum circuits

NASA Astrophysics Data System (ADS)

Fujii, Keisuke; Tamate, Shuhei

2016-05-01

It is often said that the transition from quantum to classical worlds is caused by decoherence originated from an interaction between a system of interest and its surrounding environment. Here we establish a computational quantum-classical boundary from the viewpoint of classical simulatability of a quantum system under decoherence. Specifically, we consider commuting quantum circuits being subject to decoherence. Or equivalently, we can regard them as measurement-based quantum computation on decohered weighted graph states. To show intractability of classical simulation in the quantum side, we utilize the postselection argument and crucially strengthen it by taking noise effect into account. Classical simulatability in the classical side is also shown constructively by using both separable criteria in a projected-entangled-pair-state picture and the Gottesman-Knill theorem for mixed state Clifford circuits. We found that when each qubit is subject to a single-qubit complete-positive-trace-preserving noise, the computational quantum-classical boundary is sharply given by the noise rate required for the distillability of a magic state. The obtained quantum-classical boundary of noisy quantum dynamics reveals a complexity landscape of controlled quantum systems. This paves a way to an experimentally feasible verification of quantum mechanics in a high complexity limit beyond classically simulatable region.

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

PubMed

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. © 2016 Wiley Periodicals, Inc.

Dynamics and Chemistry in Jovian Atmospheres: 2D Hydrodynamical Simulations

NASA Astrophysics Data System (ADS)

Bordwell, B. R.; Brown, B. P.; Oishi, J.

2016-12-01

A key component of our understanding of the formation and evolution of planetary systems is chemical composition. Problematically, however, in the atmospheres of cooler gas giants, dynamics on the same timescale as chemical reactions pull molecular abundances out of thermochemical equilibrium. These disequilibrium abundances are treated using what is known as the "quench" approximation, based upon the mixing length theory of convection. The validity of this approximation is questionable, though, as the atmospheres of gas giants encompass two distinct dynamic regimes: convective and radiative. To resolve this issue, we conduct 2D hydrodynamical simulations using the state-of-the-art pseudospectral simulation framework Dedalus. In these simulations, we solve the fully compressible equations of fluid motion in a local slab geometry that mimics the structure of a planetary atmosphere (convective zone underlying a radiative zone). Through the inclusion of passive tracers, we explore the transport properties of both regimes, and assess the validity of the classical eddy diffusion parameterization. With the addition of active tracers, we examine the interactions between dynamical and chemical processes, and generate prescriptions for the observational community. By providing insight into mixing and feedback mechanisms in Jovian atmospheres, this research lays a solid foundation for future global simulations and the construction of physically-sound models for current and future observations.

Computer simulation of liquid metals

NASA Astrophysics Data System (ADS)

Belashchenko, D. K.

2013-12-01

Methods for and the results of the computer simulation of liquid metals are reviewed. Two basic methods, classical molecular dynamics with known interparticle potentials and the ab initio method, are considered. Most attention is given to the simulated results obtained using the embedded atom model (EAM). The thermodynamic, structural, and diffusion properties of liquid metal models under normal and extreme (shock) pressure conditions are considered. Liquid-metal simulated results for the Groups I - IV elements, a number of transition metals, and some binary systems (Fe - C, Fe - S) are examined. Possibilities for the simulation to account for the thermal contribution of delocalized electrons to energy and pressure are considered. Solidification features of supercooled metals are also discussed.

Oligopolies with contingent workforce and unemployment insurance systems

NASA Astrophysics Data System (ADS)

Matsumoto, Akio; Merlone, Ugo; Szidarovszky, Ferenc

2015-10-01

In the recent literature the introduction of modified cost functions has added reality into the classical oligopoly analysis. Furthermore, the market evolution requires much more flexibility to firms, and in several countries contingent workforce plays an important role in the production choices by the firms. Therefore, an analysis of dynamic adjustment costs is in order to understand oligopoly dynamics. In this paper, dynamic single-product oligopolies without product differentiation are first examined with the additional consideration of production adjustment costs. Linear inverse demand and cost functions are considered and it is assumed that the firms adjust their outputs partially toward best response. The set of the steady states is characterized by a system of linear inequalities and there are usually infinitely many steady states. The asymptotic behavior of the output trajectories is examined by using computer simulation. The numerical results indicate that the resulting dynamics is richer than in the case of the classical Cournot model. This model and results are then compared to oligopolies with unemployment insurance systems when the additional cost is considered if firms do not use their maximum capacities.

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

A multi-state trajectory method for non-adiabatic dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Guohua, E-mail: taogh@pkusz.edu.cn

2016-03-07

A multi-state trajectory approach is proposed to describe nuclear-electron coupled dynamics in nonadiabatic simulations. In this approach, each electronic state is associated with an individual trajectory, among which electronic transition occurs. The set of these individual trajectories constitutes a multi-state trajectory, and nuclear dynamics is described by one of these individual trajectories as the system is on the corresponding state. The total nuclear-electron coupled dynamics is obtained from the ensemble average of the multi-state trajectories. A variety of benchmark systems such as the spin-boson system have been tested and the results generated using the quasi-classical version of the method showmore » reasonably good agreement with the exact quantum calculations. Featured in a clear multi-state picture, high efficiency, and excellent numerical stability, the proposed method may have advantages in being implemented to realistic complex molecular systems, and it could be straightforwardly applied to general nonadiabatic dynamics involving multiple states.« less

Molecular dynamics simulation of square graphene-nanoflake oscillator on graphene nanoribbon.

PubMed

Kang, Jeong Won; Lee, Kang Whan

2014-12-01

Graphene nanoflakes (GNFs) have been of interest for a building block in order to develop electromechanical devices on a nanometer scale. Here, we present the oscillation motions of a square GNF oscillator on graphene nanoribbon (GNR) in the retracting-motions by performing classical molecular dynamics simulations. The simulation results showed that the GNF oscillators can be considered as a building block for nanoelectromechanical systems such as carbon-nanotube (CNT) oscillators. The oscillation dynamics of the GNF oscillator were similar to those of the CNT oscillators. When the square GNF had an initial velocity as impulse dynamics, its oscillation motions on the GNR were achieved from its self-retracting van der Waals force. For low initial velocity, its translational motions were dominant in its motions rather than its rotational motions. The kinetic energy damping ratio rapidly decreased as initial velocity increased and the kinetic energy for the translational motion of the GNF oscillator rapidly transferred into that for its rotational motion. The oscillation frequency of the GNF oscillator was dependent on its initial velocity.

Universal self-similar dynamics of relativistic and nonrelativistic field theories near nonthermal fixed points

NASA Astrophysics Data System (ADS)

Piñeiro Orioli, Asier; Boguslavski, Kirill; Berges, Jürgen

2015-07-01

We investigate universal behavior of isolated many-body systems far from equilibrium, which is relevant for a wide range of applications from ultracold quantum gases to high-energy particle physics. The universality is based on the existence of nonthermal fixed points, which represent nonequilibrium attractor solutions with self-similar scaling behavior. The corresponding dynamic universality classes turn out to be remarkably large, encompassing both relativistic as well as nonrelativistic quantum and classical systems. For the examples of nonrelativistic (Gross-Pitaevskii) and relativistic scalar field theory with quartic self-interactions, we demonstrate that infrared scaling exponents as well as scaling functions agree. We perform two independent nonperturbative calculations, first by using classical-statistical lattice simulation techniques and second by applying a vertex-resummed kinetic theory. The latter extends kinetic descriptions to the nonperturbative regime of overoccupied modes. Our results open new perspectives to learn from experiments with cold atoms aspects about the dynamics during the early stages of our universe.

Femtosecond dynamics and laser control of charge transport in trans-polyacetylene.

PubMed

Franco, Ignacio; Shapiro, Moshe; Brumer, Paul

2008-06-28

The induction of dc electronic transport in rigid and flexible trans-polyacetylene oligomers according to the omega versus 2omega coherent control scenario is investigated using a quantum-classical mean field approximation. The approach involves running a large ensemble of mixed quantum-classical trajectories under the influence of omega+2omega laser fields and choosing the initial conditions by sampling the ground-state Wigner distribution function for the nuclei. The vibronic couplings are shown to change the mean single-particle spectrum, introduce ultrafast decoherence, and enhance intramolecular vibrational and electronic relaxation. Nevertheless, even in the presence of significant couplings, limited coherent control of the electronic dynamics is still viable, the most promising route involving the use of femtosecond pulses with a duration that is comparable to the electronic dephasing time. The simulations offer a realistic description of the behavior of a simple coherent control scenario in a complex system and provide a detailed account of the femtosecond photoinduced vibronic dynamics of a conjugated polymer.

Translational, rotational and vibrational relaxation dynamics of a solute molecule in a non-interacting solvent.

PubMed

Grubb, Michael P; Coulter, Philip M; Marroux, Hugo J B; Hornung, Balazs; McMullen, Ryan S; Orr-Ewing, Andrew J; Ashfold, Michael N R

2016-11-01

Spectroscopically observing the translational and rotational motion of solute molecules in liquid solutions is typically impeded by their interactions with the solvent, which conceal spectral detail through linewidth broadening. Here we show that unique insights into solute dynamics can be made with perfluorinated solvents, which interact weakly with solutes and provide a simplified liquid environment that helps to bridge the gap in our understanding of gas- and liquid-phase dynamics. Specifically, we show that in such solvents, the translational and rotational cooling of an energetic CN radical can be observed directly using ultrafast transient absorption spectroscopy. We observe that translational-energy dissipation within these liquids can be modelled through a series of classic collisions, whereas classically simulated rotational-energy dissipation is shown to be distinctly faster than experimentally measured. We also observe the onset of rotational hindering from nearby solvent molecules, which arises as the average rotational energy of the solute falls below the effective barrier to rotation induced by the solvent.

Scaling relationships for nonadiabatic energy relaxation times in warm dense matter: toward understanding the equation of state.

PubMed

Pradhan, Ekadashi; Magyar, Rudolph J; Akimov, Alexey V

2016-11-30

Understanding the dynamics of electron-ion energy transfer in warm dense (WD) matter is important to the measurement of equation of state (EOS) properties and for understanding the energy balance in dynamic simulations. In this work, we present a comprehensive investigation of nonadiabatic electron relaxation and thermal excitation dynamics in aluminum under high pressure and temperature. Using quantum-classical trajectory surface hopping approaches, we examine the role of nonadiabatic couplings and electronic decoherence in electron-nuclear energy transfer in WD aluminum. The computed timescales range from 400 fs to 4.0 ps and are consistent with existing experimental studies. We have derived general scaling relationships between macroscopic parameters of WD systems such as temperature or mass density and the timescales of energy redistribution between quantum and classical degrees of freedom. The scaling laws are supported by computational results. We show that electronic decoherence plays essential role and can change the functional dependencies qualitatively. The established scaling relationships can be of use in modelling of WD matter.

Simulations of population dynamics of hemlock woolly adelgid and potential impact of biological control agents

Treesearch

Joseph S. Elkinton; Robert T. Trotter; Ann F. Paradis

2011-01-01

The hemlock woolly adelgid (Adelges tsugae) is a small invasive Hemipteran herbivore that threatens the continued presence and abundance of hemlock in eastern North America. Efforts to control the adelgid have focused on the introduction of classical biological control agents. These biological controls include six different species of predatory...

Linking Well-Tempered Metadynamics Simulations with Experiments

PubMed Central

Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele

2010-01-01

Abstract Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data. PMID:20441734

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Mechanism Responsible for Intercalation of Dimethyl Sulfoxide in Kaolinite: Molecular Dynamics Simulations.

PubMed

Zhang, Shuai; Liu, Qinfu; Cheng, Hongfei; Gao, Feng; Liu, Cun; Teppen, Brian J

2018-01-01

Intercalation is the promising strategy to expand the interlayer region of kaolinite for their further applications. Herein, the adaptive biasing force (ABF) accelerated molecular dynamics simulations were performed to calculate the free energies involved in the kaolinite intercalation by dimethyl sulfoxide (DMSO). Additionally, the classical all atom molecular dynamics simulations were carried out to calculate the interfacial interactions between kaolinite interlayer surfaces and DMSO with the aim at exploring the underlying force that drives the DMSO to enter the interlayer space. The results showed that the favorable interaction of DMSO with both kaolinite interlayer octahedral surface and tetrahedral surface can help in introducing DMSO enter kaolinite interlayer. The hydroxyl groups on octahedral surface functioned as H-donors attracting the S=O groups of DMSO through hydrogen bonding interaction. The tetrahedral surface featuring hydrophobic property attracted the methyl groups of DMSO through hydrophobic interaction. The results provided a detailed picture of the energetics and interlayer structure of kaolinite-DMSO intercalate.

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis.

PubMed

Euro, Liliya; Haapanen, Outi; Róg, Tomasz; Vattulainen, Ilpo; Suomalainen, Anu; Sharma, Vivek

2017-03-07

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

Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

NASA Astrophysics Data System (ADS)

Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

2018-05-01

Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.

Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)

NASA Astrophysics Data System (ADS)

Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido

2018-04-01

Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.

Liquid Water from First Principles: Validation of Different Sampling Approaches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mundy, C J; Kuo, W; Siepmann, J

2004-05-20

A series of first principles molecular dynamics and Monte Carlo simulations were carried out for liquid water to assess the validity and reproducibility of different sampling approaches. These simulations include Car-Parrinello molecular dynamics simulations using the program CPMD with different values of the fictitious electron mass in the microcanonical and canonical ensembles, Born-Oppenheimer molecular dynamics using the programs CPMD and CP2K in the microcanonical ensemble, and Metropolis Monte Carlo using CP2K in the canonical ensemble. With the exception of one simulation for 128 water molecules, all other simulations were carried out for systems consisting of 64 molecules. It is foundmore » that the structural and thermodynamic properties of these simulations are in excellent agreement with each other as long as adiabatic sampling is maintained in the Car-Parrinello molecular dynamics simulations either by choosing a sufficiently small fictitious mass in the microcanonical ensemble or by Nos{acute e}-Hoover thermostats in the canonical ensemble. Using the Becke-Lee-Yang-Parr exchange and correlation energy functionals and norm-conserving Troullier-Martins or Goedecker-Teter-Hutter pseudopotentials, simulations at a fixed density of 1.0 g/cm{sup 3} and a temperature close to 315 K yield a height of the first peak in the oxygen-oxygen radial distribution function of about 3.0, a classical constant-volume heat capacity of about 70 J K{sup -1} mol{sup -1}, and a self-diffusion constant of about 0.1 Angstroms{sup 2}/ps.« less

Controlling protein molecular dynamics: How to accelerate folding while preserving the native state

NASA Astrophysics Data System (ADS)

Jensen, Christian H.; Nerukh, Dmitry; Glen, Robert C.

2008-12-01

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1μs. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

A fictitious domain approach for the simulation of dense suspensions

NASA Astrophysics Data System (ADS)

Gallier, Stany; Lemaire, Elisabeth; Lobry, Laurent; Peters, François

2014-01-01

Low Reynolds number concentrated suspensions do exhibit an intricate physics which can be partly unraveled by the use of numerical simulation. To this end, a Lagrange multiplier-free fictitious domain approach is described in this work. Unlike some methods recently proposed, the present approach is fully Eulerian and therefore does not need any transfer between the Eulerian background grid and some Lagrangian nodes attached to particles. Lubrication forces between particles play an important role in the suspension rheology and have been properly accounted for in the model. A robust and effective lubrication scheme is outlined which consists in transposing the classical approach used in Stokesian Dynamics to our present direct numerical simulation. This lubrication model has also been adapted to account for solid boundaries such as walls. Contact forces between particles are modeled using a classical Discrete Element Method (DEM), a widely used method in granular matter physics. Comprehensive validations are presented on various one-particle, two-particle or three-particle configurations in a linear shear flow as well as some O(103) and O(104) particle simulations.

Polynomial-time quantum algorithm for the simulation of chemical dynamics

PubMed Central

Kassal, Ivan; Jordan, Stephen P.; Love, Peter J.; Mohseni, Masoud; Aspuru-Guzik, Alán

2008-01-01

The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can be applied only to small systems. By contrast, we demonstrate that quantum computers could exactly simulate chemical reactions in polynomial time. Our algorithm uses the split-operator approach and explicitly simulates all electron-nuclear and interelectronic interactions in quadratic time. Surprisingly, this treatment is not only more accurate than the Born–Oppenheimer approximation but faster and more efficient as well, for all reactions with more than about four atoms. This is the case even though the entire electronic wave function is propagated on a grid with appropriately short time steps. Although the preparation and measurement of arbitrary states on a quantum computer is inefficient, here we demonstrate how to prepare states of chemical interest efficiently. We also show how to efficiently obtain chemically relevant observables, such as state-to-state transition probabilities and thermal reaction rates. Quantum computers using these techniques could outperform current classical computers with 100 qubits. PMID:19033207

Modeling and simulating industrial land-use evolution in Shanghai, China

NASA Astrophysics Data System (ADS)

Qiu, Rongxu; Xu, Wei; Zhang, John; Staenz, Karl

2018-01-01

This study proposes a cellular automata-based Industrial and Residential Land Use Competition Model to simulate the dynamic spatial transformation of industrial land use in Shanghai, China. In the proposed model, land development activities in a city are delineated as competitions among different land-use types. The Hedonic Land Pricing Model is adopted to implement the competition framework. To improve simulation results, the Land Price Agglomeration Model was devised to simulate and adjust classic land price theory. A new evolutionary algorithm-based parameter estimation method was devised in place of traditional methods. Simulation results show that the proposed model closely resembles actual land transformation patterns and the model can not only simulate land development, but also redevelopment processes in metropolitan areas.

Event-driven Monte Carlo: Exact dynamics at all time scales for discrete-variable models

NASA Astrophysics Data System (ADS)

Mendoza-Coto, Alejandro; Díaz-Méndez, Rogelio; Pupillo, Guido

2016-06-01

We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found, with no need to define any other phase-space construction. However, unlike existing methods, the present algorithm does not assume any particular statistical distribution to perform moves or to advance the time, and thus is a unique tool for the numerical exploration of fast and ultra-fast dynamical regimes. By decomposing the problem in a set of two-level subsystems, we find a natural variable step size, that is well defined from the normalization condition of the transition probabilities between the levels. We successfully test the algorithm with known exact solutions for non-equilibrium dynamics and equilibrium thermodynamical properties of Ising-spin models in one and two dimensions, and compare to standard implementations of kinetic Monte Carlo methods. The present algorithm is directly applicable to the study of the real-time dynamics of a large class of classical Markovian chains, and particularly to short-time situations where the exact evolution is relevant.

Molecular dynamics studies of electron-ion temperature equilibration in hydrogen plasmas within the coupled-mode regime

DOE PAGES

Benedict, Lorin X.; Surh, Michael P.; Stanton, Liam G.; ...

2017-04-10

Here, we use classical molecular dynamics (MD) to study electron-ion temperature equilibration in two-component plasmas in regimes for which the presence of coupled collective modes has been predicted to substantively reduce the equilibration rate. Guided by previous kinetic theory work, we examine hydrogen plasmas at a density of n = 10 26cm –3, T i = 10 5K, and 10 7 K < Te < 10 9K. The nonequilibrium classical MD simulations are performed with interparticle interactions modeled by quantum statistical potentials (QSPs). Our MD results indicate (i) a large effect from time-varying potential energy, which we quantify by appealingmore » to an adiabatic two-temperature equation of state, and (ii) a notable deviation in the energy equilibration rate when compared to calculations from classical Lenard-Balescu theory including the QSPs. In particular, it is shown that the energy equilibration rates from MD are more similar to those of the theory when coupled modes are neglected. We suggest possible reasons for this surprising result and propose directions of further research along these lines.« less

Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods.

PubMed

Sevgen, Emre; Giberti, Federico; Sidky, Hythem; Whitmer, Jonathan K; Galli, Giulia; Gygi, Francois; de Pablo, Juan J

2018-05-14

We present a seamless coupling of a suite of codes designed to perform advanced sampling simulations, with a first-principles molecular dynamics (MD) engine. As an illustrative example, we discuss results for the free energy and potential surfaces of the alanine dipeptide obtained using both local and hybrid density functionals (DFT), and we compare them with those of a widely used classical force field, Amber99sb. In our calculations, the efficiency of first-principles MD using hybrid functionals is augmented by hierarchical sampling, where hybrid free energy calculations are initiated using estimates obtained with local functionals. We find that the free energy surfaces obtained from classical and first-principles calculations differ. Compared to DFT results, the classical force field overestimates the internal energy contribution of high free energy states, and it underestimates the entropic contribution along the entire free energy profile. Using the string method, we illustrate how these differences lead to different transition pathways connecting the metastable minima of the alanine dipeptide. In larger peptides, those differences would lead to qualitatively different results for the equilibrium structure and conformation of these molecules.

Quantum dynamical simulation of the scattering of Ar from a frozen LiF(100) surface based on a first principles interaction potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azuri, Asaf; Pollak, Eli, E-mail: eli.pollak@weizmann.ac.il

2015-07-07

In-plane two and three dimensional diffraction patterns are computed for the vertical scattering of an Ar atom from a frozen LiF(100) surface. Suitable collimation of the incoming wavepacket serves to reveal the quantum mechanical diffraction. The interaction potential is based on a fit to an ab initio potential calculated using density functional theory with dispersion corrections. Due to the potential coupling found between the two horizontal surface directions, there are noticeable differences between the quantum angular distributions computed for two and three dimensional scattering. The quantum results are compared to analogous classical Wigner computations on the same surface and withmore » the same conditions. The classical dynamics largely provides the envelope for the quantum diffractive scattering. The classical results also show that the corrugation along the [110] direction of the surface is smaller than along the [100] direction, in qualitative agreement with experimental observations of unimodal and bimodal scattering for the [110] and [100] directions, respectively.« less

Shortcuts to adiabaticity using flow fields

NASA Astrophysics Data System (ADS)

Patra, Ayoti; Jarzynski, Christopher

2017-12-01

A shortcut to adiabaticity is a recipe for generating adiabatic evolution at an arbitrary pace. Shortcuts have been developed for quantum, classical and (most recently) stochastic dynamics. A shortcut might involve a counterdiabatic (CD) Hamiltonian that causes a system to follow the adiabatic evolution at all times, or it might utilize a fast-forward (FF) potential, which returns the system to the adiabatic path at the end of the process. We develop a general framework for constructing shortcuts to adiabaticity from flow fields that describe the desired adiabatic evolution. Our approach encompasses quantum, classical and stochastic dynamics, and provides surprisingly compact expressions for both CD Hamiltonians and FF potentials. We illustrate our method with numerical simulations of a model system, and we compare our shortcuts with previously obtained results. We also consider the semiclassical connections between our quantum and classical shortcuts. Our method, like the FF approach developed by previous authors, is susceptible to singularities when applied to excited states of quantum systems; we propose a simple, intuitive criterion for determining whether these singularities will arise, for a given excited state.

