Theory and application of quantum molecular dynamics
Zeng Hui Zhang, John
1999-01-01
This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli
Quantum molecular dynamics simulations of dense matter
Energy Technology Data Exchange (ETDEWEB)
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Quantum dynamics of bio-molecular systems in noisy environments
Huelga S.F.; Plenio M.B.
2012-01-01
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...
A quantum molecular dynamics study of aqueous solvation dynamics
Videla, Pablo E.; Rossky, Peter J.; Laria, D.
2013-10-01
Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Approximation of quantum observables by molecular dynamics simulations
Sandberg, Mattias
2016-01-06
In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.
Extension of Isospin Dependent Quantum Molecular Dynamics
Institute of Scientific and Technical Information of China (English)
FengZhaoqing; ZhangFengshou; LiWenfei; JinGenming
2003-01-01
Isospin dependent molecular dynamics (IQMD) has been used with success for studying isospin effects in heavy ion collisions at intermediate energies[1,2]. However, this model meets difficulty to study heavy ion collisions at low energies near Coulomb barrier since unsuitable dealing with the deformation, such as surface term induced by deformation during approaching projectile and target, which is not important at high energies, and it results in the calculated cross sections with IQMD which are much smaller than the experimental data at low energies. In this report, we propose a new method in which the surface term in the mean field is included in a proper way, the switch function method.
Quantum dynamics of bio-molecular systems in noisy environments
Plenio, M B
2012-01-01
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.
Molecular quantum dynamics from theory to applications
Gatti, Fabien
2014-01-01
Emphasizing fundamental educational concepts, this book offers an accessible introduction that covers eigenstates, wave packets, quantum mechanical resonances and more. Examples show that high-level experiments and theory must work closely together.
Quantum Trajectory Approach to Molecular Dynamics Simulation with Surface Hopping
Feng, Wei; Li, Xin-Qi; Fang, Weihai
2012-01-01
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic state. In this work we propose a quantum trajectory approach to the MD simulation with surface hopping, from an insight that an effective "observation" is actually implied in theMDsimulation through tracking the forces experienced, just like checking the meter's result in the quantum measurement process. This treatment can build the nonadiabatic surface hopping on a dynamical foundation, instead of the usual artificial and conceptually inconsistent hopping algorithms. The effects and advantages of the proposed scheme are preliminarily illustrated by a two-surface model system.
The classical and quantum dynamics of molecular spins on graphene
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2015-01-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
Electronically coarse-grained molecular dynamics using quantum Drude oscillators
Jones, A. P.; Crain, J.; Cipcigan, F. S.; Sokhan, V. P.; Modani, M.; Martyna, G. J.
2013-12-01
Standard molecular dynamics (MD) simulations generally make use of a basic description of intermolecular forces which consists of fixed, pairwise, atom-centred Coulomb, van der Waals and short-range repulsive terms. Important interactions such as many-body polarisation and many-body dispersion which are sensitive to changes in the environment are usually neglected, and their effects treated effectively within mean-field approximations to reproduce a single thermodynamic state point or physical environment. This leads to difficulties in modelling the complex interfaces of interest today where the behaviour may be quite different from the regime of parameterisation. Here, we describe the construction and properties of a Gaussian coarse-grained electronic structure, which naturally generates many-body polarisation and dispersion interactions. The electronic structure arises from a fully quantum mechanical treatment of a set of distributed quantum Drude oscillators (QDOs), harmonic atoms which interact with each other and other moieties via electrostatic (Coulomb) interactions; this coarse-grained approach is capable of describing many-body polarisation and dispersion but not short-range interactions which must be parametrised. We describe how on-the-fly forces due to this exchange-free Gaussian model may be generated with linear scale in the number of atoms in the system using an adiabatic path integral molecular dynamics for quantum Drude oscillators technique (APIMD-QDO). We demonstrate the applicability of the QDO approach to realistic systems via a study of the liquid-vapour interface of water.
Zimmermann, Tomas
2011-01-01
We propose to measure nonadiabaticity of molecular quantum dynamics rigorously with the quantum fidelity between the Born-Oppenheimer and fully nonadiabatic dynamics. It is shown that this measure of nonadiabaticity applies in situations where other criteria, such as the energy gap criterion or the extent of population transfer, fail. We further propose to estimate this quantum fidelity efficiently with a generalization of the dephasing representation to multiple surfaces. Two variants of the multiple-surface dephasing representation (MSDR) are introduced, in which the nuclei are propagated either with the fewest-switches surface hopping (FSSH) or with the locally mean field dynamics (LMFD). The LMFD can be interpreted as the Ehrenfest dynamics of an ensemble of nuclear trajectories, and has been used previously in the nonadiabatic semiclassical initial value representation. In addition to propagating an ensemble of classical trajectories, the MSDR requires evaluating nonadiabatic couplings and solving the Sc...