Non-classical nuclei and growth kinetics of Cr precipitates in FeCr alloys during ageing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yulan; Hu, Shenyang Y.; Zhang, Lei

2014-01-10

In this manuscript, we quantitatively calculated the thermodynamic properties of critical nuclei of Cr precipitates in FeCr alloys. The concentration profiles of the critical nuclei and nucleation energy barriers were predicted by the constrained shrinking dimer dynamics (CSDD) method. It is found that Cr concentration distribution in the critical nuclei strongly depend on the overall Cr concentration as well as temperature. The critical nuclei are non-classical because the concentration in the nuclei is smaller than the thermodynamic equilibrium value. These results are in agreement with atomic probe observation. The growth kinetics of both classical and non-classical nuclei was investigated bymore » the phase field approach. The simulations of critical nucleus evolution showed a number of interesting phenomena: 1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; 2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics. 3) a critical classical nucleus grows faster at the earlier growth stage than the non-classical nucleus. All of these results demonstrate that it is critical to introduce the correct critical nuclei in order to correctly capture the kinetics of precipitation.« less

Computation and Dynamics: Classical and Quantum

NASA Astrophysics Data System (ADS)

Kisil, Vladimir V.

2010-05-01

We discuss classical and quantum computations in terms of corresponding Hamiltonian dynamics. This allows us to introduce quantum computations which involve parallel processing of both: the data and programme instructions. Using mixed quantum-classical dynamics we look for a full cost of computations on quantum computers with classical terminals.

Exploring the 7:4 mean motion resonance—I: Dynamical evolution of classical transneptunian objects

NASA Astrophysics Data System (ADS)

Lykawka, Patryk Sofia; Mukai, Tadashi

2005-09-01

In the transneptunian classical region ( 42AU10°. Taking into account those particles still locked in the resonance at the end of the simulations, we determined a retainability of 12-15% for real 7:4 resonant transneptunian objects (TNOs). Lastly, our results demonstrate that classical TNOs associated with the 7:4 mean motion resonance have been evolving continuously until present with non-negligible mixing of populations.

Exact and approximate stochastic simulation of intracellular calcium dynamics.

PubMed

Wieder, Nicolas; Fink, Rainer H A; Wegner, Frederic von

2011-01-01

In simulations of chemical systems, the main task is to find an exact or approximate solution of the chemical master equation (CME) that satisfies certain constraints with respect to computation time and accuracy. While Brownian motion simulations of single molecules are often too time consuming to represent the mesoscopic level, the classical Gillespie algorithm is a stochastically exact algorithm that provides satisfying results in the representation of calcium microdomains. Gillespie's algorithm can be approximated via the tau-leap method and the chemical Langevin equation (CLE). Both methods lead to a substantial acceleration in computation time and a relatively small decrease in accuracy. Elimination of the noise terms leads to the classical, deterministic reaction rate equations (RRE). For complex multiscale systems, hybrid simulations are increasingly proposed to combine the advantages of stochastic and deterministic algorithms. An often used exemplary cell type in this context are striated muscle cells (e.g., cardiac and skeletal muscle cells). The properties of these cells are well described and they express many common calcium-dependent signaling pathways. The purpose of the present paper is to provide an overview of the aforementioned simulation approaches and their mutual relationships in the spectrum ranging from stochastic to deterministic algorithms.

Proton relays in anomalous carbocations dictate spectroscopy, stability, and mechanisms: case studies on C2H5+ and C3H3.

PubMed

Sager, LeeAnn M; Iyengar, Srinivasan S

2017-10-18

We present a detailed analysis of the anomalous carbocations: C 2 H 5 + and C 3 H 3 + . This work involves (a) probing electronic structural properties, (b) ab initio dynamics simulations over a range of internal energies, (c) analysis of reduced dimensional potential surfaces directed along selected conformational transition pathways, (d) dynamically averaged vibrational spectra computed from ab initio dynamics trajectories, and (e) two-dimensional time-frequency analysis to probe conformational dynamics. Key findings are as follows: (i) as noted in our previous study on C 2 H 3 + , it appears that these non-classical carbocations are stabilized by delocalized nuclear frameworks and "proton shuttles". We analyze this nuclear delocalization and find critical parallels between conformational changes in C 2 H 3 + , C 2 H 5 + , and C 3 H 3 + . (ii) The vibrational signatures of C 2 H 5 + are dominated by the "bridge-proton" conformation, but also show critical contributions from the "classical" configuration, which is a transition state at almost all levels of theory. This result is further substantiated through two-dimensional time-frequency analysis and is at odds with earlier explanations of the experimental spectra, where frequencies close to the classical region were thought to arise from an impurity. While this is still possible, our results here indicate an additional (perhaps more likely) explanation that involves the "classical" isomer. (iii) Finally, in the case of C 3 H 3 + our explanation of the experimental result includes the presence of multiple, namely, "cyclic", "straight", and propargyl, configurations. Proton shuttles and nuclear delocalization, reminiscent of those seen in the case of C 2 H 3 + , were seen all through and have a critical role in all our observations.

Discovery of new class of methoxy carrying isoxazole derivatives as COX-II inhibitors: Investigation of a detailed molecular dynamics study

NASA Astrophysics Data System (ADS)

Joy, Monu; Elrashedy, Ahmed A.; Mathew, Bijo; Pillay, Ashona Singh; Mathews, Annie; Dev, Sanal; Soliman, Mahmoud E. S.; Sudarsanakumar, C.

2018-04-01

Two novel isoxazole derivatives were synthesized and characterized by NMR and single crystal X-ray crystallography techniques. The methoxy and dimethoxy functionalized variants of isoxazole were screened for its anti-inflammatory profile using cyclooxygenase fluorescent inhibitor screening assay methods along with standard drugs, Celecoxib and Diclofenac. The potent and selective nature of the two isoxazole derivatives on COX-II isoenzyme with a greater magnitude of inhibitory concentration, as compared to the standard drugs and further exploited through molecular dynamics (MD) simulation. Classical, accelerated and multiple MD simulations were performed to investigate the actual binding mode of the two non-steroidal anti-inflammatory drug candidates and addressed their functional selectivity towards COX-II enzyme inhibitory nature.

Modeling and 2-D discrete simulation of dislocation dynamics for plastic deformation of metal

NASA Astrophysics Data System (ADS)

Liu, Juan; Cui, Zhenshan; Ou, Hengan; Ruan, Liqun

2013-05-01

Two methods are employed in this paper to investigate the dislocation evolution during plastic deformation of metal. One method is dislocation dynamic simulation of two-dimensional discrete dislocation dynamics (2D-DDD), and the other is dislocation dynamics modeling by means of nonlinear analysis. As screw dislocation is prone to disappear by cross-slip, only edge dislocation is taken into account in simulation. First, an approach of 2D-DDD is used to graphically simulate and exhibit the collective motion of a large number of discrete dislocations. In the beginning, initial grains are generated in the simulation cells according to the mechanism of grain growth and the initial dislocation is randomly distributed in grains and relaxed under the internal stress. During the simulation process, the externally imposed stress, the long range stress contribution of all dislocations and the short range stress caused by the grain boundaries are calculated. Under the action of these forces, dislocations begin to glide, climb, multiply, annihilate and react with each other. Besides, thermal activation process is included. Through the simulation, the distribution of dislocation and the stress-strain curves can be obtained. On the other hand, based on the classic dislocation theory, the variation of the dislocation density with time is described by nonlinear differential equations. Finite difference method (FDM) is used to solve the built differential equations. The dislocation evolution at a constant strain rate is taken as an example to verify the rationality of the model.

Computational simulations of hydrogen circular migration in protonated acetylene induced by circularly polarized light

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Xuetao; Li, Wen; Schlegel, H. Bernhard, E-mail: hbs@chem.wayne.edu

2016-08-28

The hydrogens in protonated acetylene are very mobile and can easily migrate around the C{sub 2} core by moving between classical and non-classical structures of the cation. The lowest energy structure is the T-shaped, non-classical cation with a hydrogen bridging the two carbons. Conversion to the classical H{sub 2}CCH{sup +} ion requires only 4 kcal/mol. The effect of circularly polarized light on the migration of hydrogens in oriented C{sub 2}H{sub 3}{sup +} has been simulated by Born-Oppenheimer molecular dynamics. Classical trajectory calculations were carried out with the M062X/6-311+G(3df,2pd) level of theory using linearly and circularly polarized 32 cycle 7 μmmore » cosine squared pulses with peak intensity of 5.6 × 10{sup 13} W/cm{sup 2} and 3.15 × 10{sup 13} W/cm{sup 2}, respectively. These linearly and circularly polarized pulses transfer similar amounts of energy and total angular momentum to C{sub 2}H{sub 3}{sup +}. The average angular momentum vectors of the three hydrogens show opposite directions of rotation for right and left circularly polarized light, but no directional preference for linearly polarized light. This difference results in an appreciable amount of angular displacement of the three hydrogens relative to the C{sub 2} core for circularly polarized light, but only an insignificant amount for linearly polarized light. Over the course of the simulation with circularly polarized light, this corresponds to a propeller-like motion of the three hydrogens around the C{sub 2} core of protonated acetylene.« less

Quantum diffusion of H/D on Ni(111)—A partially adiabatic centroid MD study

NASA Astrophysics Data System (ADS)

Hopkinson, A. R.; Probert, M. I. J.

2018-03-01

We present the results of a theoretical study of H/D diffusion on a Ni(111) surface at a range of temperatures, from 250 K to 75 K. The diffusion is studied using both classical molecular dynamics and the partially adiabatic centroid molecular dynamics method. The calculations are performed with the hydrogen (or deuterium) moving in 3D across a static nickel surface using a novel Fourier interpolated potential energy surface which has been parameterized to density functional theory calculations. The results of the classical simulations are that the calculated diffusion coefficients are far too small and with too large a variation with temperature compared with experiment. By contrast, the quantum simulations are in much better agreement with experiment and show that quantum effects in the diffusion of hydrogen are significant at all temperatures studied. There is also a crossover to a quantum-dominated diffusive regime for temperatures below ˜150 K for hydrogen and ˜85 K for deuterium. The quantum diffusion coefficients are found to accurately reproduce the spread in values with temperature, but with an absolute value that is a little high compared with experiment.

Solvent effects on the properties of hyperbranched polythiophenes.

PubMed

Torras, Juan; Zanuy, David; Aradilla, David; Alemán, Carlos

2016-09-21

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties-conformational flexibility relationships in all-Th dendrimers.

Universal attractor in a highly occupied non-Abelian plasma

NASA Astrophysics Data System (ADS)

Berges, J.; Boguslavski, K.; Schlichting, S.; Venugopalan, R.

2014-06-01

We study the thermalization process in highly occupied non-Abelian plasmas at weak coupling. The nonequilibrium dynamics of such systems is classical in nature and can be simulated with real-time lattice gauge theory techniques. We provide a detailed discussion of this framework and elaborate on the results reported in J. Berges, K. Boguslavski, S. Schlichting, and R. Venugopalan, Phys. Rev. D 89, 074011 (2014), 10.1103/PhysRevD.89.074011 along with novel findings. We demonstrate the emergence of universal attractor solutions, which govern the nonequilibrium evolution on large time scales both for nonexpanding and expanding non-Abelian plasmas. The turbulent attractor for a nonexpanding plasma drives the system close to thermal equilibrium on a time scale t ˜Q-1αs-7/4. The attractor solution for an expanding non-Abelian plasma leads to a strongly interacting albeit highly anisotropic system at the transition to the low-occupancy or quantum regime. This evolution in the classical regime is, within the uncertainties of our simulations, consistent with the "bottom up" thermalization scenario [R. Baier, A. H. Mueller, D. Schiff, and D. T. Son, Phys. Lett. B 502, 51 (2001), 10.1016/S0370-2693(01)00191-5]. While the focus of this paper is to understand the nonequilibrium dynamics in weak coupling asymptotics, we also discuss the relevance of our results for larger couplings in the early time dynamics of heavy ion collision experiments.

Unveiling the Interplay Between Diffusing CO2 and Ethanol Molecules in Champagne Wines by Classical Molecular Dynamics and (13)C NMR Spectroscopy.

PubMed

Bonhommeau, David A; Perret, Alexandre; Nuzillard, Jean-Marc; Cilindre, Clara; Cours, Thibaud; Alijah, Alexander; Liger-Belair, Gérard

2014-12-18

The diffusion coefficients of carbon dioxide (CO2) and ethanol (EtOH) in carbonated hydroalcoholic solutions and Champagne wines are evaluated as a function of temperature by classical molecular dynamics (MD) simulations and (13)C NMR spectroscopy measurements. The excellent agreement between theoretical and experimental diffusion coefficients suggest that ethanol is the main molecule, apart from water, responsible for the value of the CO2 diffusion coefficients in typical Champagne wines, a result that could likely be extended to most sparkling wines with alike ethanol concentrations. CO2 and EtOH hydrodynamical radii deduced from viscometry measurements by applying the Stokes-Einstein relationship are found to be mostly constant and in close agreement with MD predictions. The reliability of our approach should be of interest to physical chemists aiming to model transport phenomena in supersaturated aqueous solutions or water/alcohol mixtures.

Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco

2016-09-13

The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.

Preparation of two-qubit steady entanglement through driving a single qubit.

PubMed

Shen, Li-Tuo; Chen, Rong-Xin; Yang, Zhen-Biao; Wu, Huai-Zhi; Zheng, Shi-Biao

2014-10-15

Inspired by a recent paper [J. Phys. B 47, 055502 (2014)], we propose a simplified scheme to generate and stabilize a Bell state of two qubits coupled to a resonator. In the scheme only one qubit is needed to be driven by external classical fields, and the entanglement dynamics is independent of the phases of these fields and insensitive to their amplitude fluctuations. This is a distinct advantage as compared with the previous ones that require each qubit to be addressed by well-controlled classical fields. Numerical simulation shows that the steady singlet state with high fidelity can be obtained with currently available techniques in circuit quantum electrodynamics.

Molecular dynamics studies of displacement cascades in Fe-Y{sub 2}TiO{sub 5} system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dholakia, Manan, E-mail: manan@igcar.gov.in; Chandra, Sharat; Jaya, S. Mathi

The effect of displacement cascade on Fe-Y{sub 2}TiO{sub 5} bilayer is studied using classical molecular dynamics simulations. Different PKA species – Fe, Y, Ti and O – with the same PKA energy of 8 keV are used to produce displacement cascades that encompass the interface. It is shown that Ti atom has the highest movement in the ballistic regime of cascades which can lead to Ti atoms moving out of the oxide clusters into the Fe matrix in ODS alloys.

The Sharma-Parthasarathy stochastic two-body problem

NASA Astrophysics Data System (ADS)

Cresson, J.; Pierret, F.; Puig, B.

2015-03-01

We study the Sharma-Parthasarathy stochastic two-body problem introduced by Sharma and Parthasarathy in ["Dynamics of a stochastically perturbed two-body problem," Proc. R. Soc. A 463, 979-1003 (2007)]. In particular, we focus on the preservation of some fundamental features of the classical two-body problem like the Hamiltonian structure and first integrals in the stochastic case. Numerical simulations are performed which illustrate the dynamical behaviour of the osculating elements as the semi-major axis, the eccentricity, and the pericenter. We also derive a stochastic version of Gauss's equations in the planar case.

From crater functions to partial differential equations: a new approach to ion bombardment induced nonequilibrium pattern formation.

PubMed

Norris, Scott A; Brenner, Michael P; Aziz, Michael J

2009-06-03

We develop a methodology for deriving continuum partial differential equations for the evolution of large-scale surface morphology directly from molecular dynamics simulations of the craters formed from individual ion impacts. Our formalism relies on the separation between the length scale of ion impact and the characteristic scale of pattern formation, and expresses the surface evolution in terms of the moments of the crater function. We demonstrate that the formalism reproduces the classical Bradley-Harper results, as well as ballistic atomic drift, under the appropriate simplifying assumptions. Given an actual set of converged molecular dynamics moments and their derivatives with respect to the incidence angle, our approach can be applied directly to predict the presence and absence of surface morphological instabilities. This analysis represents the first work systematically connecting molecular dynamics simulations of ion bombardment to partial differential equations that govern topographic pattern-forming instabilities.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

Solute-defect interactions in Al-Mg alloys from diffusive variational Gaussian calculations

NASA Astrophysics Data System (ADS)

Dontsova, E.; Rottler, J.; Sinclair, C. W.

2014-11-01

Resolving atomic-scale defect topologies and energetics with accurate atomistic interaction models provides access to the nonlinear phenomena inherent at atomic length and time scales. Coarse graining the dynamics of such simulations to look at the migration of, e.g., solute atoms, while retaining the rich atomic-scale detail required to properly describe defects, is a particular challenge. In this paper, we present an adaptation of the recently developed "diffusive molecular dynamics" model to describe the energetics and kinetics of binary alloys on diffusive time scales. The potential of the technique is illustrated by applying it to the classic problems of solute segregation to a planar boundary (stacking fault) and edge dislocation in the Al-Mg system. Our approach provides fully dynamical solutions in situations with an evolving energy landscape in a computationally efficient way, where atomistic kinetic Monte Carlo simulations are difficult or impractical to perform.

Linking well-tempered metadynamics simulations with experiments.

PubMed

Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele

2010-05-19

Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

PubMed

Ilott, Andrew J; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R

2013-10-10

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Diffusion and interactions of interstitials in hard-sphere interstitial solid solutions

NASA Astrophysics Data System (ADS)

van der Meer, Berend; Lathouwers, Emma; Smallenburg, Frank; Filion, Laura

2017-12-01

Using computer simulations, we study the dynamics and interactions of interstitial particles in hard-sphere interstitial solid solutions. We calculate the free-energy barriers associated with their diffusion for a range of size ratios and densities. By applying classical transition state theory to these free-energy barriers, we predict the diffusion coefficients, which we find to be in good agreement with diffusion coefficients as measured using event-driven molecular dynamics simulations. These results highlight that transition state theory can capture the interstitial dynamics in the hard-sphere model system. Additionally, we quantify the interactions between the interstitials. We find that, apart from excluded volume interactions, the interstitial-interstitial interactions are almost ideal in our system. Lastly, we show that the interstitial diffusivity can be inferred from the large-particle fluctuations alone, thus providing an empirical relationship between the large-particle fluctuations and the interstitial diffusivity.

Classical black holes: the nonlinear dynamics of curved spacetime.

PubMed

Thorne, Kip S

2012-08-03

Numerical simulations have revealed two types of physical structures, made from curved spacetime, that are attached to black holes: tendexes, which stretch or squeeze anything they encounter, and vortexes, which twist adjacent inertial frames relative to each other. When black holes collide, their tendexes and vortexes interact and oscillate (a form of nonlinear dynamics of curved spacetime). These oscillations generate gravitational waves, which can give kicks up to 4000 kilometers per second to the merged black hole. The gravitational waves encode details of the spacetime dynamics and will soon be observed and studied by the Laser Interferometer Gravitational Wave Observatory and its international partners.

CLASSICAL AREAS OF PHENOMENOLOGY: Correcting dynamic residual aberrations of conformal optical systems using AO technology

NASA Astrophysics Data System (ADS)

Li, Yan; Li, Lin; Huang, Yi-Fan; Du, Bao-Lin

2009-07-01

This paper analyses the dynamic residual aberrations of a conformal optical system and introduces adaptive optics (AO) correction technology to this system. The image sharpening AO system is chosen as the correction scheme. Communication between MATLAB and Code V is established via ActiveX technique in computer simulation. The SPGD algorithm is operated at seven zoom positions to calculate the optimized surface shape of the deformable mirror. After comparison of performance of the corrected system with the baseline system, AO technology is proved to be a good way of correcting the dynamic residual aberration in conformal optical design.

Classical Black Holes: The Nonlinear Dynamics of Curved Spacetime

NASA Astrophysics Data System (ADS)

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.

Enstrophy Cascade in Decaying Two-Dimensional Quantum Turbulence

NASA Astrophysics Data System (ADS)

Reeves, Matthew T.; Billam, Thomas P.; Yu, Xiaoquan; Bradley, Ashton S.

2017-11-01

We report evidence for an enstrophy cascade in large-scale point-vortex simulations of decaying two-dimensional quantum turbulence. Devising a method to generate quantum vortex configurations with kinetic energy narrowly localized near a single length scale, the dynamics are found to be well characterized by a superfluid Reynolds number Res that depends only on the number of vortices and the initial kinetic energy scale. Under free evolution the vortices exhibit features of a classical enstrophy cascade, including a k-3 power-law kinetic energy spectrum, and constant enstrophy flux associated with inertial transport to small scales. Clear signatures of the cascade emerge for N ≳500 vortices. Simulating up to very large Reynolds numbers (N =32 768 vortices), additional features of the classical theory are observed: the Kraichnan-Batchelor constant is found to converge to C'≈1.6 , and the width of the k-3 range scales as Res1 /2 .

Molecular Growth Inside of Polycyclic Aromatic Hydrocarbon Clusters Induced by Ion Collisions.

PubMed

Delaunay, Rudy; Gatchell, Michael; Rousseau, Patrick; Domaracka, Alicja; Maclot, Sylvain; Wang, Yang; Stockett, Mark H; Chen, Tao; Adoui, Lamri; Alcamí, Manuel; Martín, Fernando; Zettergren, Henning; Cederquist, Henrik; Huber, Bernd A

2015-05-07

The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan.

THERMODYNAMICS OF FE-CU ALLOYS AS DESCRIBED BY A CLASSIC POTENTIALS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caro, A; Caro, M; Lopasso, E M

2005-04-14

The Fe-Cu system is of relevance to the nuclear industry because of the deleterious consequences of Cu precipitates in the mechanical properties of Fe. Several sets of classical potentials are used in molecular dynamics simulations studies of this system, in particular that proposed by Ludwig et al. (Modelling Simul. Mater. Sci. Eng. 6, 19 (1998)). In this work we extract thermodynamic information from this interatomic potentials. We obtain equilibrium phase diagram and find a reasonable agreement with the experimental phases in the regions of relevance to radiation damage studies. We compare the results with the predicted phase diagram based onmore » other potential, as calculated in previous work. We discuss the disagreements found between the phase diagram calculated here and experimental results, focusing on the pure components and discuss the applicability of these potentials; finally we suggest an approach to improve existing potentials for this system.« less

On the onset of surface condensation: formation and transition mechanisms of condensation mode

PubMed Central

Sheng, Qiang; Sun, Jie; Wang, Qian; Wang, Wen; Wang, Hua Sheng

2016-01-01

Molecular dynamics simulations have been carried out to investigate the onset of surface condensation. On surfaces with different wettability, we snapshot different condensation modes (no-condensation, dropwise condensation and filmwise condensation) and quantitatively analyze their characteristics by temporal profiles of surface clusters. Two different types of formation of nanoscale droplets are identified, i.e. the formations with and without film-like condensate. We exhibit the effect of surface tensions on the formations of nanoscale droplets and film. We reveal the formation mechanisms of different condensation modes at nanoscale based on our simulation results and classical nucleation theory, which supplements the ‘classical hypotheses’ of the onset of dropwise condensation. We also reveal the transition mechanism between different condensation modes based on the competition between surface tensions and reveal that dropwise condensation represents the transition states from no-condensation to filmwise condensation. PMID:27481071

On the onset of surface condensation: formation and transition mechanisms of condensation mode.

PubMed

Sheng, Qiang; Sun, Jie; Wang, Qian; Wang, Wen; Wang, Hua Sheng

2016-08-02

Molecular dynamics simulations have been carried out to investigate the onset of surface condensation. On surfaces with different wettability, we snapshot different condensation modes (no-condensation, dropwise condensation and filmwise condensation) and quantitatively analyze their characteristics by temporal profiles of surface clusters. Two different types of formation of nanoscale droplets are identified, i.e. the formations with and without film-like condensate. We exhibit the effect of surface tensions on the formations of nanoscale droplets and film. We reveal the formation mechanisms of different condensation modes at nanoscale based on our simulation results and classical nucleation theory, which supplements the 'classical hypotheses' of the onset of dropwise condensation. We also reveal the transition mechanism between different condensation modes based on the competition between surface tensions and reveal that dropwise condensation represents the transition states from no-condensation to filmwise condensation.

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

PubMed

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

PubMed

Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R

2016-09-13

The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.

Emergence of coherence and the dynamics of quantum phase transitions

PubMed Central

Braun, Simon; Friesdorf, Mathis; Hodgman, Sean S.; Schreiber, Michael; Ronzheimer, Jens Philipp; Riera, Arnau; del Rey, Marco; Bloch, Immanuel; Eisert, Jens

2015-01-01

The dynamics of quantum phase transitions pose one of the most challenging problems in modern many-body physics. Here, we study a prototypical example in a clean and well-controlled ultracold atom setup by observing the emergence of coherence when crossing the Mott insulator to superfluid quantum phase transition. In the 1D Bose–Hubbard model, we find perfect agreement between experimental observations and numerical simulations for the resulting coherence length. We, thereby, perform a largely certified analog quantum simulation of this strongly correlated system reaching beyond the regime of free quasiparticles. Experimentally, we additionally explore the emergence of coherence in higher dimensions, where no classical simulations are available, as well as for negative temperatures. For intermediate quench velocities, we observe a power-law behavior of the coherence length, reminiscent of the Kibble–Zurek mechanism. However, we find nonuniversal exponents that cannot be captured by this mechanism or any other known model. PMID:25775515

Concurrence of dynamical phase transitions at finite temperature in the fully connected transverse-field Ising model

NASA Astrophysics Data System (ADS)

Lang, Johannes; Frank, Bernhard; Halimeh, Jad C.

2018-05-01

We construct the finite-temperature dynamical phase diagram of the fully connected transverse-field Ising model from the vantage point of two disparate concepts of dynamical criticality. An analytical derivation of the classical dynamics and exact diagonalization simulations are used to study the dynamics after a quantum quench in the system prepared in a thermal equilibrium state. The different dynamical phases characterized by the type of nonanalyticities that emerge in an appropriately defined Loschmidt-echo return rate directly correspond to the dynamical phases determined by the spontaneous breaking of Z2 symmetry in the long-time steady state. The dynamical phase diagram is qualitatively different depending on whether the initial thermal state is ferromagnetic or paramagnetic. Whereas the former leads to a dynamical phase diagram that can be directly related to its equilibrium counterpart, the latter gives rise to a divergent dynamical critical temperature at vanishing final transverse-field strength.

Creation of deuterium protective layer below the tungsten surface

NASA Astrophysics Data System (ADS)

Krstic, Predrag; Kaganovich, Igor; Startsev, Edward

2014-10-01

By cumulative irradiation of both pre-damaged and virgin surfaces of monocrystal tungsten by deuterium atoms of impact energy of few tens of eV, we simulate by classical molecular dynamics the creation of a deuterium protective layer. The depth and width of the layer depend on the deuterium impact energy and the diffusion rate of deuterium in tungsten, the latter being influenced by the tungsten temperature and damage. Found simulation results are in concert with the experimental results, found recently in DIFFER. Support of the PPPL LDRD project acknowledged.

Zero point energy leakage in condensed phase dynamics: An assessment of quantum simulation methods for liquid water

NASA Astrophysics Data System (ADS)

Habershon, Scott; Manolopoulos, David E.

2009-12-01

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Zero point energy leakage in condensed phase dynamics: an assessment of quantum simulation methods for liquid water.

PubMed

Habershon, Scott; Manolopoulos, David E

2009-12-28

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Structure, thermodynamic and transport properties of imidazolium-based bis(trifluoromethylsulfonyl)imide ionic liquids from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Androulaki, Eleni; Vergadou, Niki; Ramos, Javier; Economou, Ioannis G.

2012-06-01

Molecular dynamics (MD) simulations have been performed in order to investigate the properties of [C n mim+][Tf2N-] (n = 4, 8, 12) ionic liquids (ILs) in a wide temperature range (298.15-498.15 K) and at atmospheric pressure (1 bar). A previously developed methodology for the calculation of the charge distribution that incorporates ab initio quantum mechanical calculations based on density functional theory (DFT) was used to calculate the partial charges for the classical molecular simulations. The wide range of time scales that characterize the segmental dynamics of these ILs, especially at low temperatures, required very long MD simulations, on the order of several tens of nanoseconds, to calculate the thermodynamic (density, thermal expansion, isothermal compressibility), structural (radial distribution functions between the centers of mass of ions and between individual sites, radial-angular distribution functions) and dynamic (relaxation times of the reorientation of the bonds and the torsion angles, self-diffusion coefficients, shear viscosity) properties. The influence of the temperature and the cation's alkyl chain length on the above-mentioned properties was thoroughly investigated. The calculated thermodynamic (primary and derivative) and structural properties are in good agreement with the experimental data, while the extremely sluggish dynamics of the ILs under study renders the calculation of their transport properties a very complicated and challenging task, especially at low temperatures.

Fault Gauge Numerical Simulation : Dynamic Rupture Propagation and Local Energy Partitioning

NASA Astrophysics Data System (ADS)

Mollon, G.

2017-12-01

In this communication, we present dynamic simulations of the local (centimetric) behaviour of a fault filled with a granular gauge submitted to dynamic rupture. The numerical tool (Fig. 1) combines classical Discrete Element Modelling (albeit with the ability to deal with arbitrary grain shapes) for the simualtion of the gauge, and continuous modelling for the simulation of the acoustic waves emission and propagation. In a first part, the model is applied to the simulation of steady-state shearing of the fault under remote displacement boudary conditions, in order to observe the shear accomodation at the interface (R1 cracks, localization, wear, etc.). It also makes it possible to fit to desired values the Rate and State Friction properties of the granular gauge by adapting the contact laws between grains. Such simulations provide quantitative insight in the steady-state energy partitionning between fracture, friction and acoustic emissions as a function of the shear rate. In a second part, the model is submitted to dynamic rupture. For that purpose, the fault is elastically preloaded just below rupture, and a displacement pulse is applied at one end of the sample (and on only one side of the fault). This allows to observe the propagation of the instability along the fault and the interplay between this propagation and the local granular phenomena. Energy partitionning is then observed both in space and time.

State of the Art Assessment of Simulation in Advanced Materials Development

NASA Technical Reports Server (NTRS)

Wise, Kristopher E.

2008-01-01

Advances in both the underlying theory and in the practical implementation of molecular modeling techniques have increased their value in the advanced materials development process. The objective is to accelerate the maturation of emerging materials by tightly integrating modeling with the other critical processes: synthesis, processing, and characterization. The aims of this report are to summarize the state of the art of existing modeling tools and to highlight a number of areas in which additional development is required. In an effort to maintain focus and limit length, this survey is restricted to classical simulation techniques including molecular dynamics and Monte Carlo simulations.

The Propulsive-Only Flight Control Problem

NASA Technical Reports Server (NTRS)

Blezad, Daniel J.

1996-01-01

Attitude control of aircraft using only the throttles is investigated. The long time constants of both the engines and of the aircraft dynamics, together with the coupling between longitudinal and lateral aircraft modes make piloted flight with failed control surfaces hazardous, especially when attempting to land. This research documents the results of in-flight operation using simulated failed flight controls and ground simulations of piloted propulsive-only control to touchdown. Augmentation control laws to assist the pilot are described using both optimal control and classical feedback methods. Piloted simulation using augmentation shows that simple and effective augmented control can be achieved in a wide variety of failed configurations.

Active control and sound synthesis--two different ways to investigate the influence of the modal parameters of a guitar on its sound.

PubMed

Benacchio, Simon; Mamou-Mani, Adrien; Chomette, Baptiste; Finel, Victor

2016-03-01

The vibrational behavior of musical instruments is usually studied using physical modeling and simulations. Recently, active control has proven its efficiency to experimentally modify the dynamical behavior of musical instruments. This approach could also be used as an experimental tool to systematically study fine physical phenomena. This paper proposes to use modal active control as an alternative to sound simulation to study the complex case of the coupling between classical guitar strings and soundboard. A comparison between modal active control and sound simulation investigates the advantages, the drawbacks, and the limits of these two approaches.

Computer simulation of surface and film processes

NASA Technical Reports Server (NTRS)

Tiller, W. A.; Halicioglu, M. T.

1984-01-01

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

NASA Astrophysics Data System (ADS)

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; Ho, Kai-Ming; Travesset, Alex

2018-04-01

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu64.5Zr35.5, and pair correlation function g (r) of liquid Ni3Al. Our code scales well with the size of the simulating system on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. The source code can be accessed through the HOOMD-blue web page for free by any interested user.

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.

PubMed

Sultan, Mohammad M; Kiss, Gert; Shukla, Diwakar; Pande, Vijay S

2014-12-09

Given the large number of crystal structures and NMR ensembles that have been solved to date, classical molecular dynamics (MD) simulations have become powerful tools in the atomistic study of the kinetics and thermodynamics of biomolecular systems on ever increasing time scales. By virtue of the high-dimensional conformational state space that is explored, the interpretation of large-scale simulations faces difficulties not unlike those in the big data community. We address this challenge by introducing a method called clustering based feature selection (CB-FS) that employs a posterior analysis approach. It combines supervised machine learning (SML) and feature selection with Markov state models to automatically identify the relevant degrees of freedom that separate conformational states. We highlight the utility of the method in the evaluation of large-scale simulations and show that it can be used for the rapid and automated identification of relevant order parameters involved in the functional transitions of two exemplary cell-signaling proteins central to human disease states.

Quantum vs Classical Mechanics for a 'Simple' Dissociation Reaction. Should They Give the Same Results?

NASA Astrophysics Data System (ADS)

Holloway, Stephen

1997-03-01

When performing molecular dynamical simulations on light systems at low energies, there is always the risk of producing data that bear no similarity to experiment. Indeed, John Barker himself was particularly anxious about treating Ar scattering from surfaces using classical mechanics where it had been shown experimentally in his own lab that diffraction occurs. In such cases, the correct procedure is probably to play the trump card "... well of course, quantum effects will modify this so that....." and retire gracefully. For our particular interests, the tables are turned in that we are interested in gas-surface dynamical studies for highly quantized systems, but would be interested to know when it is possible to use classical mechanics in order that a greater dimensionality might be treated. For molecular dissociation and scattering, it has been oft quoted that the greater the number of degrees of freedom, the more appropriate is classical mechanics, primarily because of the mass averaging over the quantized dimensions. Is this true? We have been investigating the dissociation of hydrogen molecules at surfaces and in this talk I will present quantum results for dissociation and scattering, along with a novel method for their interpretation based upon adiabatic potential energy surfaces. Comparison with classical calculations will be made and conclusions drawn. a novel method for their interpretation based upon adiabatic potential energy surfaces

The polymer physics of single DNA confined in nanochannels.

PubMed

Dai, Liang; Renner, C Benjamin; Doyle, Patrick S

2016-06-01

In recent years, applications and experimental studies of DNA in nanochannels have stimulated the investigation of the polymer physics of DNA in confinement. Recent advances in the physics of confined polymers, using DNA as a model polymer, have moved beyond the classic Odijk theory for the strong confinement, and the classic blob theory for the weak confinement. In this review, we present the current understanding of the behaviors of confined polymers while briefly reviewing classic theories. Three aspects of confined DNA are presented: static, dynamic, and topological properties. The relevant simulation methods are also summarized. In addition, comparisons of confined DNA with DNA under tension and DNA in semidilute solution are made to emphasize universal behaviors. Finally, an outlook of the possible future research for confined DNA is given. Copyright © 2015 Elsevier B.V. All rights reserved.

Applications of Density Functional Theory in Soft Condensed Matter

NASA Astrophysics Data System (ADS)

Löwen, Hartmut

Applications of classical density functional theory (DFT) to soft matter systems like colloids, liquid crystals and polymer solutions are discussed with a focus on the freezing transition and on nonequilibrium Brownian dynamics. First, after a brief reminder of equilibrium density functional theory, DFT is applied to the freezing transition of liquids into crystalline lattices. In particular, spherical particles with radially symmetric pair potentials will be treated (like hard spheres, the classical one-component plasma or Gaussian-core particles). Second, the DFT will be generalized towards Brownian dynamics in order to tackle nonequilibrium problems. After a general introduction to Brownian dynamics using the complementary Smoluchowski and Langevin pictures appropriate for the dynamics of colloidal suspensions, the dynamical density functional theory (DDFT) will be derived from the Smoluchowski equation. This will be done first for spherical particles (e.g. hard spheres or Gaussian-cores) without hydrodynamic interactions. Then we show how to incorporate hydrodynamic interactions between the colloidal particles into the DDFT framework and compare to Brownian dynamics computer simulations. Third orientational degrees of freedom (rod-like particles) will be considered as well. In the latter case, the stability of intermediate liquid crystalline phases (isotropic, nematic, smectic-A, plastic crystals etc) can be predicted. Finally, the corresponding dynamical extension of density functional theory towards orientational degrees of freedom is proposed and the collective behaviour of "active" (self-propelled) Brownian particles is briefly discussed.

First-Principles Molecular Dynamics Simulations of NaCl in Water: Performance of Advanced Exchange-Correlation Approximations in Density Functional Theory

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

Our ability to correctly model the association of oppositely charged ions in water is fundamental in physical chemistry and essential to various technological and biological applications of molecular dynamics (MD) simulations. MD simulations using classical force fields often show strong clustering of NaCl in the aqueous ionic solutions as a consequence of a deep contact pair minimum in the potential of mean force (PMF) curve. First-Principles Molecular Dynamics (FPMD) based on Density functional theory (DFT) with the popular PBE exchange-correlation approximation, on the other hand, show a different result with a shallow contact pair minimum in the PMF. We employed two of most promising exchange-correlation approximations, ωB97xv by Mardiorossian and Head-Gordon and SCAN by Sun, Ruzsinszky and Perdew, to examine the PMF using FPMD simulations. ωB97xv is highly empirically and optimized in the space of range-separated hybrid functional with a dispersion correction while SCAN is the most recent meta-GGA functional that is constructed by satisfying various known conditions in well-defined physical limits. We will discuss our findings for PMF, charge transfer, water dipoles, etc.

The impact of dynamic data assimilation on the numerical simulations of the QE II cyclone and an analysis of the jet streak influencing the precyclogenetic environment

NASA Technical Reports Server (NTRS)

Manobianco, John; Uccellini, Louis W.; Brill, Keith F.; Kuo, Ying-Hwa

1992-01-01

A mesoscale numerical model is combined with a dynamic data assimilation via Newtonian relaxation, or 'nudging', to provide initial conditions for subsequent simulations of the QE II cyclone. Both the nudging technique and the inclusion of supplementary data are shown to have a large positive impact on the simulation of the QE II cyclone during the initial phase of rapid cyclone development. Within the initial development period (from 1200 to 1800 UTC 9 September 1978), the dynamic assimilation of operational and bogus data yields a coherent two-layer divergence pattern that is not well defined in the model run using only the operational data and static initialization. Diagnostic analysis based on the simulations show that the initial development of the QE II storm between 0000 UTC 9 September and 0000 UTC 10 September was embedded within an indirect circulation of an intense 300-hPa jet streak, was related to baroclinic processes extending throughout a deep portion of the troposphere, and was associated with a classic two-layer mass-divergence profile expected for an extratropical cyclone.

Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

2016-03-01

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

Dynamic behaviors of cavitation bubble for the steady cavitating flow

NASA Astrophysics Data System (ADS)

Cai, Jun; Huai, Xiulan; Li, Xunfeng

2009-12-01

In this paper, by introducing the flow velocity item into the classical Rayleigh-Plesset dynamic equation, a new equation, which does not involve the time term and can describe the motion of cavitation bubble in the steady cavitating flow, has been obtained. By solving the new motion equation using Runge-Kutta fourth order method with adaptive step size control, the dynamic behaviors of cavitation bubble driven by the varying pressure field downstream of a venturi cavitation reactor are numerically simulated. The effects of liquid temperature (corresponding to the saturated vapor pressure of liquid), cavitation number and inlet pressure of venturi on radial motion of bubble and pressure pulse due to the radial motion are analyzed and discussed in detail. Some dynamic behaviors of bubble different from those in previous papers are displayed. In addition, the internal relationship between bubble dynamics and process intensification is also discussed. The simulation results reported in this work reveal the variation laws of cavitation intensity with the flow conditions of liquid, and will lay a foundation for the practical application of hydrodynamic cavitation technology.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulationsmore » as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water. Published by AIP Publishing.« less

A general stochastic model for studying time evolution of transition networks

NASA Astrophysics Data System (ADS)

Zhan, Choujun; Tse, Chi K.; Small, Michael

2016-12-01

We consider a class of complex networks whose nodes assume one of several possible states at any time and may change their states from time to time. Such networks represent practical networks of rumor spreading, disease spreading, language evolution, and so on. Here, we derive a model describing the dynamics of this kind of network and a simulation algorithm for studying the network evolutionary behavior. This model, derived at a microscopic level, can reveal the transition dynamics of every node. A numerical simulation is taken as an ;experiment; or ;realization; of the model. We use this model to study the disease propagation dynamics in four different prototypical networks, namely, the regular nearest-neighbor (RN) network, the classical Erdös-Renyí (ER) random graph, the Watts-Strogátz small-world (SW) network, and the Barabási-Albert (BA) scalefree network. We find that the disease propagation dynamics in these four networks generally have different properties but they do share some common features. Furthermore, we utilize the transition network model to predict user growth in the Facebook network. Simulation shows that our model agrees with the historical data. The study can provide a useful tool for a more thorough understanding of the dynamics networks.

Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases.

PubMed

Moffett, Alexander S; Bender, Kyle W; Huber, Steven C; Shukla, Diwakar

2017-07-28

The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and dynamic characteristics in monolayer square ice.

PubMed

Zhu, YinBo; Wang, FengChao; Wu, HengAn

2017-07-28

When water is constrained between two sheets of graphene, it becomes an intriguing monolayer solid with a square pattern due to the ultrahigh van der Waals pressure. However, the square ice phase has become a matter of debate due to the insufficient experimental interpretation and the slightly rhomboidal feature in simulated monolayer square-like structures. Here, we performed classical molecular dynamics simulations to reveal monolayer square ice in graphene nanocapillaries from the perspective of structure and dynamic characteristics. Monolayer square-like ice (instantaneous snapshot), assembled square-rhombic units with stacking faults, is a long-range ordered structure, in which the square and rhombic units are assembled in an order of alternative distribution, and the other rhombic unit forms stacking faults (polarized water chains). Spontaneous flipping of water molecules in monolayer square-like ice is intrinsic and induces transformations among different elementary units, resulting in the structural evolution of monolayer square ice in dynamics. The existence of stacking faults should be attributed to the spontaneous flipping behavior of water molecules under ambient temperature. Statistical averaging results (thermal average positions) demonstrate the inherent square characteristic of monolayer square ice. The simulated data and insight obtained here might be significant for understanding the topological structure and dynamic behavior of monolayer square ice.

Re'class'ification of 'quant'ified classical simulated annealing

NASA Astrophysics Data System (ADS)

Tanaka, Toshiyuki

2009-12-01

We discuss a classical reinterpretation of quantum-mechanics-based analysis of classical Markov chains with detailed balance, that is based on the quantum-classical correspondence. The classical reinterpretation is then used to demonstrate that it successfully reproduces a sufficient condition for cooling schedule in classical simulated annealing, which has the inverse-logarithmic scaling.

A quantum-classical theory with nonlinear and stochastic dynamics

NASA Astrophysics Data System (ADS)

Burić, N.; Popović, D. B.; Radonjić, M.; Prvanović, S.

2014-12-01

The method of constrained dynamical systems on the quantum-classical phase space is utilized to develop a theory of quantum-classical hybrid systems. Effects of the classical degrees of freedom on the quantum part are modeled using an appropriate constraint, and the interaction also includes the effects of neglected degrees of freedom. Dynamical law of the theory is given in terms of nonlinear stochastic differential equations with Hamiltonian and gradient terms. The theory provides a successful dynamical description of the collapse during quantum measurement.

Molecular Dynamics Simulation of Fission Fragment Damage in Nuclear Fuel and Surrogate Material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devanathan, Ram

ABSTRACT We have performed classical molecular dynamics simulations of swift heavy ion damage, typical of fission fragments, in nuclear fuel (UO 2) for energy deposition per unit length of 3.9 keV/nm. We did not observe amorphization. The damage mainly consisted of isolated point defects. Only about 1% of the displacements occur on the uranium sublattice. Oxygen Frenkel pairs are an order of magnitude more numerous than uranium Frenkel pairs in the primary damage state. In contrast, previous results show that the ratio of Frenkel pairs on the two sublattices is close to the stoichiometric ratio in ceria. These differences inmore » the primary damage state may lead to differences in radiation response of UO 2and CeO 2.« less

Interactions in charged colloidal suspensions: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Padidela, Uday Kumar; Behera, Raghu Nath

2017-07-01

Colloidal suspensions are extensively used in everyday life and find several applications in the pharmaceutical, chemical, food industries, etc. We present the classical molecular dynamics simulation results of the structural and transport properties of charged colloidal suspensions as a function of its size, charge and concentration. The system is viewed as a two-component (colloids and counterions) primitive model consisting of spherical colloid particle (macroion) and the counterions (micro-particles), which are treated explicitly. The solvent is treated as dielectric continuum. A systematic trend in the radial distribution functions g(r), potential of mean force W(r), different thermodynamic properties and diffusion coefficients is obtained as a function of colloid charge, size and concentration. An attractive minimum in W(r) is obtained at short interparticle distance.

Nonadiabatic nuclear dynamics of the ammonia cation studied by surface hopping classical trajectory calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belyaev, Andrey K., E-mail: belyaev@herzen.spb.ru; Domcke, Wolfgang, E-mail: wolfgang.domcke@ch.tum.de; Lasser, Caroline, E-mail: classer@ma.tum.de

The Landau–Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected formore » the nuclear dynamics: Ultrafast Jahn–Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.« less

Simulation of weak polyelectrolytes: a comparison between the constant pH and the reaction ensemble method

NASA Astrophysics Data System (ADS)

Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

2017-03-01

The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we demonstrate the similarity between both methods under certain conditions. We perform molecular dynamics simulations of a weak polyelectrolyte in order to compare the titration curves obtained by both approaches. Our findings reveal a good agreement between the methods when the reaction ensemble is used to sweep the reaction constant. Pronounced differences between the reaction ensemble and the constant pH method can be observed for stronger acids and bases in terms of adaptive pH values. These deviations are due to the presence of explicit protons in the reaction ensemble method which induce a screening of electrostatic interactions between the charged titrable groups of the polyelectrolyte. The outcomes of our simulation hint to a better applicability of the reaction ensemble method for systems in confined geometries and titrable groups in polyelectrolytes with different pKa values.

Multiscale methods for computational RNA enzymology

PubMed Central

Panteva, Maria T.; Dissanayake, Thakshila; Chen, Haoyuan; Radak, Brian K.; Kuechler, Erich R.; Giambaşu, George M.; Lee, Tai-Sung; York, Darrin M.

2016-01-01

RNA catalysis is of fundamental importance to biology and yet remains ill-understood due to its complex nature. The multi-dimensional “problem space” of RNA catalysis includes both local and global conformational rearrangements, changes in the ion atmosphere around nucleic acids and metal ion binding, dependence on potentially correlated protonation states of key residues and bond breaking/forming in the chemical steps of the reaction. The goal of this article is to summarize and apply multiscale modeling methods in an effort to target the different parts of the RNA catalysis problem space while also addressing the limitations and pitfalls of these methods. Classical molecular dynamics (MD) simulations, reference interaction site model (RISM) calculations, constant pH molecular dynamics (CpHMD) simulations, Hamiltonian replica exchange molecular dynamics (HREMD) and quantum mechanical/molecular mechanical (QM/MM) simulations will be discussed in the context of the study of RNA backbone cleavage transesterification. This reaction is catalyzed by both RNA and protein enzymes, and here we examine the different mechanistic strategies taken by the hepatitis delta virus ribozyme (HDVr) and RNase A. PMID:25726472

Molecular dynamics and charge transport in organic semiconductors: a classical approach to modeling electron transfer

DOE PAGES

Pelzer, Kenley M.; Vázquez-Mayagoitia, Álvaro; Ratcliff, Laura E.; ...

2017-01-01

Organic photovoltaics (OPVs) are a promising carbon-neutral energy conversion technology, with recent improvements pushing power conversion efficiencies over 10%. A major factor limiting OPV performance is inefficiency of charge transport in organic semiconducting materials (OSCs). Due to strong coupling with lattice degrees of freedom, the charges form polarons, localized quasi-particles comprised of charges dressed with phonons. These polarons can be conceptualized as pseudo-atoms with a greater effective mass than a bare charge. Here we propose that due to this increased mass, polarons can be modeled with Langevin molecular dynamics (LMD), a classical approach with a computational cost much lower thanmore » most quantum mechanical methods. Here we present LMD simulations of charge transfer between a pair of fullerene molecules, which commonly serve as electron acceptors in OSCs. We find transfer rates consistent with experimental measurements of charge mobility, suggesting that this method may provide quantitative predictions of efficiency when used to simulate materials on the device scale. Our approach also offers information that is not captured in the overall transfer rate or mobility: in the simulation data, we observe exactly when and why intermolecular transfer events occur. In addition, we demonstrate that these simulations can shed light on the properties of polarons in OSCs. In conclusion, much remains to be learned about these quasi-particles, and there are no widely accepted methods for calculating properties such as effective mass and friction. Lastly, our model offers a promising approach to exploring mass and friction as well as providing insight into the details of polaron transport in OSCs.« less

Dynamical Symmetries in Classical Mechanics

ERIC Educational Resources Information Center

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…

Peptide aggregation and solvent electrostriction in a simple zwitterionic dipeptide via molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Bates, S. P.

2009-07-01

We investigate the structure of the glycyl-l-alanine dipeptide in aqueous solution at a 1:20 peptide:water concentration via classical, atomistic molecular dynamics simulations using the CHARMM22 force field, and compare to recent neutron diffraction data [S. E. McLain, A. K. Soper, and A. Watts, Eur. Biophys. J. 37, 647 (2008); S. E. McLain, A. K. Soper, I. Diadone, J. C. Smith, and A. Watts, Angew. Chem. Int. Ed. 47, 9059 (2008)]. Comparison between simulations and experiments is made using the static structure factor S (Q ) . The effect of water model (TIP3P, TIP4P, and SPC/E) upon the solution structure is investigated. Agreement between experiment and simulation is generally good across the entire Q range, although some model-dependent variation is observed, particularly in the predicted intensities of features in S (Q ) . Peptide aggregation is found to be driven by "hydrophilic" (often bifurcated) hydrogen bonds formed between carboxy and amine functional groups, although simulations suggest that the degree of aggregation is less than that observed experimentally. It is found that hydrophobic association is not significant, with hydrophobic hydration being preferred to association. Detailed examination of the solute structural motifs reveals the existence of bifurcated motifs that are suggested to be an artifact of the CHARMM force field, and may imply that classical force fields provide a flawed structural and dynamical description of such molecular fluids. Investigation of the water structure reveals the presence of an electrostrictive effect which manifests itself as an increase in the number of interstitial molecules in the water second coordination shell, in contradiction to suggestions that this phenomenon arises owing to hydrogen bond bending. Detailed analysis based upon two-dimensional distribution functions suggests an intimate link between the phenomenon of electrostriction and the behavior of water under high-pressure compression. We find the magnitude of the electrostrictive effect inferred from the neutron diffraction data to be greater than that found in the simulations. Investigation of the solvation structure suggests that the CHARMM force field overhydrates the terminal carboxy group, and that this overhydration is accompanied by the presence of bifurcated hydrogen bonds.

Feedback control laws for highly maneuverable aircraft

NASA Technical Reports Server (NTRS)

Garrard, William L.; Balas, Gary J.

1995-01-01

During this year, we concentrated our efforts on the design of controllers for lateral/directional control using mu synthesis. This proved to be a more difficult task than we anticipated and we are still working on the designs. In the lateral-directional control problem, the inputs are pilot lateral stick and pedal commands and the outputs are roll rate about the velocity vector and side slip angle. The control effectors are ailerons, rudder deflection, and directional thrust vectoring vane deflection which produces a yawing moment about the body axis. Our math model does not contain any provision for thrust vectoring of rolling moment. This has resulted in limitations of performance at high angles of attack. During 1994-95, the following tasks for the lateral-directional controllers were accomplished: (1) Designed both inner and outer loop dynamic inversion controllers. These controllers are implemented using accelerometer outputs rather than an a priori model of the vehicle aerodynamics; (2) Used classical techniques to design controllers for the system linearized by dynamics inversion. These controllers acted to control roll rate and Dutch roll response; (3) Implemented the inner loop dynamic inversion and classical controllers on the six DOF simulation; (4) Developed a lateral-directional control allocation scheme based on minimizing required control effort among the ailerons, rudder, and directional thrust vectoring; and (5) Developed mu outer loop controllers combined with classical inner loop controllers.

An appraisal of the classic forest succession paradigm with the shade tolerance index.

PubMed

Lienard, Jean; Florescu, Ionut; Strigul, Nikolay

2015-01-01

In this paper we revisit the classic theory of forest succession that relates shade tolerance and species replacement and assess its validity to understand patch-mosaic patterns of forested ecosystems of the USA. We introduce a macroscopic parameter called the "shade tolerance index" and compare it to the classic continuum index in southern Wisconsin forests. We exemplify shade tolerance driven succession in White Pine-Eastern Hemlock forests using computer simulations and analyzing approximated chronosequence data from the USDA FIA forest inventory. We describe this parameter across the last 50 years in the ecoregions of mainland USA, and demonstrate that it does not correlate with the usual macroscopic characteristics of stand age, biomass, basal area, and biodiversity measures. We characterize the dynamics of shade tolerance index using transition matrices and delimit geographical areas based on the relevance of shade tolerance to explain forest succession. We conclude that shade tolerance driven succession is linked to climatic variables and can be considered as a primary driving factor of forest dynamics mostly in central-north and northeastern areas in the USA. Overall, the shade tolerance index constitutes a new quantitative approach that can be used to understand and predict succession of forested ecosystems and biogeographic patterns.

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions.

PubMed

Jiang, Hao; Haji-Akbari, Amir; Debenedetti, Pablo G; Panagiotopoulos, Athanassios Z

2018-01-28

We used molecular dynamics simulations and the path sampling technique known as forward flux sampling to study homogeneous nucleation of NaCl crystals from supersaturated aqueous solutions at 298 K and 1 bar. Nucleation rates were obtained for a range of salt concentrations for the Joung-Cheatham NaCl force field combined with the Extended Simple Point Charge (SPC/E) water model. The calculated nucleation rates are significantly lower than the available experimental measurements. The estimates for the nucleation rates in this work do not rely on classical nucleation theory, but the pathways observed in the simulations suggest that the nucleation process is better described by classical nucleation theory than an alternative interpretation based on Ostwald's step rule, in contrast to some prior simulations of related models. In addition to the size of NaCl nucleus, we find that the crystallinity of a nascent cluster plays an important role in the nucleation process. Nuclei with high crystallinity were found to have higher growth probability and longer lifetimes, possibly because they are less exposed to hydration water.

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions

NASA Astrophysics Data System (ADS)

Jiang, Hao; Haji-Akbari, Amir; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2018-01-01

We used molecular dynamics simulations and the path sampling technique known as forward flux sampling to study homogeneous nucleation of NaCl crystals from supersaturated aqueous solutions at 298 K and 1 bar. Nucleation rates were obtained for a range of salt concentrations for the Joung-Cheatham NaCl force field combined with the Extended Simple Point Charge (SPC/E) water model. The calculated nucleation rates are significantly lower than the available experimental measurements. The estimates for the nucleation rates in this work do not rely on classical nucleation theory, but the pathways observed in the simulations suggest that the nucleation process is better described by classical nucleation theory than an alternative interpretation based on Ostwald's step rule, in contrast to some prior simulations of related models. In addition to the size of NaCl nucleus, we find that the crystallinity of a nascent cluster plays an important role in the nucleation process. Nuclei with high crystallinity were found to have higher growth probability and longer lifetimes, possibly because they are less exposed to hydration water.

A new class of ensemble conserving algorithms for approximate quantum dynamics: Theoretical formulation and model problems.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Nyman, Gunnar; Rossky, Peter J

2015-06-28

We develop two classes of quasi-classical dynamics that are shown to conserve the initial quantum ensemble when used in combination with the Feynman-Kleinert approximation of the density operator. These dynamics are used to improve the Feynman-Kleinert implementation of the classical Wigner approximation for the evaluation of quantum time correlation functions known as Feynman-Kleinert linearized path-integral. As shown, both classes of dynamics are able to recover the exact classical and high temperature limits of the quantum time correlation function, while a subset is able to recover the exact harmonic limit. A comparison of the approximate quantum time correlation functions obtained from both classes of dynamics is made with the exact results for the challenging model problems of the quartic and double-well potentials. It is found that these dynamics provide a great improvement over the classical Wigner approximation, in which purely classical dynamics are used. In a special case, our first method becomes identical to centroid molecular dynamics.

Influence of velocity effects on the shape of N2 (and air) broadened H2O lines revisited with classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ngo, N. H.; Tran, H.; Gamache, R. R.; Bermejo, D.; Domenech, J.-L.

2012-08-01

The modeling of the shape of H2O lines perturbed by N2 (and air) using the Keilson-Storer (KS) kernel for collision-induced velocity changes is revisited with classical molecular dynamics simulations (CMDS). The latter have been performed for a large number of molecules starting from intermolecular-potential surfaces. Contrary to the assumption made in a previous study [H. Tran, D. Bermejo, J.-L. Domenech, P. Joubert, R. R. Gamache, and J.-M. Hartmann, J. Quant. Spectrosc. Radiat. Transf. 108, 126 (2007)], 10.1016/j.jqsrt.2007.03.009, the results of these CMDS show that the velocity-orientation and -modulus changes statistically occur at the same time scale. This validates the use of a single memory parameter in the Keilson-Storer kernel to describe both the velocity-orientation and -modulus changes. The CMDS results also show that velocity- and rotational state-changing collisions are statistically partially correlated. A partially correlated speed-dependent Keilson-Storer model has thus been used to describe the line-shape. For this, the velocity changes KS kernel parameters have been directly determined from CMDS, while the speed-dependent broadening and shifting coefficients have been calculated with a semi-classical approach. Comparisons between calculated spectra and measurements of several lines of H2O broadened by N2 (and air) in the ν3 and 2ν1 + ν2 + ν3 bands for a wide range of pressure show very satisfactory agreement. The evolution of non-Voigt effects from Doppler to collisional regimes is also presented and discussed.

Effect of pairwise additivity on finite-temperature behavior of classical ideal gas

NASA Astrophysics Data System (ADS)

Shekaari, Ashkan; Jafari, Mahmoud

2018-05-01

Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.

The quantum CP-violating kaon system reproduced in the electronic laboratory

NASA Astrophysics Data System (ADS)

Caruso, M.; Fanchiotti, H.; García Canal, C. A.; Mayosky, M.; Veiga, A.

2016-11-01

The equivalence between the Schrödinger dynamics of a quantum system with a finite number of basis states and a classical dynamics is realized in terms of electric networks. The isomorphism that connects in a univocal way both dynamical systems was applied to the case of neutral mesons, kaons in particular, and the class of electric networks univocally related to the quantum system was analysed. Moreover, under CPT invariance, the relevant ɛ parameter that measures CP violation in the kaon system is reinterpreted in terms of network parameters. All these results were explicitly shown by means of both a numerical simulation of the implied networks and by constructing the corresponding circuits.

Ares I Flight Control System Overview

NASA Technical Reports Server (NTRS)

Hall, Charles; Lee, Chong; Jackson, Mark; Whorton, Mark; West, mark; Brandon, Jay; Hall, Rob A.; Jang, Jimmy; Bedrossian, Naz; Compton, Jimmy;

Emulation of complex open quantum systems using superconducting qubits

NASA Astrophysics Data System (ADS)

Mostame, Sarah; Huh, Joonsuk; Kreisbeck, Christoph; Kerman, Andrew J.; Fujita, Takatoshi; Eisfeld, Alexander; Aspuru-Guzik, Alán

2017-02-01

With quantum computers being out of reach for now, quantum simulators are alternative devices for efficient and accurate simulation of problems that are challenging to tackle using conventional computers. Quantum simulators are classified into analog and digital, with the possibility of constructing "hybrid" simulators by combining both techniques. Here we focus on analog quantum simulators of open quantum systems and address the limit that they can beat classical computers. In particular, as an example, we discuss simulation of the chlorosome light-harvesting antenna from green sulfur bacteria with over 250 phonon modes coupled to each electronic state. Furthermore, we propose physical setups that can be used to reproduce the quantum dynamics of a standard and multiple-mode Holstein model. The proposed scheme is based on currently available technology of superconducting circuits consist of flux qubits and quantum oscillators.

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

PubMed

Chen, Yunjie; Roux, Benoît

2015-08-11

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up to 21 times for polyalanine and (AAQAA)3 in water.

Role of Dynamics in the Autoinhibition and Activation of the Exchange Protein Directly Activated by Cyclic AMP (EPAC)*

PubMed Central

VanSchouwen, Bryan; Selvaratnam, Rajeevan; Fogolari, Federico; Melacini, Giuseppe

2011-01-01

The exchange protein directly activated by cAMP (EPAC) is a key receptor of cAMP in eukaryotes and controls critical signaling pathways. Currently, no residue resolution information is available on the full-length EPAC dynamics, which are known to be pivotal determinants of allostery. In addition, no information is presently available on the intermediates for the classical induced fit and conformational selection activation pathways. Here these questions are addressed through molecular dynamics simulations on five key states along the thermodynamic cycle for the cAMP-dependent activation of a fully functional construct of EPAC2, which includes the cAMP-binding domain and the integral catalytic region. The simulations are not only validated by the agreement with the experimental trends in cAMP-binding domain dynamics determined by NMR, but they also reveal unanticipated dynamic attributes, rationalizing previously unexplained aspects of EPAC activation and autoinhibition. Specifically, the simulations show that cAMP binding causes an extensive perturbation of dynamics in the distal catalytic region, assisting the recognition of the Rap1b substrate. In addition, analysis of the activation intermediates points to a possible hybrid mechanism of EPAC allostery incorporating elements of both the induced fit and conformational selection models. In this mechanism an entropy compensation strategy results in a low free-energy pathway of activation. Furthermore, the simulations indicate that the autoinhibitory interactions of EPAC are more dynamic than previously anticipated, leading to a revised model of autoinhibition in which dynamics fine tune the stability of the autoinhibited state, optimally sensitizing it to cAMP while avoiding constitutive activation. PMID:21873431

2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre

2018-05-01

Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

Complex discrete dynamics from simple continuous population models.

PubMed

Gamarra, Javier G P; Solé, Ricard V

2002-05-01

Nonoverlapping generations have been classically modelled as difference equations in order to account for the discrete nature of reproductive events. However, other events such as resource consumption or mortality are continuous and take place in the within-generation time. We have realistically assumed a hybrid ODE bidimensional model of resources and consumers with discrete events for reproduction. Numerical and analytical approaches showed that the resulting dynamics resembles a Ricker map, including the doubling route to chaos. Stochastic simulations with a handling-time parameter for indirect competition of juveniles may affect the qualitative behaviour of the model.

Thermodynamics of a time-dependent and dissipative oval billiard: A heat transfer and billiard approach.

PubMed

Leonel, Edson D; Galia, Marcus Vinícius Camillo; Barreiro, Luiz Antonio; Oliveira, Diego F M

2016-12-01

We study some statistical properties for the behavior of the average squared velocity-hence the temperature-for an ensemble of classical particles moving in a billiard whose boundary is time dependent. We assume the collisions of the particles with the boundary of the billiard are inelastic, leading the average squared velocity to reach a steady-state dynamics for large enough time. The description of the stationary state is made by using two different approaches: (i) heat transfer motivated by the Fourier law and (ii) billiard dynamics using either numerical simulations and theoretical description.

The Sharma-Parthasarathy stochastic two-body problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cresson, J.; SYRTE/Observatoire de Paris, 75014 Paris; Pierret, F.

2015-03-15

We study the Sharma-Parthasarathy stochastic two-body problem introduced by Sharma and Parthasarathy in [“Dynamics of a stochastically perturbed two-body problem,” Proc. R. Soc. A 463, 979-1003 (2007)]. In particular, we focus on the preservation of some fundamental features of the classical two-body problem like the Hamiltonian structure and first integrals in the stochastic case. Numerical simulations are performed which illustrate the dynamical behaviour of the osculating elements as the semi-major axis, the eccentricity, and the pericenter. We also derive a stochastic version of Gauss’s equations in the planar case.

Fractional dynamics using an ensemble of classical trajectories

NASA Astrophysics Data System (ADS)

Sun, Zhaopeng; Dong, Hao; Zheng, Yujun

2018-01-01

A trajectory-based formulation for fractional dynamics is presented and the trajectories are generated deterministically. In this theoretical framework, we derive a new class of estimators in terms of confluent hypergeometric function (F11) to represent the Riesz fractional derivative. Using this method, the simulation of free and confined Lévy flight are in excellent agreement with the exact numerical and analytical results. In addition, the barrier crossing in a bistable potential driven by Lévy noise of index α is investigated. In phase space, the behavior of trajectories reveal the feature of Lévy flight in a better perspective.

Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

PubMed

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. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations.

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Dayle MA; Xiong, Yijia; Straatsma, TP

2012-05-09

Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexiblemore » in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.« less

Exploring Ultrahigh-Intensity Laser-Plasma Interaction Physics with QED Particle-in-Cell Simulations

NASA Astrophysics Data System (ADS)

Luedtke, S. V.; Yin, L.; Labun, L. A.; Albright, B. J.; Stark, D. J.; Bird, R. F.; Nystrom, W. D.; Hegelich, B. M.

2017-10-01

Next generation high-intensity lasers are reaching intensity regimes where new physics-quantum electrodynamics (QED) corrections to otherwise classical plasma dynamics-becomes important. Modeling laser-plasma interactions in these extreme settings presents a challenge to traditional particle-in-cell (PIC) codes, which either do not have radiation reaction or include only classical radiation reaction. We discuss a semi-classical approach to adding quantum radiation reaction and photon production to the PIC code VPIC. We explore these intensity regimes with VPIC, compare with results from the PIC code PSC, and report on ongoing work to expand the capability of VPIC in these regimes. This work was supported by the U.S. DOE, Los Alamos National Laboratory Science program, LDRD program, NNSA (DE-NA0002008), and AFOSR (FA9550-14-1-0045). HPC resources provided by TACC, XSEDE, and LANL Institutional Computing.

Selectivity trend of gas separation through nanoporous graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hongjun; Chen, Zhongfang; Dai, Sheng

2014-01-29

We demonstrate that porous graphene can efficiently separate gases according to their molecular sizes using molecular dynamic (MD) simulations,. The flux sequence from the classical MD simulation is H 2>CO 2>>N 2>Ar>CH 4, which generally follows the trend in the kinetic diameters. Moreover, this trend is also confirmed from the fluxes based on the computed free energy barriers for gas permeation using the umbrella sampling method and kinetic theory of gases. Both brute-force MD simulations and free-energy calcualtions lead to the flux trend consistent with experiments. Case studies of two compositions of CO 2/N 2 mixtures further demonstrate the separationmore » capability of nanoporous graphene.« less

SIVEH: numerical computing simulation of wireless energy-harvesting sensor nodes.

PubMed

Sanchez, Antonio; Blanc, Sara; Climent, Salvador; Yuste, Pedro; Ors, Rafael

2013-09-04

The paper presents a numerical energy harvesting model for sensor nodes, SIVEH (Simulator I-V for EH), based on I-V hardware tracking. I-V tracking is demonstrated to be more accurate than traditional energy modeling techniques when some of the components present different power dissipation at either different operating voltages or drawn currents. SIVEH numerical computing allows fast simulation of long periods of time-days, weeks, months or years-using real solar radiation curves. Moreover, SIVEH modeling has been enhanced with sleep time rate dynamic adjustment, while seeking energy-neutral operation. This paper presents the model description, a functional verification and a critical comparison with the classic energy approach.

SIVEH: Numerical Computing Simulation of Wireless Energy-Harvesting Sensor Nodes

PubMed Central

Sanchez, Antonio; Blanc, Sara; Climent, Salvador; Yuste, Pedro; Ors, Rafael

2013-01-01

The paper presents a numerical energy harvesting model for sensor nodes, SIVEH (Simulator I–V for EH), based on I–V hardware tracking. I–V tracking is demonstrated to be more accurate than traditional energy modeling techniques when some of the components present different power dissipation at either different operating voltages or drawn currents. SIVEH numerical computing allows fast simulation of long periods of time—days, weeks, months or years—using real solar radiation curves. Moreover, SIVEH modeling has been enhanced with sleep time rate dynamic adjustment, while seeking energy-neutral operation. This paper presents the model description, a functional verification and a critical comparison with the classic energy approach. PMID:24008287

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Dynamics of Flexible MLI-type Debris for Accurate Orbit Prediction

DTIC Science & Technology

2014-09-01

sets usually are classical orbital elements , or Keplerian elements illustrated in Fig. 3. Fig. 3. Orbital elements ... elements in Table 2, for 10 orbits . Orbit of the objects is simulated by equation (3.9) and set the initial equation in Table 2. Gravitational...depending upon the parameters selected and the orbit to be propagated. For this reason, other sets of elements were defined and used in the

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pang, Yuan-Ping, E-mail: pang@mayo.edu

Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its nativemore » conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.« less

Molecular Dynamics Investigation of Each Bubble Behavior in Coarsening of Cavitation Bubbles in a Finite Space

NASA Astrophysics Data System (ADS)

Tsuda, Shin-Ichi; Nakano, Yuta; Watanabe, Satoshi

2017-11-01

Recently, several studies using Molecular Dynamics (MD) simulation have been conducted for investigation of Ostwald ripening of cavitation bubbles in a finite space. The previous studies focused a characteristic length of bubbles as one of the spatially-averaged quantities, but each bubble behavior was not been investigated in detail. The objective of this study is clarification of the characteristics of each bubble behavior in Ostwald ripening, and we conducted MD simulation of a Lennard-Jones fluid in a semi-confined space. As a result, the time dependency of the characteristic length of bubbles as a spatially-averaged quantity suggested that the driving force of the Ostwald ripening is Evaporation/Condensation (EC) across liquid-vapor surface, which is the same result as the previous works. The radius change of the relatively larger bubbles also showed the same tendency to a classical EC model. However, the sufficiently smaller bubbles than the critical size, e.g., the bubbles just before collapsing, showed a different characteristic from the classical EC model. Those smaller bubbles has a tendency to be limited by mechanical non-equilibrium in which viscosity of liquid is dominant rather than by EC across liquid-vapor surface. This work was supported by JSPS KAKENHI Grant Number JP16K06085.

N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

NASA Astrophysics Data System (ADS)

Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

2015-03-01

We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

Quasi-Geostrophic Diagnosis of Mixed-Layer Dynamics Embedded in a Mesoscale Turbulent Field

NASA Astrophysics Data System (ADS)

Chavanne, C. P.; Klein, P.

2016-02-01

A new quasi-geostrophic model has been developed to diagnose the three-dimensional circulation, including the vertical velocity, in the upper ocean from high-resolution observations of sea surface height and buoyancy. The formulation for the adiabatic component departs from the classical surface quasi-geostrophic framework considered before since it takes into account the stratification within the surface mixed-layer that is usually much weaker than that in the ocean interior. To achieve this, the model approximates the ocean with two constant-stratification layers : a finite-thickness surface layer (or the mixed-layer) and an infinitely-deep interior layer. It is shown that the leading-order adiabatic circulation is entirely determined if both the surface streamfunction and buoyancy anomalies are considered. The surface layer further includes a diabatic dynamical contribution. Parameterization of diabatic vertical velocities is based on their restoring impacts of the thermal-wind balance that is perturbed by turbulent vertical mixing of momentum and buoyancy. The model skill in reproducing the three-dimensional circulation in the upper ocean from surface data is checked against the output of a high-resolution primitive-equation numerical simulation. Correlation between simulated and diagnosed vertical velocities are significantly improved in the mixed-layer for the new model compared to the classical surface quasi-geostrophic model, reaching 0.9 near the surface.

Hierarchical Multiscale Modeling of Macromolecules and their Assemblies

PubMed Central

Ortoleva, P.; Singharoy, A.; Pankavich, S.

2013-01-01

Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character of such systems often makes traditional molecular dynamics simulation impractical, a multiscale approach has been presented that allows for long-time simulation with atomic detail based on the co-evolution of slowly-varying order parameters (OPs) with the quasi-equilibrium probability density of atomic configurations. However, this approach breaks down when the structural change is extreme, or when nearest-neighbor connectivity of atoms is not maintained. In the current study, a self-consistent approach is presented wherein OPs and a reference structure co-evolve slowly to yield long-time simulation for dynamical soft-matter phenomena such as structural transitions and self-assembly. The development begins with the Liouville equation for N classical atoms and an ansatz on the form of the associated N-atom probability density. Multiscale techniques are used to derive Langevin equations for the coupled OP-configurational dynamics. The net result is a set of equations for the coupled stochastic dynamics of the OPs and centers of mass of the subsystems that constitute a soft material body. The theory is based on an all-atom methodology and an interatomic force field, and therefore enables calibration-free simulations of soft matter, such as macromolecular assemblies. PMID:23671457

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Perspective: Memcomputing: Leveraging memory and physics to compute efficiently

NASA Astrophysics Data System (ADS)

Di Ventra, Massimiliano; Traversa, Fabio L.

2018-05-01

It is well known that physical phenomena may be of great help in computing some difficult problems efficiently. A typical example is prime factorization that may be solved in polynomial time by exploiting quantum entanglement on a quantum computer. There are, however, other types of (non-quantum) physical properties that one may leverage to compute efficiently a wide range of hard problems. In this perspective, we discuss how to employ one such property, memory (time non-locality), in a novel physics-based approach to computation: Memcomputing. In particular, we focus on digital memcomputing machines (DMMs) that are scalable. DMMs can be realized with non-linear dynamical systems with memory. The latter property allows the realization of a new type of Boolean logic, one that is self-organizing. Self-organizing logic gates are "terminal-agnostic," namely, they do not distinguish between the input and output terminals. When appropriately assembled to represent a given combinatorial/optimization problem, the corresponding self-organizing circuit converges to the equilibrium points that express the solutions of the problem at hand. In doing so, DMMs take advantage of the long-range order that develops during the transient dynamics. This collective dynamical behavior, reminiscent of a phase transition, or even the "edge of chaos," is mediated by families of classical trajectories (instantons) that connect critical points of increasing stability in the system's phase space. The topological character of the solution search renders DMMs robust against noise and structural disorder. Since DMMs are non-quantum systems described by ordinary differential equations, not only can they be built in hardware with the available technology, they can also be simulated efficiently on modern classical computers. As an example, we will show the polynomial-time solution of the subset-sum problem for the worst cases, and point to other types of hard problems where simulations of DMMs' equations of motion on classical computers have already demonstrated substantial advantages over traditional approaches. We conclude this article by outlining further directions of study.

Ultimate open pit stochastic optimization

NASA Astrophysics Data System (ADS)

Marcotte, Denis; Caron, Josiane

2013-02-01

Classical open pit optimization (maximum closure problem) is made on block estimates, without directly considering the block grades uncertainty. We propose an alternative approach of stochastic optimization. The stochastic optimization is taken as the optimal pit computed on the block expected profits, rather than expected grades, computed from a series of conditional simulations. The stochastic optimization generates, by construction, larger ore and waste tonnages than the classical optimization. Contrary to the classical approach, the stochastic optimization is conditionally unbiased for the realized profit given the predicted profit. A series of simulated deposits with different variograms are used to compare the stochastic approach, the classical approach and the simulated approach that maximizes expected profit among simulated designs. Profits obtained with the stochastic optimization are generally larger than the classical or simulated pit. The main factor controlling the relative gain of stochastic optimization compared to classical approach and simulated pit is shown to be the information level as measured by the boreholes spacing/range ratio. The relative gains of the stochastic approach over the classical approach increase with the treatment costs but decrease with mining costs. The relative gains of the stochastic approach over the simulated pit approach increase both with the treatment and mining costs. At early stages of an open pit project, when uncertainty is large, the stochastic optimization approach appears preferable to the classical approach or the simulated pit approach for fair comparison of the values of alternative projects and for the initial design and planning of the open pit.

Dynamic Modeling and Simulation of a Rotational Inverted Pendulum

NASA Astrophysics Data System (ADS)

Duart, J. L.; Montero, B.; Ospina, P. A.; González, E.

2017-01-01

This paper presents an alternative way to the dynamic modeling of a rotational inverted pendulum using the classic mechanics known as Euler-Lagrange allows to find motion equations that describe our model. It also has a design of the basic model of the system in SolidWorks software, which based on the material and dimensions of the model provides some physical variables necessary for modeling. In order to verify the theoretical results, It was made a contrast between the solutions obtained by simulation SimMechanics-Matlab and the system of equations Euler-Lagrange, solved through ODE23tb method included in Matlab bookstores for solving equations systems of the type and order obtained. This article comprises a pendulum trajectory analysis by a phase space diagram that allows the identification of stable and unstable regions of the system.

Comparison of Quantum and Classical Monte Carlo on a Simple Model Phase Transition

NASA Astrophysics Data System (ADS)

Cohen, D. E.; Cohen, R. E.

2005-12-01

Most simulations of phase transitions in minerals use classical molecular dynamics or classical Monte Carlo. However, it is known that in some cases, quantum effects are quite large, even for perovskite oxides [1]. We have studied the simplest model of a phase transition where this can be tested, that of interacting of double wells with an infinite- range interaction. The energy is E = ∑i (-A xi2 + B xi4 + ξ xi) . We used the same parameters used in a study of vibrational spectra and soft- mode behavior [4], A=0.01902, B=0.14294, ξ=0.025 in Hartree atomic units. This gives Tc of about 400 K. We varied the oscillator mass from 18 to 100. Classical Monte Carlo and path integral Monte Carlo (PIMC) were performed on this model. The maximum effect was for the lightest mass, in which PIMC gave a 75K lower Tc than the classical simulation. This is similar to the reduction in Tc observed in PIMC simulations for BaTiO3 at zero pressure [1]. We will explore the effects of varying the well depths. Shallower wells would show a greater quantum effect, as was seen in the high pressure BaTiO3 simulations, since pressure reduces the double well depths [5]. [1] Iniguez, J. & Vanderbilt, D. First-principles study of the temperature-pressure phase diagram of BaTiO3. Phys. Rev. Lett. 89, 115503 (2002). [2] Gillis, N. S. & Koehler, T. R. Phase transitions in a simple model ferroelectric-- -comparison of exact and variational treatments of a molecular-field Hamiltonian. Phys. Rev. B 9, 3806 (1974). [3] Koehler, T. R. & Gillis, N. S. Phase Transitions in a Model of Interacting Anharmonic Oscillators. Phys. Rev. B 7, 4980 (1973). [4] Flocken, J. W., Guenther, R. A., Hardy, J. R. & Boyer, L. L. Dielectric response spectrum of a damped one-dimensional double-well oscillator. Phys. Rev. B 40, 11496-11501 (1989). [5] Cohen, R. E. Origin of ferroelectricity in oxide ferroelectrics and the difference in ferroelectric behavior of BaTiO3 and PbTiO3. Nature 358, 136-138 (1992).

Anomalous Chained Turbulence in Actively Driven Flows on Spheres

NASA Astrophysics Data System (ADS)

Mickelin, Oscar; Słomka, Jonasz; Burns, Keaton J.; Lecoanet, Daniel; Vasil, Geoffrey M.; Faria, Luiz M.; Dunkel, Jörn

2018-04-01

Recent experiments demonstrate the importance of substrate curvature for actively forced fluid dynamics. Yet, the covariant formulation and analysis of continuum models for nonequilibrium flows on curved surfaces still poses theoretical challenges. Here, we introduce and study a generalized covariant Navier-Stokes model for fluid flows driven by active stresses in nonplanar geometries. The analytical tractability of the theory is demonstrated through exact stationary solutions for the case of a spherical bubble geometry. Direct numerical simulations reveal a curvature-induced transition from a burst phase to an anomalous turbulent phase that differs distinctly from externally forced classical 2D Kolmogorov turbulence. This new type of active turbulence is characterized by the self-assembly of finite-size vortices into linked chains of antiferromagnetic order, which percolate through the entire fluid domain, forming an active dynamic network. The coherent motion of the vortex chain network provides an efficient mechanism for upward energy transfer from smaller to larger scales, presenting an alternative to the conventional energy cascade in classical 2D turbulence.

Shock melting method to determine melting curve by molecular dynamics: Cu, Pd, and Al.

PubMed

Liu, Zhong-Li; Zhang, Xiu-Lu; Cai, Ling-Cang

2015-09-21

A melting simulation method, the shock melting (SM) method, is proposed and proved to be able to determine the melting curves of materials accurately and efficiently. The SM method, which is based on the multi-scale shock technique, determines melting curves by preheating and/or prepressurizing materials before shock. This strategy was extensively verified using both classical and ab initio molecular dynamics (MD). First, the SM method yielded the same satisfactory melting curve of Cu with only 360 atoms using classical MD, compared to the results from the Z-method and the two-phase coexistence method. Then, it also produced a satisfactory melting curve of Pd with only 756 atoms. Finally, the SM method combined with ab initio MD cheaply achieved a good melting curve of Al with only 180 atoms, which agrees well with the experimental data and the calculated results from other methods. It turned out that the SM method is an alternative efficient method for calculating the melting curves of materials.

Shock melting method to determine melting curve by molecular dynamics: Cu, Pd, and Al

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Zhong-Li, E-mail: zl.liu@163.com; Zhang, Xiu-Lu; Cai, Ling-Cang

A melting simulation method, the shock melting (SM) method, is proposed and proved to be able to determine the melting curves of materials accurately and efficiently. The SM method, which is based on the multi-scale shock technique, determines melting curves by preheating and/or prepressurizing materials before shock. This strategy was extensively verified using both classical and ab initio molecular dynamics (MD). First, the SM method yielded the same satisfactory melting curve of Cu with only 360 atoms using classical MD, compared to the results from the Z-method and the two-phase coexistence method. Then, it also produced a satisfactory melting curvemore » of Pd with only 756 atoms. Finally, the SM method combined with ab initio MD cheaply achieved a good melting curve of Al with only 180 atoms, which agrees well with the experimental data and the calculated results from other methods. It turned out that the SM method is an alternative efficient method for calculating the melting curves of materials.« less

Crystal-melt interface mobility in bcc Fe: Linking molecular dynamics to phase-field and phase-field crystal modeling

NASA Astrophysics Data System (ADS)

Guerdane, M.; Berghoff, M.

2018-04-01

By combining molecular dynamics (MD) simulations with phase-field (PF) and phase-field crystal (PFC) modeling we study collision-controlled growth kinetics from the melt for pure Fe. The MD/PF comparison shows, on the one hand, that the PF model can be properly designed to reproduce quantitatively different aspects of the growth kinetics and anisotropy of planar and curved solid-liquid interfaces. On the other hand, this comparison demonstrates the ability of classical MD simulations to predict morphology and dynamics of moving curved interfaces up to a length scale of about 0.15 μ m . After mapping the MD model to the PF one, the latter permits to analyze the separate contribution of different anisotropies to the interface morphology. The MD/PFC agreement regarding the growth anisotropy and morphology extends the trend already observed for the here used PFC model in describing structural and elastic properties of bcc Fe.

Dynamical Defects in Rotating Magnetic Skyrmion Lattices

NASA Astrophysics Data System (ADS)

Pöllath, S.; Wild, J.; Heinen, L.; Meier, T. N. G.; Kronseder, M.; Tutsch, L.; Bauer, A.; Berger, H.; Pfleiderer, C.; Zweck, J.; Rosch, A.; Back, C. H.

2017-05-01

The chiral magnet Cu2 OSeO3 hosts a Skyrmion lattice that may be equivalently described as a superposition of plane waves or a lattice of particlelike topological objects. A thermal gradient may break up the Skyrmion lattice and induce rotating domains, raising the question of which of these scenarios better describes the violent dynamics at the domain boundaries. Here, we show that in an inhomogeneous temperature gradient caused by illumination in a Lorentz transmission electron microscope different parts of the Skyrmion lattice can be set into motion with different angular velocities. Tracking the time dependence, we show that the constant rearrangement of domain walls is governed by dynamic 5-7 defects arranging into lines. An analysis of the associated defect density is described by Frank's equation and agrees well with classical 2D Monte Carlo simulations. Fluctuations of boundaries show a surgelike rearrangement of Skyrmion clusters driven by defect rearrangement consistent with simulations treating Skyrmions as point particles. Our findings underline the particle character of the Skyrmion.

Multiple molecular dynamics simulations of human LOX-1 and Trp150Ala mutant reveal the structural determinants causing the full deactivation of the receptor.

PubMed

Iacovelli, Federico; Tucci, Fabio Giovanni; Macari, Gabriele; Falconi, Mattia

2017-10-01

Multiple classical molecular dynamics simulations have been applied to the human LOX-1 receptor to clarify the role of the Trp150Ala mutation in the loss of binding activity. Results indicate that the substitution of this crucial residue, located at the dimer interface, markedly disrupts the wild-type receptor dynamics. The mutation causes an irreversible rearrangement of the subunits interaction pattern that in the wild-type protein allows the maintaining of a specific symmetrical motion of the monomers. The subunits dislocation determines a loss of linearity of the arginines residues composing the basic spine and a consequent alteration of the long-range electrostatic attraction of the substrate. Moreover, the anomalous subunits arrangement observed in the mutated receptor also affects the integrity of the hydrophobic tunnel, actively involved in the short-range hydrophobic recognition of the substrate. The combined effect of these structural rearrangements generates the impairing of the receptor function. © 2017 Wiley Periodicals, Inc.

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

PubMed

Shokuhfar, Ali; Arab, Behrouz

2013-09-01

Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA) with diethylenetriamine (DETA) curing agent, and to study the behavior of resulted epoxy polymer with different conversion rates. The constant-strain (static) approach was then applied to calculate the mechanical properties (Bulk, shear and Young's moduli, elastic stiffness constants, and Poisson's ratio) of the uncured and cross-linked systems. Estimated material properties were found to be in good agreement with experimental observations. Moreover, the dependency of mechanical properties on the cross linking density was investigated and revealed improvements in the mechanical properties with increasing the cross linking density. The radial distribution function (RDF) was also used to study the evolution of local structures of the simulated systems as a function of cross linking density.

A cut-cell immersed boundary technique for fire dynamics simulation

NASA Astrophysics Data System (ADS)

Vanella, Marcos; McDermott, Randall; Forney, Glenn

2015-11-01

Fire simulation around complex geometry is gaining increasing attention in performance based design of fire protection systems, fire-structure interaction and pollutant transport in complex terrains, among others. This presentation will focus on our present effort in improving the capability of FDS (Fire Dynamics Simulator, developed at the Fire Research Division, NIST. https://github.com/firemodels/fds-smv) to represent fire scenarios around complex bodies. Velocities in the vicinity of the bodies are reconstructed using a classical immersed boundary scheme (Fadlun and co-workers, J. Comput. Phys., 161:35-60, 2000). Also, a conservative treatment of scalar transport equations (i.e. for chemical species) will be presented. In our method, discrete conservation and no penetration of species across solid boundaries are enforced using a cut-cell finite volume scheme. The small cell problem inherent to the method is tackled using explicit-implicit domain decomposition for scalar, within the FDS time integration scheme. Some details on the derivation, implementation and numerical tests of this numerical scheme will be discussed.

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

DOE PAGES

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; ...

2018-01-12

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

Molecular Dynamics Simulation Study of the Capacitive Performance of a Binary Mixture of Ionic Liquids near an Onion-like Carbon Electrode.

PubMed

Li, Song; Feng, Guang; Fulvio, Pasquale F; Hillesheim, Patrick C; Liao, Chen; Dai, Sheng; Cummings, Peter T

2012-09-06

An equimolar mixture of 1-methyl-1-propylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([C3mpy][Tf2N]), 1-methyl-1-butylpiperidinium bis(trifluoromethylsulfonyl)imide ([C4mpip][Tf2N]) was investigated by classic molecular dynamics (MD) simulation. Differential scanning calorimetry (DSC) measurements verified that the binary mixture exhibited lower glass transition temperature than either of the pure room-temperature ionic liquids (RTILs). Moreover, the binary mixture gave rise to higher conductivity than the neat RTILs at lower temperature range. In order to study its capacitive performance in supercapacitors, simulations were performed of the mixture, and the neat RTILs used as electrolytes near an onion-like carbon (OLC) electrode at varying temperatures. The differential capacitance exhibited independence of the electrical potential applied for three electrolytes, which is in agreement with previous work on OLC electrodes in a different RTILs. Positive temperature dependence of the differential capacitance was observed, and it was dominated by the electrical double layer (EDL) thickness, which is for the first time substantiated in MD simulation.

Simulations of the Neutron Gas in the Inner Crust of Neutron Stars

NASA Astrophysics Data System (ADS)

Vandegriff, Elizabeth; Horowitz, Charles; Caplan, Matthew

2017-09-01

Inside neutron stars, the structures known as `nuclear pasta' are found in the crust. This pasta forms near nuclear density as nucleons arrange in spaghetti- or lasagna-like structures to minimize their energy. We run classical molecular dynamics simulations to visualize the geometry of this pasta and study the distribution of nucleons. In the simulations, we observe that the pasta is embedded in a gas of neutrons, which we call the `sauce'. In this work, we developed two methods for determining the density of neutrons in the gas, one which is accurate at low temperatures and a second which justifies an extrapolation at high temperatures. Running simulations with no Coulomb interactions, we find that the neutron density increases linearly with temperature for every proton fraction we simulated. NSF REU Grant PHY-1460882 at Indiana University.

Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

PubMed

Kreck, Cara A; Mancera, Ricardo L

2014-02-20

Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.

Data Analysis Approaches for the Risk-Informed Safety Margins Characterization Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mandelli, Diego; Alfonsi, Andrea; Maljovec, Daniel P.

2016-09-01

In the past decades, several numerical simulation codes have been employed to simulate accident dynamics (e.g., RELAP5-3D, RELAP-7, MELCOR, MAAP). In order to evaluate the impact of uncertainties into accident dynamics, several stochastic methodologies have been coupled with these codes. These stochastic methods range from classical Monte-Carlo and Latin Hypercube sampling to stochastic polynomial methods. Similar approaches have been introduced into the risk and safety community where stochastic methods (such as RAVEN, ADAPT, MCDET, ADS) have been coupled with safety analysis codes in order to evaluate the safety impact of timing and sequencing of events. These approaches are usually calledmore » Dynamic PRA or simulation-based PRA methods. These uncertainties and safety methods usually generate a large number of simulation runs (database storage may be on the order of gigabytes or higher). The scope of this paper is to present a broad overview of methods and algorithms that can be used to analyze and extract information from large data sets containing time dependent data. In this context, “extracting information” means constructing input-output correlations, finding commonalities, and identifying outliers. Some of the algorithms presented here have been developed or are under development within the RAVEN statistical framework.« less

Molecular dynamics and charge transport in organic semiconductors: a classical approach to modeling electron transfer† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04547b Click here for additional data file.

PubMed Central

Vázquez-Mayagoitia, Álvaro; Ratcliff, Laura E.; Tretiak, Sergei; Bair, Raymond A.; Gray, Stephen K.; Van Voorhis, Troy; Larsen, Ross E.; Darling, Seth B.

2017-01-01

Organic photovoltaics (OPVs) are a promising carbon-neutral energy conversion technology, with recent improvements pushing power conversion efficiencies over 10%. A major factor limiting OPV performance is inefficiency of charge transport in organic semiconducting materials (OSCs). Due to strong coupling with lattice degrees of freedom, the charges form polarons, localized quasi-particles comprised of charges dressed with phonons. These polarons can be conceptualized as pseudo-atoms with a greater effective mass than a bare charge. We propose that due to this increased mass, polarons can be modeled with Langevin molecular dynamics (LMD), a classical approach with a computational cost much lower than most quantum mechanical methods. Here we present LMD simulations of charge transfer between a pair of fullerene molecules, which commonly serve as electron acceptors in OSCs. We find transfer rates consistent with experimental measurements of charge mobility, suggesting that this method may provide quantitative predictions of efficiency when used to simulate materials on the device scale. Our approach also offers information that is not captured in the overall transfer rate or mobility: in the simulation data, we observe exactly when and why intermolecular transfer events occur. In addition, we demonstrate that these simulations can shed light on the properties of polarons in OSCs. Much remains to be learned about these quasi-particles, and there are no widely accepted methods for calculating properties such as effective mass and friction. Our model offers a promising approach to exploring mass and friction as well as providing insight into the details of polaron transport in OSCs. PMID:28553494

Out-of-time-ordered measurements as a probe of quantum dynamics

NASA Astrophysics Data System (ADS)

Bordia, Pranjal; Alet, Fabien; Hosur, Pavan

2018-03-01

Probing the out-of-equilibrium dynamics of quantum matter has gained renewed interest owing to immense experimental progress in artificial quantum systems. Dynamical quantum measures such as the growth of entanglement entropy and out-of-time-ordered correlators (OTOCs) have been shown to provide great insight by exposing subtle quantum features invisible to traditional measures such as mass transport. However, measuring them in experiments requires either identical copies of the system, an ancilla qubit coupled to the whole system, or many measurements on a single copy, thereby making scalability extremely complex and hence, severely limiting their potential. Here, we introduce an alternative quantity, the out-of-time-ordered measurement (OTOM), which involves measuring a single observable on a single copy of the system, while retaining the distinctive features of the OTOCs. We show, theoretically, that OTOMs are closely related to OTOCs in a doubled system with the same quantum statistical properties as the original system. Using exact diagonalization, we numerically simulate classical mass transport, as well as quantum dynamics through computations of the OTOC, the OTOM, and the entanglement entropy in quantum spin chain models in various interesting regimes (including chaotic and many-body localized systems). Our results demonstrate that an OTOM can successfully reveal subtle aspects of quantum dynamics hidden to classical measures and, crucially, provide experimental access to them.

Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations

PubMed Central

Hine, Nicholas D. M.; Mostofi, Arash A.; Yarovsky, Irene

2013-01-01

Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth. PMID:24339760

Shock compression of strongly correlated oxides: A liquid-regime equation of state for cerium(IV) oxide

NASA Astrophysics Data System (ADS)

Weck, Philippe F.; Cochrane, Kyle R.; Root, Seth; Lane, J. Matthew D.; Shulenburger, Luke; Carpenter, John H.; Sjostrom, Travis; Mattsson, Thomas R.; Vogler, Tracy J.

2018-03-01

The shock Hugoniot for full-density and porous CeO2 was investigated in the liquid regime using ab initio molecular dynamics (AIMD) simulations with Erpenbeck's approach based on the Rankine-Hugoniot jump conditions. The phase space was sampled by carrying out NVT simulations for isotherms between 6000 and 100 000 K and densities ranging from ρ =2.5 to 20 g /cm3 . The impact of on-site Coulomb interaction corrections +U on the equation of state (EOS) obtained from AIMD simulations was assessed by direct comparison with results from standard density functional theory simulations. Classical molecular dynamics (CMD) simulations were also performed to model atomic-scale shock compression of larger porous CeO2 models. Results from AIMD and CMD compression simulations compare favorably with Z-machine shock data to 525 GPa and gas-gun data to 109 GPa for porous CeO2 samples. Using results from AIMD simulations, an accurate liquid-regime Mie-Grüneisen EOS was built for CeO2. In addition, a revised multiphase SESAME-type EOS was constrained using AIMD results and experimental data generated in this work. This study demonstrates the necessity of acquiring data in the porous regime to increase the reliability of existing analytical EOS models.

Computational studies of thermal and quantum phase transitions approached through non-equilibrium quenching

NASA Astrophysics Data System (ADS)

Liu, Cheng-Wei

Phase transitions and their associated critical phenomena are of fundamental importance and play a crucial role in the development of statistical physics for both classical and quantum systems. Phase transitions embody diverse aspects of physics and also have numerous applications outside physics, e.g., in chemistry, biology, and combinatorial optimization problems in computer science. Many problems can be reduced to a system consisting of a large number of interacting agents, which under some circumstances (e.g., changes of external parameters) exhibit collective behavior; this type of scenario also underlies phase transitions. The theoretical understanding of equilibrium phase transitions was put on a solid footing with the establishment of the renormalization group. In contrast, non-equilibrium phase transition are relatively less understood and currently a very active research topic. One important milestone here is the Kibble-Zurek (KZ) mechanism, which provides a useful framework for describing a system with a transition point approached through a non-equilibrium quench process. I developed two efficient Monte Carlo techniques for studying phase transitions, one is for classical phase transition and the other is for quantum phase transitions, both are under the framework of KZ scaling. For classical phase transition, I develop a non-equilibrium quench (NEQ) simulation that can completely avoid the critical slowing down problem. For quantum phase transitions, I develop a new algorithm, named quasi-adiabatic quantum Monte Carlo (QAQMC) algorithm for studying quantum quenches. I demonstrate the utility of QAQMC quantum Ising model and obtain high-precision results at the transition point, in particular showing generalized dynamic scaling in the quantum system. To further extend the methods, I study more complex systems such as spin-glasses and random graphs. The techniques allow us to investigate the problems efficiently. From the classical perspective, using the NEQ approach I verify the universality class of the 3D Ising spin-glasses. I also investigate the random 3-regular graphs in terms of both classical and quantum phase transitions. I demonstrate that under this simulation scheme, one can extract information associated with the classical and quantum spin-glass transitions without any knowledge prior to the simulation.

Transition from fractional to classical Stokes-Einstein behaviour in simple fluids.

PubMed

Coglitore, Diego; Edwardson, Stuart P; Macko, Peter; Patterson, Eann A; Whelan, Maurice

2017-12-01

An optical technique for tracking single particles has been used to evaluate the particle diameter at which diffusion transitions from molecular behaviour described by the fractional Stokes-Einstein relationship to particle behaviour described by the classical Stokes-Einstein relationship. The results confirm a prior prediction from molecular dynamic simulations that there is a particle size at which transition occurs and show it is inversely dependent on concentration and viscosity but independent of particle density. For concentrations in the range 5 × 10 -3 to 5 × 10 -6  mg ml -1 and viscosities from 0.8 to 150 mPa s, the transition was found to occur in the diameter range 150-300 nm.

Vortex Dynamics and Shear-Layer Instability in High-Intensity Cyclotrons.

PubMed

Cerfon, Antoine J

2016-04-29

We show that the space-charge dynamics of high-intensity beams in the plane perpendicular to the magnetic field in cyclotrons is described by the two-dimensional Euler equations for an incompressible fluid. This analogy with fluid dynamics gives a unified and intuitive framework to explain the beam spiraling and beam breakup behavior observed in experiments and in simulations. Specifically, we demonstrate that beam breakup is the result of a classical instability occurring in fluids subject to a sheared flow. We give scaling laws for the instability and predict the nonlinear evolution of beams subject to it. Our work suggests that cyclotrons may be uniquely suited for the experimental study of shear layers and vortex distributions that are not achievable in Penning-Malmberg traps.

Critical analysis of partial discharge dynamics in air filled spherical voids

NASA Astrophysics Data System (ADS)

Callender, G.; Golosnoy, I. O.; Rapisarda, P.; Lewin, P. L.

2018-03-01

In this paper partial discharge (PD) is investigated inside a spherical air filled void at atmospheric pressure using a drift diffusion model. Discharge dynamics consisted of an electron avalanche transitioning into positive streamer, in agreement with earlier work on dielectric barrier discharges. Different model configurations were utilised to test many of the concepts employed in semi-analytical PD activity models, which use simplistic descriptions of the discharge dynamics. The results showed that many of these concepts may be erroneous, with significant discrepancies between the canonical reasoning and the simulation results. For example, the residual electric field, the electric field after a discharge, is significantly lower than the estimates used by classical PD activity models in the literature.

Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

NASA Astrophysics Data System (ADS)

Palczynski, Karol; Wilke, Andreas; Paeschke, Manfred; Dzubiella, Joachim

2017-09-01

Linking the experimentally accessible macroscopic properties of thermoplastic polymers to their microscopic static and dynamic properties is a key requirement for targeted material design. Classical molecular dynamics simulations enable us to study the structural and dynamic behavior of molecules on microscopic scales, and statistical physics provides a framework for relating these properties to the macroscopic properties. We take a first step toward creating an automated workflow for the theoretical prediction of thermoplastic material properties by developing an expeditious method for parameterizing a simple yet surprisingly powerful coarse-grained bisphenol-A polycarbonate model which goes beyond previous coarse-grained models and successfully reproduces the thermal expansion behavior, the glass transition temperature as a function of the molecular weight, and several elastic properties.

Kinetics of the chiral phase transition in a linear σ model

NASA Astrophysics Data System (ADS)

Wesp, Christian; van Hees, Hendrik; Meistrenko, Alex; Greiner, Carsten

2018-02-01

We study the dynamics of the chiral phase transition in a linear quark-meson σ model using a novel approach based on semiclassical wave-particle duality. The quarks are treated as test particles in a Monte Carlo simulation of elastic collisions and the coupling to the σ meson, which is treated as a classical field, via a kinetic approach motivated by wave-particle duality. The exchange of energy and momentum between particles and fields is described in terms of appropriate Gaussian wave packets. It has been demonstrated that energy-momentum conservation and the principle of detailed balance are fulfilled, and that the dynamics leads to the correct equilibrium limit. First schematic studies of the dynamics of matter produced in heavy-ion collisions are presented.

Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ionmore » diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.« less

Pasta Nucleosynthesis: Molecular dynamics simulations of nuclear statistical equilibrium

NASA Astrophysics Data System (ADS)

Caplan, Matthew; Horowitz, Charles; da Silva Schneider, Andre; Berry, Donald

2014-09-01

We simulate the decompression of cold dense nuclear matter, near the nuclear saturation density, in order to study the role of nuclear pasta in r-process nucleosynthesis in neutron star mergers. Our simulations are performed using a classical molecular dynamics model with 51 200 and 409 600 nucleons, and are run on GPUs. We expand our simulation region to decompress systems from initial densities of 0.080 fm-3 down to 0.00125 fm-3. We study proton fractions of YP = 0.05, 0.10, 0.20, 0.30, and 0.40 at T = 0.5, 0.75, and 1 MeV. We calculate the composition of the resulting systems using a cluster algorithm. This composition is in good agreement with nuclear statistical equilibrium models for temperatures of 0.75 and 1 MeV. However, for proton fractions greater than YP = 0.2 at a temperature of T = 0.5 MeV, the MD simulations produce non-equilibrium results with large rod-like nuclei. Our MD model is valid at higher densities than simple nuclear statistical equilibrium models and may help determine the initial temperatures and proton fractions of matter ejected in mergers.

Global water dynamics: issues for the 21st century.

PubMed

Simonovic, Slobodan P

2002-01-01

The WorldWater system dynamics model has been developed for modeling the global world water balance and capturing the dynamic character of the main variables affecting water availability and use in the future. Despite not being a novel approach, system dynamics offers a new way of addressing complex systems. WorldWater simulations are clearly demonstrating the strong feedback relation between water availability and different aspects of world development. Results of numerous simulations are contradictory to the assumption made by many global modelers that water is not an issue on the global scale. Two major observations can be made from early simulations: (a) the use of clean water for dilution and transport of wastewater, if not dealt with in other ways, imposes a major stress on the global world water balance; and (b) water use by different sectors is demonstrating quite different dynamics than predicted by classical forecasting tools and other water-models. Inherent linkages between water quantity and quality sectors with food, industry, persistent pollution, technology, and non-renewable resources sectors of the model create shoot and collapse behavior in water use dynamics. This paper discusses a number of different water-related scenarios and their implications on the global water balance. In particular, two extreme scenarios (business as usual - named "Chaos", and unlimited desalination - named "Ocean") are presented in the paper. Based on the conclusions derived from these two extreme cases a set of more moderate and realistic scenarios (named "Conservation") is proposed and their consequences on the global water balance are evaluated.

Modeling hydrodynamic self-propulsion with Stokesian Dynamics. Or teaching Stokesian Dynamics to swim

NASA Astrophysics Data System (ADS)

Swan, James W.; Brady, John F.; Moore, Rachel S.; ChE 174

2011-07-01

We develop a general framework for modeling the hydrodynamic self-propulsion (i.e., swimming) of bodies (e.g., microorganisms) at low Reynolds number via Stokesian Dynamics simulations. The swimming body is composed of many spherical particles constrained to form an assembly that deforms via relative motion of its constituent particles. The resistance tensor describing the hydrodynamic interactions among the individual particles maps directly onto that for the assembly. Specifying a particular swimming gait and imposing the condition that the swimming body is force- and torque-free determine the propulsive speed. The body's translational and rotational velocities computed via this methodology are identical in form to that from the classical theory for the swimming of arbitrary bodies at low Reynolds number. We illustrate the generality of the method through simulations of a wide array of swimming bodies: pushers and pullers, spinners, the Taylor/Purcell swimming toroid, Taylor's helical swimmer, Purcell's three-link swimmer, and an amoeba-like body undergoing large-scale deformation. An open source code is a part of the supplementary material and can be used to simulate the swimming of a body with arbitrary geometry and swimming gait.

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

NASA Astrophysics Data System (ADS)

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

2017-09-01

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations.

PubMed

Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

2017-09-14

The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

Modeling of crack growth under mixed-mode loading by a molecular dynamics method and a linear fracture mechanics approach

NASA Astrophysics Data System (ADS)

Stepanova, L. V.

2017-12-01

Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is the Embedded Atom Method (EAM) potential. Plane specimens with an initial central crack are subjected to mixed-mode loadings. The simulation cell contains 400,000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide range of temperatures (from 0.1 K to 800 K) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields. The multi-parameter fracture criteria are based on the multi-parameter stress field description taking into account the higher order terms of the Williams series expansion of the crack tip fields.

A thermodynamically consistent discontinuous Galerkin formulation for interface separation

DOE PAGES

Versino, Daniele; Mourad, Hashem M.; Dávila, Carlos G.; ...

2015-07-31

Our paper describes the formulation of an interface damage model, based on the discontinuous Galerkin (DG) method, for the simulation of failure and crack propagation in laminated structures. The DG formulation avoids common difficulties associated with cohesive elements. Specifically, it does not introduce any artificial interfacial compliance and, in explicit dynamic analysis, it leads to a stable time increment size which is unaffected by the presence of stiff massless interfaces. This proposed method is implemented in a finite element setting. Convergence and accuracy are demonstrated in Mode I and mixed-mode delamination in both static and dynamic analyses. Significantly, numerical resultsmore » obtained using the proposed interface model are found to be independent of the value of the penalty factor that characterizes the DG formulation. By contrast, numerical results obtained using a classical cohesive method are found to be dependent on the cohesive penalty stiffnesses. The proposed approach is shown to yield more accurate predictions pertaining to crack propagation under mixed-mode fracture because of the advantage. Furthermore, in explicit dynamic analysis, the stable time increment size calculated with the proposed method is found to be an order of magnitude larger than the maximum allowable value for classical cohesive elements.« less

Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin.

PubMed

Orlowski, Slawomir; Nowak, Wieslaw

2007-07-01

Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.

An Appraisal of the Classic Forest Succession Paradigm with the Shade Tolerance Index

PubMed Central

Lienard, Jean; Florescu, Ionut; Strigul, Nikolay

2015-01-01

In this paper we revisit the classic theory of forest succession that relates shade tolerance and species replacement and assess its validity to understand patch-mosaic patterns of forested ecosystems of the USA. We introduce a macroscopic parameter called the “shade tolerance index” and compare it to the classic continuum index in southern Wisconsin forests. We exemplify shade tolerance driven succession in White Pine-Eastern Hemlock forests using computer simulations and analyzing approximated chronosequence data from the USDA FIA forest inventory. We describe this parameter across the last 50 years in the ecoregions of mainland USA, and demonstrate that it does not correlate with the usual macroscopic characteristics of stand age, biomass, basal area, and biodiversity measures. We characterize the dynamics of shade tolerance index using transition matrices and delimit geographical areas based on the relevance of shade tolerance to explain forest succession. We conclude that shade tolerance driven succession is linked to climatic variables and can be considered as a primary driving factor of forest dynamics mostly in central-north and northeastern areas in the USA. Overall, the shade tolerance index constitutes a new quantitative approach that can be used to understand and predict succession of forested ecosystems and biogeographic patterns. PMID:25658092

Study of the Time Response of a Simulated Hydroelectric System

NASA Astrophysics Data System (ADS)

Simani, S.; Alvisi, S.; Venturini, M.

2014-12-01

This paper addresses the design of an advanced control strategy for a typical hydroelectric dynamic process, performed in the Matlab and Simulink environments. The hydraulic system consists of a high water head and a long penstock with upstream and downstream surge tanks, and is equipped with a Francis turbine. The nonlinear characteristics of hydraulic turbine and the inelastic water hammer effects were considered to calculate and simulate the hydraulic transients. With reference to the control solution, the proposed methodology relies on an adaptive control designed by means of the on-line identification of the system model under monitoring. Extensive simulations and comparison with respect to a classic hydraulic turbine speed PID regulator show the effectiveness of the proposed modelling and control tools.

Report on the Implementation of Homogeneous Nucleation Scheme in MARMOT-based Phase Field Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2013-09-30

In this report, we summarized our effort in developing mesoscale phase field models for predicting precipitation kinetics in alloys during thermal aging and/or under irradiation in nuclear reactors. The first part focused on developing a method to predict the thermodynamic properties of critical nuclei such as the sizes and concentration profiles of critical nuclei, and nucleation barrier. These properties are crucial for quantitative simulations of precipitate evolution kinetics with phase field models. Fe-Cr alloy was chosen as a model alloy because it has valid thermodynamic and kinetic data as well as it is an important structural material in nuclear reactors.more » A constrained shrinking dimer dynamics (CSDD) method was developed to search for the energy minimum path during nucleation. With the method we are able to predict the concentration profiles of the critical nuclei of Cr-rich precipitates and nucleation energy barriers. Simulations showed that Cr concentration distribution in the critical nucleus strongly depends on the overall Cr concentration as well as temperature. The Cr concentration inside the critical nucleus is much smaller than the equilibrium concentration calculated by the equilibrium phase diagram. This implies that a non-classical nucleation theory should be used to deal with the nucleation of Cr precipitates in Fe-Cr alloys. The growth kinetics of both classical and non-classical nuclei was investigated by the phase field approach. A number of interesting phenomena were observed from the simulations: 1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; 2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics. 3) a critical classical nucleus grows faster at the earlier growth stage than the non-classical nucleus. All of these results demonstrated that it is critical to introduce the correct critical nuclei into phase field modeling in order to correctly capture the kinetics of precipitation. In most alloys the matrix phase and precipitate phase have different concentrations as well as different crystal structures. For example, Cu precipitates in FeCu alloys have fcc crystal structure while the matrix Fe-Cu solid solution has bcc structure at low temperature. The WBM model and KimS model, where both concentrations and order parameters are chosen to describe the microstructures, are commonly used to model precipitations in such alloys. The WBM and KimS models have not been implemented into Marmot yet. In the second part of this report, we focused on implementing the WBM and KimS models into Marmot. The Fe-Cu alloys, which are important structure materials in nuclear reactors, was taken as the model alloys to test the models.« less

Multinuclear NMR of CaSiO(3) glass: simulation from first-principles.

PubMed

Pedone, Alfonso; Charpentier, Thibault; Menziani, Maria Cristina

2010-06-21

An integrated computational method which couples classical molecular dynamics simulations with density functional theory calculations is used to simulate the solid-state NMR spectra of amorphous CaSiO(3). Two CaSiO(3) glass models are obtained by shell-model molecular dynamics simulations, successively relaxed at the GGA-PBE level of theory. The calculation of the NMR parameters (chemical shielding and quadrupolar parameters), which are then used to simulate solid-state 1D and 2D-NMR spectra of silicon-29, oxygen-17 and calcium-43, is achieved by the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods. It is shown that the limitations due to the finite size of the MD models can be overcome using a Kernel Estimation Density (KDE) approach to simulate the spectra since it better accounts for the disorder effects on the NMR parameter distribution. KDE allows reconstructing a smoothed NMR parameter distribution from the MD/GIPAW data. Simulated NMR spectra calculated with the present approach are found to be in excellent agreement with the experimental data. This further validates the CaSiO(3) structural model obtained by MD simulations allowing the inference of relationships between structural data and NMR response. The methods used to simulate 1D and 2D-NMR spectra from MD GIPAW data have been integrated in a package (called fpNMR) freely available on request.

Entanglement in Self-Supervised Dynamics

NASA Technical Reports Server (NTRS)

Zak, Michail

2011-01-01

A new type of correlation has been developed similar to quantum entanglement in self-supervised dynamics (SSD). SSDs have been introduced as a quantum-classical hybrid based upon the Madelung equation in which the quantum potential is replaced by an information potential. As a result, SSD preserves the quantum topology along with superposition, entanglement, and wave-particle duality. At the same time, it can be implemented in any scale including the Newtonian scale. The main properties of SSD associated with simulating intelligence have been formulated. The attention with this innovation is focused on intelligent agents interaction based upon the new fundamental non-New tonian effect; namely, entanglement.

LES models for incompressible magnetohydrodynamics derived from the variational multiscale formulation

NASA Astrophysics Data System (ADS)

Sondak, David; Oberai, Assad

2012-10-01

Novel large eddy simulation (LES) models are developed for incompressible magnetohydrodynamics (MHD). These models include the application of the variational multiscale formulation (VMS) of LES to the equations of incompressible MHD, a new residual-based eddy viscosity model (RBEVM,) and a mixed LES model that combines the strengths of both of these models. The new models result in a consistent numerical method that is relatively simple to implement. A dynamic procedure for determining model coefficients is no longer required. The new LES models are tested on a decaying Taylor-Green vortex generalized to MHD and benchmarked against classical and state-of-the art LES turbulence models as well as direct numerical simulations (DNS). These new models are able to account for the essential MHD physics which is demonstrated via comparisons of energy spectra. We also compare the performance of our models to a DNS simulation by A. Pouquet et al., for which the ratio of DNS modes to LES modes is 262,144. Additionally, we extend these models to a finite element setting in which boundary conditions play a role. A classic problem on which we test these models is turbulent channel flow, which in the case of MHD, is called Hartmann flow.

Heat Transfer Enhancement of Laminar Nanofluids Flow in a Circular Tube Fitted with Parabolic-Cut Twisted Tape Inserts

PubMed Central

Salman, Sami D.; Kadhum, Abdul Amir H.; Takriff, Mohd S.; Mohamad, Abu Bakar

2014-01-01

Numerical investigation has been carried out on heat transfer and friction factor characteristics of copper-water nanofluid flow in a constant heat-fluxed tube with the existence of new configuration of vortex generator using Computational Fluid Dynamics (CFD) simulation. Two types of swirl flow generator: Classical twisted tape (CTT) and Parabolic-cut twisted tape (PCT) with a different twist ratio (y = 2.93, 3.91 and 4.89) and different cut depth (w = 0.5, 1.0 and 1.5 cm) with 2% and 4% volume concentration of CuO nanofluid were used for simulation. The effect of different parameters such as flow Reynolds number, twist ratio, cut depth and nanofluid were considered. The results show that the enhancement of heat transfer rate and the friction factor induced by the Classical (CTT) and Parabolic-cut (PCT) inserts increases with twist ratio and cut depth decreases. The results also revealed that the heat transfer enhancement increases with an increase in the volume fraction of the CuO nanoparticle. Furthermore, the twisted tape with twist ratio (y = 2.93) and cut depth w = 0.5 cm offered 10% enhancement of the average Nusselt number with significant increases in friction factor than those of Classical twisted tape. PMID:24605055

Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration.

PubMed

Furmanchuk, Al'ona; Isayev, Olexandr; Gorb, Leonid; Shishkin, Oleg V; Hovorun, Dmytro M; Leszczynski, Jerzy

2011-03-14

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.

Experimental validation of docking and capture using space robotics testbeds

NASA Technical Reports Server (NTRS)

Spofford, John; Schmitz, Eric; Hoff, William

1991-01-01

This presentation describes the application of robotic and computer vision systems to validate docking and capture operations for space cargo transfer vehicles. Three applications are discussed: (1) air bearing systems in two dimensions that yield high quality free-flying, flexible, and contact dynamics; (2) validation of docking mechanisms with misalignment and target dynamics; and (3) computer vision technology for target location and real-time tracking. All the testbeds are supported by a network of engineering workstations for dynamic and controls analyses. Dynamic simulation of multibody rigid and elastic systems are performed with the TREETOPS code. MATRIXx/System-Build and PRO-MATLAB/Simulab are the tools for control design and analysis using classical and modern techniques such as H-infinity and LQG/LTR. SANDY is a general design tool to optimize numerically a multivariable robust compensator with a user-defined structure. Mathematica and Macsyma are used to derive symbolically dynamic and kinematic equations.

MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

PubMed Central

2014-01-01

Background Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes. PMID:25077693

MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories.

PubMed

Abdel-Azeim, Safwat; Chermak, Edrisse; Vangone, Anna; Oliva, Romina; Cavallo, Luigi

2014-01-01

Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

Application of quantum master equation for long-term prognosis of asset-prices

NASA Astrophysics Data System (ADS)

Khrennikova, Polina

2016-05-01

This study combines the disciplines of behavioral finance and an extension of econophysics, namely the concepts and mathematical structure of quantum physics. We apply the formalism of quantum theory to model the dynamics of some correlated financial assets, where the proposed model can be potentially applied for developing a long-term prognosis of asset price formation. At the informational level, the asset price states interact with each other by the means of a ;financial bath;. The latter is composed of agents' expectations about the future developments of asset prices on the finance market, as well as financially important information from mass-media, society, and politicians. One of the essential behavioral factors leading to the quantum-like dynamics of asset prices is the irrationality of agents' expectations operating on the finance market. These expectations lead to a deeper type of uncertainty concerning the future price dynamics of the assets, than given by a classical probability theory, e.g., in the framework of the classical financial mathematics, which is based on the theory of stochastic processes. The quantum dimension of the uncertainty in price dynamics is expressed in the form of the price-states superposition and entanglement between the prices of the different financial assets. In our model, the resolution of this deep quantum uncertainty is mathematically captured with the aid of the quantum master equation (its quantum Markov approximation). We illustrate our model of preparation of a future asset price prognosis by a numerical simulation, involving two correlated assets. Their returns interact more intensively, than understood by a classical statistical correlation. The model predictions can be extended to more complex models to obtain price configuration for multiple assets and portfolios.

Multistructure index in revealing complexity of regulatory mechanisms of human cardiovascular system at rest and orthostatic stress in healthy humans

NASA Astrophysics Data System (ADS)

Makowiec, Danuta; Graff, Beata; Struzik, Zbigniew R.

2017-02-01

Biological regulation is sufficiently complex to pose an enduring challenge for characterization of both its equilibrium and transient non-equilibrium dynamics. Two univariate but coupled observables, heart rate and systolic blood pressure, are commonly characterized in the benchmark example of the human cardiovascular regulatory system. Asymmetric distributions of accelerations and decelerations of heart rate, as well as rises and falls in systolic blood pressure, recorded in humans during a head-up tilt test provide insights into the dynamics of cardiovascular response to a rapid, controlled deregulation of the system's homeostasis. The baroreflex feedback loop is assumed to be the fundamental physiological mechanism for ensuring homeostatic blood supply to distant organs at rest and during orthostatic stress, captured in a classical beat-to-beat autoregressive model of baroreflex by de Boer et al. (1987). For model corroboration, a multistructure index statistic is proposed, seamlessly evaluating the size spectrum of magnitudes of neural reflexes such as baroreflex, responsible for maintaining the homeostatic dynamics. The multistructure index exposes a distinctly different dynamics of multiscale asymmetry between results obtained from real-life signals recorded from healthy subjects and those simulated using both the classical and perturbed versions of the model. Nonlinear effects observed suggest the pronounced presence of complex mechanisms resulting from baroreflex regulation when a human is at rest, which is aggravated in the system's response to orthostatic stress. Using our methodology of multistructure index, we therefore show a marked difference between model and real-life scenarios, which we attribute to multiscale asymmetry of non-linear origin in real-life signals, which we are not reproducible by the classical model.

Study on the tumor-induced angiogenesis using mathematical models.

PubMed

Suzuki, Takashi; Minerva, Dhisa; Nishiyama, Koichi; Koshikawa, Naohiko; Chaplain, Mark Andrew Joseph

2018-01-01

We studied angiogenesis using mathematical models describing the dynamics of tip cells. We reviewed the basic ideas of angiogenesis models and its numerical simulation technique to produce realistic computer graphics images of sprouting angiogenesis. We examined the classical model of Anderson-Chaplain using fundamental concepts of mass transport and chemical reaction with ECM degradation included. We then constructed two types of numerical schemes, model-faithful and model-driven ones, where new techniques of numerical simulation are introduced, such as transient probability, particle velocity, and Boolean variables. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

A theoretical model for the collective motion of proteins by means of principal component analysis

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2011-02-01

A coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations have been studied for the Bovine Pancreatic Trypsin Inhibitor. We analyzed the stability of the method by studying structural fluctuations of the C a atoms obtained from a 20 ns molecular dynamics simulation. Subsequently, the dynamics of the collective coordinates of protein were characterized by calculating the dynamical friction coefficient and diffusion coefficients along with time-dependent correlation functions of collective coordinates. A dual diffusion behavior was observed with a fast relaxation time of short diffusion regime 0.2-0.4 ps and slow relaxation time of long diffusion about 1-2 ps. In addition, we observed a power law decay of dynamical friction coefficient with exponent for the first five collective coordinates varying from -0.746 to -0.938 for the real part and from -0.528 to -0.665 for its magnitude. It was found that only the first ten collective coordinates are responsible for configuration transitions occurring on time scale longer than 50 ps.

Modeling and simulation of dynamic ant colony's labor division for task allocation of UAV swarm

NASA Astrophysics Data System (ADS)

Wu, Husheng; Li, Hao; Xiao, Renbin; Liu, Jie

2018-02-01

The problem of unmanned aerial vehicle (UAV) task allocation not only has the intrinsic attribute of complexity, such as highly nonlinear, dynamic, highly adversarial and multi-modal, but also has a better practicability in various multi-agent systems, which makes it more and more attractive recently. In this paper, based on the classic fixed response threshold model (FRTM), under the idea of "problem centered + evolutionary solution" and by a bottom-up way, the new dynamic environmental stimulus, response threshold and transition probability are designed, and a dynamic ant colony's labor division (DACLD) model is proposed. DACLD allows a swarm of agents with a relatively low-level of intelligence to perform complex tasks, and has the characteristic of distributed framework, multi-tasks with execution order, multi-state, adaptive response threshold and multi-individual response. With the proposed model, numerical simulations are performed to illustrate the effectiveness of the distributed task allocation scheme in two situations of UAV swarm combat (dynamic task allocation with a certain number of enemy targets and task re-allocation due to unexpected threats). Results show that our model can get both the heterogeneous UAVs' real-time positions and states at the same time, and has high degree of self-organization, flexibility and real-time response to dynamic environments.

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Molecular dynamics simulation of shock-wave loading of copper and titanium

NASA Astrophysics Data System (ADS)

Bolesta, A. V.; Fomin, V. M.

2017-10-01

At extreme pressures and temperatures common materials form new dense phases with compacted atomic arrangements. By classical molecular dynamics simulation we observe that FCC copper undergo phase transformation to BCC structure. The transition occurs under shock wave loading at the pressures above 80 GPa and corresponding temperatures above 2000 K. We calculate phase diagram, show that at these pressures and low temperature FCC phase of copper is still stable and discuss the thermodynamic reason for phase transformation at high temperature shock wave regime. Titanium forms new hexagonal phase at high pressure as well. We calculate the structure of shock wave in titanium and observe that shock front splits in three parts: elastic, plastic and phase transformation. The possibility of using a phase transition behind a shock wave with further unloading for designing nanocrystalline materials with a reduced grain size is also shown.

Molecular Dynamics Simulations of the Initial-State Predict Product Distributions of Dediazoniation of Aryldiazonium in Binary Solvents.

PubMed

Cruz, Gustavo N; Lima, Filipe S; Dias, Luís G; El Seoud, Omar A; Horinek, Dominik; Chaimovich, Hernan; Cuccovia, Iolanda M

2015-09-04

The dediazoniation of aryldiazonium salts in mixed solvents proceeds by a borderline SN1 and SN2 pathway, and product distribution should be proportional to the composition of the solvation shell of the carbon attached to the -N2 group (ipso carbon). The rates of dediazoniation of 2,4,6-trimethylbenzenediazonium in water, methanol, ethanol, propanol, and acetonitrile were similar, but measured product distributions were noticeably dependent on the nature of the water/cosolvent mixture. Here we demonstrated that solvent distribution in the first solvation shell of the ipso carbon, calculated from classical molecular dynamics simulations, is equal to the measured product distribution. Furthermore, we showed that regardless of the charge distribution of the initial state, i.e., whether the positive charge is smeared over the molecule or localized on phenyl moiety, the solvent distribution around the reaction center is nearly the same.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

PubMed

Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V

2014-08-21

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

Dynamic Modeling and Simulation of an Underactuated System

NASA Astrophysics Data System (ADS)

Libardo Duarte Madrid, Juan; Ospina Henao, P. A.; González Querubín, E.

2017-06-01

In this paper, is used the Lagrangian classical mechanics for modeling the dynamics of an underactuated system, specifically a rotary inverted pendulum that will have two equations of motion. A basic design of the system is proposed in SOLIDWORKS 3D CAD software, which based on the material and dimensions of the model provides some physical variables necessary for modeling. In order to verify the results obtained, a comparison the CAD model simulated in the environment SimMechanics of MATLAB software with the mathematical model who was consisting of Euler-Lagrange’s equations implemented in Simulink MATLAB, solved with the ODE23tb method, included in the MATLAB libraries for the solution of systems of equations of the type and order obtained. This article also has a topological analysis of pendulum trajectories through a phase space diagram, which allows the identification of stable and unstable regions of the system.

Atomistic simulation of Al-graphene thin film growth on polycrystalline Al substrate

NASA Astrophysics Data System (ADS)

Zhang, Lan; Zhu, Yongchao; Li, Na; Rong, Yan; Xia, Huimin; Ma, Huizhong

2018-03-01

The growth of Al-Graphene composite coatings on polycrystalline Al substrate was investigated by using classical molecular dynamics (MD) simulations. Unlike the diffusion behaviors on single crystal surface, most of adatoms were easily bound by the steps on polycrystalline Al surface, owing to the local accelerated energy. Both Ehrlich-Schwoebel (ES) barriers and the steering effect backed up the volmer-weber growth mode, which was consistent with the dynamic growth process observed in the deposit. The morphology of composite coatings was significantly affected by graphene flakes. Enrichment of graphene flakes gave rise to an increase of the local thickness, and graphene flakes only existed in Al grain boundaries. The size of Al grains in the composite coating visibly decreased when compared with that in the pure Al coating. This grain refinement and the mechanical property can be reinforced by the increase of graphene flakes.

Molecular dynamics simulations of bubble formation and cavitation in liquid metals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Insepov, Z.; Hassanein, A.; Bazhirov, T. T.

2007-11-01

Thermodynamics and kinetics of nano-scale bubble formation in liquid metals such as Li and Pb were studied by molecular dynamics (MD) simulations at pressures typical for magnetic and inertial fusion. Two different approaches to bubble formation were developed. In one method, radial densities, pressures, surface tensions, and work functions of the cavities in supercooled liquid lithium were calculated and compared with the surface tension experimental data. The critical radius of a stable cavity in liquid lithium was found for the first time. In the second method, the cavities were created in the highly stretched region of the liquid phase diagram;more » and then the stability boundary and the cavitation rates were calculated in liquid lead. The pressure dependences of cavitation frequencies were obtained over the temperature range 700-2700 K in liquid Pb. The results of MD calculations for cavitation rate were compared with estimates of classical nucleation theory (CNT).« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

A matrix-free implicit unstructured multigrid finite volume method for simulating structural dynamics and fluid structure interaction

NASA Astrophysics Data System (ADS)

Lv, X.; Zhao, Y.; Huang, X. Y.; Xia, G. H.; Su, X. H.

2007-07-01

A new three-dimensional (3D) matrix-free implicit unstructured multigrid finite volume (FV) solver for structural dynamics is presented in this paper. The solver is first validated using classical 2D and 3D cantilever problems. It is shown that very accurate predictions of the fundamental natural frequencies of the problems can be obtained by the solver with fast convergence rates. This method has been integrated into our existing FV compressible solver [X. Lv, Y. Zhao, et al., An efficient parallel/unstructured-multigrid preconditioned implicit method for simulating 3d unsteady compressible flows with moving objects, Journal of Computational Physics 215(2) (2006) 661-690] based on the immersed membrane method (IMM) [X. Lv, Y. Zhao, et al., as mentioned above]. Results for the interaction between the fluid and an immersed fixed-free cantilever are also presented to demonstrate the potential of this integrated fluid-structure interaction approach.

Segregation formation, thermal and electronic properties of ternary cubic CdZnTe clusters: MD simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Kurban, Mustafa; Erkoç, Şakir

2017-04-01

Surface and core formation, thermal and electronic properties of ternary cubic CdZnTe clusters are investigated by using classical molecular dynamics (MD) simulations and density functional theory (DFT) calculations. In this work, MD simulations of the CdZnTe clusters are performed by means of LAMMPS by using bond order potential (BOP). MD simulations are carried out at different temperatures to study the segregation phenomena of Cd, Zn and Te atoms, and deviation of clusters and heat capacity. After that, using optimized geometries obtained, excess charge on atoms, dipole moments, highest occupied molecular orbitals, lowest unoccupied molecular orbitals, HOMO-LUMO gaps (Eg) , total energies, spin density and the density of states (DOS) have been calculated with DFT. Simulation results such as heat capacity and segregation formation are compared with experimental bulk and theoretical results.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

PubMed

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Effective dynamics of a classical point charge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polonyi, Janos, E-mail: polonyi@iphc.cnrs.fr

2014-03-15

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 quantum 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-polemore » of perturbative QED. Similarity between the dynamical breakdown of the time reversal invariance and dynamical symmetry breaking is pointed out. -- Highlights: •Extension of the classical action principle for dissipative systems. •New derivation of the Abraham–Lorentz force for a point charge. •Absence of a runaway solution of the Abraham–Lorentz force. •Acausality in classical electrodynamics. •Renormalization of classical electrodynamics of point charges.« less

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

Molecular simulations, based on atomistic force fields are a standard theoretical tool in materials, polymers and biosciences. While various methods, with quantum chemistry incorporated, have been developed for condensed phase simulations during the last decade, there is another line of development with the purpose to bridge the time and length scales based on coarse-graining. This is expected to lead to some very interesting breakthroughs in the near future. In this lecture we will first give some background to common atomistic force fields. After that, we review a few common simple techniques for reducing the number of motional degrees of freedom to speed up the simulations. Finally, we present a powerful method for reducing uninteresting degrees of freedom. This is done by solving the Inverse Problem to obtain the interaction potentials. More precisely, we make use of the radial distribution functions, and by using the method of Inverse Monte Carlo [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)], we can construct effective potentials which are consistent with the original RDFs. This makes it possible to simulate much larger system than would have been possible by using atomistic force fields. We present many examples: How to simulate aqueous electrolyte solutions without any water molecules but still having the hydration structure around the ions - at the speed of a primitive electrolyte model calculation. We demonstrate how a coarse-grained model can be constructed for a double-helix DNA and how it can be used. It is accurate enough to reproduce the experimental results for ion condensation around DNA for several different counterions. We also show how we can construct site-site potentials for large-scale atomistic classical simulations of arbitrary liquids from smaller scale ab initio simulations. This methodology allows us to start from a simulation with the electrons and atomic nuclei, to construct a set of atomistic effective interaction potentials, and to use them in classical simulations. As a next step we can construct a new set of potentials beyond the atomistic description and carry out mesoscopic simulations, for example by using Dissipative Particle Dynamics. In this way we can tie together three different levels of description. The Dissipative Particle Dynamics method appears as a very promising tool to use with our coarse-grained potentials.

Poincaré resonances and the limits of trajectory dynamics.

PubMed Central

Petrosky, T; Prigogine, I

1993-01-01

In previous papers we have shown that the elimination of the resonance divergences in large Poincare systems leads to complex irreducible spectral representations for the Liouville-von Neumann operator. Complex means that time symmetry is broken and irreducibility means that this representation is implementable only by statistical ensembles and not by trajectories. We consider in this paper classical potential scattering. Our theory applies to persistent scattering. Numerical simulations show quantitative agreement with our predictions. PMID:11607428

Current Status of Protein Force Fields for Molecular Dynamics

PubMed Central

Lopes, Pedro E.M.; Guvench, Olgun

2015-01-01

Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

Exploring the Temperature Dependent Solid-State ALC Spectrum of the C6H6Mu• Radical with Ab-Initio Simulation Techniques

NASA Astrophysics Data System (ADS)

Sturniolo, S.; Liborio, L.; Pratt, F. L.; Cottrell, S. P.; Jochym, D. B.; Montanari, B.

The longitudinal field Avoided Level Crossing (ALC) muon spectrum of crystalline benzene is found to exhibit multiple complex features that strongly depend on temperature. In this work, a number of different computational techniques were used in conjunction to explain this behavior. An overall picture emerges in which the spectrum appears to be the result of an interplay of multiple dynamical effects, both classical and quantum mechanical.

Quantum Game of Life

NASA Astrophysics Data System (ADS)

Glick, Aaron; Carr, Lincoln; Calarco, Tommaso; Montangero, Simone

2014-03-01

In order to investigate the emergence of complexity in quantum systems, we present a quantum game of life, inspired by Conway's classic game of life. Through Matrix Product State (MPS) calculations, we simulate the evolution of quantum systems, dictated by a Hamiltonian that defines the rules of our quantum game. We analyze the system through a number of measures which elicit the emergence of complexity in terms of spatial organization, system dynamics, and non-local mutual information within the network. Funded by NSF

A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits.

PubMed

Shiraishi, Emi; Maeda, Kazuhiro; Kurata, Hiroyuki

2009-02-01

Numerical simulation of differential equation systems plays a major role in the understanding of how metabolic network models generate particular cellular functions. On the other hand, the classical and technical problems for stiff differential equations still remain to be solved, while many elegant algorithms have been presented. To relax the stiffness problem, we propose new practical methods: the gradual update of differential-algebraic equations based on gradual application of the steady-state approximation to stiff differential equations, and the gradual update of the initial values in differential-algebraic equations. These empirical methods show a high efficiency for simulating the steady-state solutions for the stiff differential equations that existing solvers alone cannot solve. They are effective in extending the applicability of dynamic simulation to biochemical network models.

Drama in Dynamics: Boom, Splash, and Speed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Netzloff, Heather Marie

2004-12-19

The full nature of chemistry and physics cannot be captured by static calculations alone. Dynamics calculations allow the simulation of time-dependent phenomena. This facilitates both comparisons with experimental data and the prediction and interpretation of details not easily obtainable from experiments. Simulations thus provide a direct link between theory and experiment, between microscopic details of a system and macroscopic observed properties. Many types of dynamics calculations exist. The most important distinction between the methods and the decision of which method to use can be described in terms of the size and type of molecule/reaction under consideration and the type andmore » level of accuracy required in the final properties of interest. These considerations must be balanced with available computational codes and resources as simulations to mimic ''real-life'' may require many time steps. As indicated in the title, the theme of this thesis is dynamics. The goal is to utilize the best type of dynamics for the system under study while trying to perform dynamics in the most accurate way possible. As a quantum chemist, this involves some level of first principles calculations by default. Very accurate calculations of small molecules and molecular systems are now possible with relatively high-level ab initio quantum chemistry. For example, a quantum chemical potential energy surface (PES) can be developed ''on-the-fly'' with dynamic reaction path (DRP) methods. In this way a classical trajectory is developed without prior knowledge of the PES. In order to treat solvation processes and the condensed phase, large numbers of molecules are required, especially in predicting bulk behavior. The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute and an ''effective fragment'' region that contains the remaining solvent molecules. But, despite the reduced cost relative to fully QM calculations, the EFP method, due to its complex, QM-based potential, does require more computation time than simple interaction potentials, especially when the method is used for large scale molecular dynamics simulations. Thus, the EFP method was parallelized to facilitate these calculations within the quantum chemistry program GAMESS. The EFP method provides relative energies and structures that are in excellent agreement with the analogous fully quantum results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. Molecular dynamics simulations can provide properties that are directly comparable with experimental results, for example radial distribution functions. The molecular PES is a fundamental starting point for chemical reaction dynamics. Many methods can be used to obtain a PES; for example, assuming a global functional form for the PES or, as mentioned above, performing ''on-the-fly'' dynamics with Al or semi-empirical calculations at every molecular configuration. But as the size of the system grows, using electronic structure theory to build a PES and, therefore, study reaction dynamics becomes virtually impossible. The program Grow builds a PES as an interpolation of Al data; the goal is to attempt to produce an accurate PES with the smallest number of Al calculations. The Grow-GAMESS interface was developed to obtain the Al data from GAMESS. Classical or quantum dynamics can be performed on the resulting surface. The interface includes the novel capability to build multi-reference PESs; these types of calculations are applicable to problems ranging from atmospheric chemistry to photochemical reaction mechanisms in organic and inorganic chemistry to fundamental biological phenomena such as photosynthesis.« less

Chaotic scattering in an open vase-shaped cavity: Topological, numerical, and experimental results

NASA Astrophysics Data System (ADS)

Novick, Jaison Allen

We present a study of trajectories in a two-dimensional, open, vase-shaped cavity in the absence of forces The classical trajectories freely propagate between elastic collisions. Bound trajectories, regular scattering trajectories, and chaotic scattering trajectories are present in the vase. Most importantly, we find that classical trajectories passing through the vase's mouth escape without return. In our simulations, we propagate bursts of trajectories from point sources located along the vase walls. We record the time for escaping trajectories to pass through the vase's neck. Constructing a plot of escape time versus the initial launch angle for the chaotic trajectories reveals a vastly complicated recursive structure or a fractal. This fractal structure can be understood by a suitable coordinate transform. Reducing the dynamics to two dimensions reveals that the chaotic dynamics are organized by a homoclinic tangle, which is formed by the union of infinitely long, intersecting stable and unstable manifolds. This study is broken down into three major components. We first present a topological theory that extracts the essential topological information from a finite subset of the tangle and encodes this information in a set of symbolic dynamical equations. These equations can be used to predict a topologically forced minimal subset of the recursive structure seen in numerically computed escape time plots. We present three applications of the theory and compare these predictions to our simulations. The second component is a presentation of an experiment in which the vase was constructed from Teflon walls using an ultrasound transducer as a point source. We compare the escaping signal to a classical simulation and find agreement between the two. Finally, we present an approximate solution to the time independent Schrodinger Equation for escaping waves. We choose a set of points at which to evaluate the wave function and interpolate trajectories connecting the source point to each "detector point". We then construct the wave function directly from these classical trajectories using the two-dimensional WKB approximation. The wave function is Fourier Transformed using a Fast Fourier Transform algorithm resulting in a spectrum in which each peak corresponds to an interpolated trajectory. Our predictions are based on an imagined experiment that uses microwave propagation within an electromagnetic waveguide. Such an experiment exploits the fact that under suitable conditions both Maxwell's Equations and the Schrodinger Equation can be reduced to the Helmholtz Equation. Therefore, our predictions, while compared to the electromagnetic experiment, contain information about the quantum system. Identifying peaks in the transmission spectrum with chaotic trajectories will allow for an additional experimental verification of the intermediate recursive structure. Finally, we summarize our results and discuss possible extensions of this project.

Classic-Ada(TM)

NASA Technical Reports Server (NTRS)

Valley, Lois

1989-01-01

The SPS product, Classic-Ada, is a software tool that supports object-oriented Ada programming with powerful inheritance and dynamic binding. Object Oriented Design (OOD) is an easy, natural development paradigm, but it is not supported by Ada. Following the DOD Ada mandate, SPS developed Classic-Ada to provide a tool which supports OOD and implements code in Ada. It consists of a design language, a code generator and a toolset. As a design language, Classic-Ada supports the object-oriented principles of information hiding, data abstraction, dynamic binding, and inheritance. It also supports natural reuse and incremental development through inheritance, code factoring, and Ada, Classic-Ada, dynamic binding and static binding in the same program. Only nine new constructs were added to Ada to provide object-oriented design capabilities. The Classic-Ada code generator translates user application code into fully compliant, ready-to-run, standard Ada. The Classic-Ada toolset is fully supported by SPS and consists of an object generator, a builder, a dictionary manager, and a reporter. Demonstrations of Classic-Ada and the Classic-Ada Browser were given at the workshop.

Autonomous rotor heat engine

NASA Astrophysics Data System (ADS)

Roulet, Alexandre; Nimmrichter, Stefan; Arrazola, Juan Miguel; Seah, Stella; Scarani, Valerio

2017-06-01

The triumph of heat engines is their ability to convert the disordered energy of thermal sources into useful mechanical motion. In recent years, much effort has been devoted to generalizing thermodynamic notions to the quantum regime, partly motivated by the promise of surpassing classical heat engines. Here, we instead adopt a bottom-up approach: we propose a realistic autonomous heat engine that can serve as a test bed for quantum effects in the context of thermodynamics. Our model draws inspiration from actual piston engines and is built from closed-system Hamiltonians and weak bath coupling terms. We analytically derive the performance of the engine in the classical regime via a set of nonlinear Langevin equations. In the quantum case, we perform numerical simulations of the master equation. Finally, we perform a dynamic and thermodynamic analysis of the engine's behavior for several parameter regimes in both the classical and quantum case and find that the latter exhibits a consistently lower efficiency due to additional noise.

Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase

PubMed Central

Patra, Niladri; Ioannidis, Efthymios I.

2016-01-01

Catechol O-methyltransferase (COMT) is a SAM- and Mg2+-dependent methyltransferase that regulates neurotransmitters through methylation. Simulations and experiments have identified divergent catecholamine substrate orientations in the COMT active site: molecular dynamics simulations have favored a monodentate coordination of catecholate substrates to the active site Mg2+, and crystal structures instead preserve bidentate coordination along with short (2.65 Å) methyl donor-acceptor distances. We carry out longer dynamics (up to 350 ns) to quantify interconversion between bidentate and monodentate binding poses. We provide a systematic determination of the relative free energy of the monodentate and bidentate structures in order to identify whether structural differences alter the nature of the methyl transfer mechanism and source of enzymatic rate enhancement. We demonstrate that the bidentate and monodentate binding modes are close in energy but separated by a 7 kcal/mol free energy barrier. Analysis of interactions in the two binding modes reveals that the driving force for monodentate catecholate orientations in classical molecular dynamics simulations is derived from stronger electrostatic stabilization afforded by alternate Mg2+ coordination with strongly charged active site carboxylates. Mixed semi-empirical-classical (SQM/MM) substrate C-O distances (2.7 Å) for the bidentate case are in excellent agreement with COMT X-ray crystal structures, as long as charge transfer between the substrates, Mg2+, and surrounding ligands is permitted. SQM/MM free energy barriers for methyl transfer from bidentate and monodentate catecholate configurations are comparable at around 21–22 kcal/mol, in good agreement with experiment (18–19 kcal/mol). Overall, the work suggests that both binding poses are viable for methyl transfer, and accurate descriptions of charge transfer and electrostatics are needed to provide balanced relative barriers when multiple binding poses are accessible, for example in other transferases. PMID:27564542

Toward a 3D dynamic model of a faulty duplex ball bearing

NASA Astrophysics Data System (ADS)

Kogan, Gideon; Klein, Renata; Kushnirsky, Alex; Bortman, Jacob

2015-03-01

Bearings are vital components for safe and proper operation of machinery. Increasing efficiency of bearing diagnostics usually requires training of health and usage monitoring systems via expensive and time-consuming ground calibration tests. The main goal of this research, therefore, is to improve bearing dynamics modeling tools in order to reduce the time and budget needed to implement the health and usage monitoring approach. The proposed three-dimensional ball bearing dynamic model is based on the classic dynamic and kinematic equations. Interactions between the bodies are simulated using non-linear springs combined with dampers described by Hertz-type contact relation. The force friction is simulated using the hyperbolic-tangent function. The model allows simulation of a wide range of mechanical faults. It is validated by comparison to known bearing behavior and to experimental results. The model results are verified by demonstrating numerical convergence. The model results for the two cases of single and duplex angular ball bearings with axial deformation in the outer ring are presented. The qualitative investigation provides insight into bearing dynamics, the sensitivity study generalizes the qualitative findings for similar cases, and the comparison to the test results validates model reliability. The article demonstrates the variety of the cases that the 3D bearing model can simulate and the findings to which it may lead. The research allowed the identification of new patterns generated by single and duplex bearings with axially deformed outer race. It also enlightened the difference between single and duplex bearing manifestation. In the current research the dynamic model enabled better understanding of the physical behavior of the faulted bearings. Therefore, it is expected that the modeling approach has the potential to simplify and improve the development process of diagnostic algorithms. • A deformed outer race of a single axially loaded bearing is simulated. • The model results are subjected to a sensitivity study. • Duplex bearing with deformed outer race is simulated as well as tested. • The simulation results are in a good agreement with the experimental results.

A modular architecture for transparent computation in recurrent neural networks.

PubMed

Carmantini, Giovanni S; Beim Graben, Peter; Desroches, Mathieu; Rodrigues, Serafim

2017-01-01

Computation is classically studied in terms of automata, formal languages and algorithms; yet, the relation between neural dynamics and symbolic representations and operations is still unclear in traditional eliminative connectionism. Therefore, we suggest a unique perspective on this central issue, to which we would like to refer as transparent connectionism, by proposing accounts of how symbolic computation can be implemented in neural substrates. In this study we first introduce a new model of dynamics on a symbolic space, the versatile shift, showing that it supports the real-time simulation of a range of automata. We then show that the Gödelization of versatile shifts defines nonlinear dynamical automata, dynamical systems evolving on a vectorial space. Finally, we present a mapping between nonlinear dynamical automata and recurrent artificial neural networks. The mapping defines an architecture characterized by its granular modularity, where data, symbolic operations and their control are not only distinguishable in activation space, but also spatially localizable in the network itself, while maintaining a distributed encoding of symbolic representations. The resulting networks simulate automata in real-time and are programmed directly, in the absence of network training. To discuss the unique characteristics of the architecture and their consequences, we present two examples: (i) the design of a Central Pattern Generator from a finite-state locomotive controller, and (ii) the creation of a network simulating a system of interactive automata that supports the parsing of garden-path sentences as investigated in psycholinguistics experiments. Copyright © 2016 Elsevier Ltd. All rights reserved.

The surprising dynamics of a chain on a pulley: lift off and snapping

PubMed Central

Audoly, Basile

2016-01-01

The motion of weights attached to a chain or string moving on a frictionless pulley is a classic problem of introductory physics used to understand the relationship between force and acceleration. Here, we consider the dynamics of the chain when one of the weights is removed and, thus, one end is pulled with constant acceleration. This simple change has dramatic consequences for the ensuing motion: at a finite time, the chain ‘lifts off’ from the pulley, and the free end subsequently accelerates faster than the end that is pulled. Eventually, the chain undergoes a dramatic reversal of curvature reminiscent of the crack or snap, of a whip. We combine experiments, numerical simulations and theoretical arguments to explain key aspects of this dynamical problem. PMID:27436987

Extrapolating dynamic leidenfrost principles to metallic nanodroplets on asymmetrically textured surfaces

DOE PAGES

Horne, Joseph E.; Lavrik, Nickolay V.; Terrones, Humberto; ...

2015-06-30

In an effort to enhance our knowledge on how to control the movement of metallic nanodroplets, here we have used classical molecular dynamics simulations to investigate whether Cu nanostructures deposited on nanopillared substrates can be made to jump at desired angles. We find that such control is possible, especially for Cu nanostructures that are symmetric; for asymmetric nanostructures, however, control is more uncertain. The work presented here borrows ideas from two seemingly different fields, metallic droplets and water droplets in the dynamic Leidenfrost regime. Despite the differences in the respective systems, we find common ground in their behavior on nanostructuredmore » surfaces. As a result, we suggest that the ongoing research in Leidenfrost droplets is a fertile area for scientists working on metallic nanodroplets.« less

Hydrodynamic limit of the Yukawa one-component plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salin, Gwenaeel

This paper presents a detailed mathematical analysis of the dynamical correlation of density fluctuations of the Yukawa one component plasma in the framework of linearized hydrodynamics. In particular, expressions for the hydrodynamic modes which hold both for the plasma and the neutral fluid are derived. This work constitutes an extension of the computation of the dynamical structure factor in the hydrodynamic limit done by Vieillefosse and Hansen [Phys. Rev. A 12, 1106 (1975)]. As a typical result of Yukawa plasma, a coupling appears between thermal and mechanical effects in the damping of the sound modes, which does not exist inmore » the classical one component plasma. Theoretical and numerical results obtained by means of equilibrium molecular-dynamic simulations in the microcanonical ensemble are compared and discussed.« less

The surprising dynamics of a chain on a pulley: lift off and snapping.

PubMed

Brun, P-T; Audoly, Basile; Goriely, Alain; Vella, Dominic

2016-06-01

The motion of weights attached to a chain or string moving on a frictionless pulley is a classic problem of introductory physics used to understand the relationship between force and acceleration. Here, we consider the dynamics of the chain when one of the weights is removed and, thus, one end is pulled with constant acceleration. This simple change has dramatic consequences for the ensuing motion: at a finite time, the chain 'lifts off' from the pulley, and the free end subsequently accelerates faster than the end that is pulled. Eventually, the chain undergoes a dramatic reversal of curvature reminiscent of the crack or snap, of a whip. We combine experiments, numerical simulations and theoretical arguments to explain key aspects of this dynamical problem.

Classical strongly coupled quark-gluon plasma. VII. Energy loss

NASA Astrophysics Data System (ADS)

Cho, Sungtae; Zahed, Ismail

2010-12-01

We use linear response analysis and the fluctuation-dissipation theorem to derive the energy loss of a heavy quark in the SU(2) classical Coulomb plasma in terms of the l=1 monopole and nonstatic structure factor. The result is valid for all Coulomb couplings Γ=V/K, the ratio of the mean potential to kinetic energy. We use the Liouville equation in the collisionless limit to assess the SU(2) nonstatic structure factor. We find the energy loss to be strongly dependent on Γ. In the liquid phase with Γ≈4, the energy loss is mostly metallic and soundless with neither a Cerenkov nor a Mach cone. Our analytical results compare favorably with the SU(2) molecular dynamics simulations at large momentum and for heavy quark masses.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

PubMed

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

NASA Astrophysics Data System (ADS)

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-01

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

PubMed Central

2015-01-01

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up to 21 times for polyalanine and (AAQAA)3 in water. PMID:26574442