Quantum molecular dynamics simulations of hydrogen production and solar cells
Mou, Weiwei
The global energy crisis presents two major challenges for scientists around the world: Producing cleaner energy which is sustainable for the environment; And improving the efficiency of energy production as well as consumption. It is crucial and yet elusive to understand the atomistic mechanisms and electronic properties, which are needed in order to tackle those challenges. Quantum molecular dynamics simulations and nonadiabatic quantum molecular dynamics are two of the dominant methods used to address the atomistic and electronic properties in various energy studies. This dissertation is an ensemble of three studies in energy research: (1) Hydrogen production from the reaction of aluminum clusters with water to provide a renewable energy cycle; (2) The photo-excited charge transfer and recombination at a quaterthiophene/zinc oxide interface to improve the power conversion efficiency of hybrid poly(3-hexylthiophene) (P3HT) /ZnO solar cells; and (3) the charge transfer at a rubrene/C60 interface to understand why phenyl groups in rubrene improve the performance of rubrene/C60 solar cells.
Massively Parallel Reactive and Quantum Molecular Dynamics Simulations
Vashishta, Priya
2015-03-01
In this talk I will discuss two simulations: Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. Quantum molecular dynamics (QMD) simulations are performed on 786,432-processor Blue Gene/Q to study on-demand production of hydrogen gas from water using Al nanoclusters. QMD simulations reveal rapid hydrogen production from water by an Al nanocluster. We find a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production. I will also discuss on-demand production of hydrogen gas from water using and LiAl alloy particles. Research reported in this lecture was carried in collaboration with Rajiv Kalia, Aiichiro Nakano and Ken-ichi Nomura from the University of Southern California, and Fuyuki Shimojo and Kohei Shimamura from Kumamoto University, Japan.
Zimmermann, Tomas
2010-01-01
We propose an approximate method for evaluating the importance of non-Born-Oppenheimer effects on the quantum dynamics of nuclei. The method uses a generalization of the dephasing representation (DR) of quantum fidelity to several diabatic potential energy surfaces and its computational cost is the cost of dynamics of a classical phase space distribution. It can be implemented easily into any molecular dynamics program and also can utilize on-the-fly ab initio electronic structure information. We test the methodology on three model problems introduced by Tully and on the photodissociation of NaI. The results show that for dynamics close to the diabatic regime the decay of fidelity due to nondiabatic effects is described accurately by the DR. In the nearly diabatic regime, unlike the mixed quantum-classical methods such as surface hopping or Ehrenfest dynamics, the DR can capture more subtle quantum effects than the population transfer between potential energy surfaces. Hence we propose using the DR to estimat...
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Makhov, Dmitry V.; Shalashilin, Dmitrii V. [Department of Chemistry, University of Leeds, Leeds LS2 9JT (United Kingdom); Glover, William J.; Martinez, Todd J. [Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture
Directory of Open Access Journals (Sweden)
Wei Feng
2014-07-01
Full Text Available Mixed-quantum-classical molecular dynamics simulation implies an effective quantum measurement on the electronic states by the classical motion of atoms. Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.
Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations
Energy Technology Data Exchange (ETDEWEB)
Giorgi, G.L., E-mail: g.giorgi@inrim.it [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy); Roncaglia, M. [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy); Raffa, F.A. [Politecnico di Torino, Dipartimento di Scienza Applicata e Tecnologia, Corso Duca degli Abruzzi 24, I-10129 Torino (Italy); Genovese, M. [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy)
2015-10-15
During the long course of evolution, nature has learnt how to exploit quantum effects. In fact, recent experiments reveal the existence of quantum processes whose coherence extends over unexpectedly long time and space ranges. In particular, photosynthetic processes in light-harvesting complexes display a typical oscillatory dynamics ascribed to quantum coherence. Here, we consider the simple model where a dimer made of two chromophores is strongly coupled with a quasi-resonant vibrational mode. We observe the occurrence of wide oscillations of genuine quantum correlations, between electronic excitations and the environment, represented by vibrational bosonic modes. Such a quantum dynamics has been unveiled through the calculation of the negativity of entanglement and the discord, indicators widely used in quantum information for quantifying the resources needed to realize quantum technologies. We also discuss the possibility of approximating additional weakly-coupled off-resonant vibrational modes, simulating the disturbances induced by the rest of the environment, by a single vibrational mode. Within this approximation, one can show that the off-resonant bath behaves like a classical source of noise.
Quantum molecular dynamics simulations of beryllium at high pressures
Desjarlais, Michael; Knudson, Marcus
2008-03-01
The phase boundaries and high pressure melt properties of beryllium have been the subject of several recent experimental and theoretical studies. The interest is motivated in part by the use of beryllium as an ablator material in inertial confinement fusion capsule designs. In this work, the high pressure melt curve, Hugoniot crossings, sound speeds, and phase boundaries of beryllium are explored with DFT based quantum molecular dynamics calculations. The entropy differences between the various phases of beryllium are extracted in the vicinity of the melt curve and agree favorably with earlier theoretical work on normal melting. High velocity flyer plate experiments with beryllium targets on Sandia's Z machine have generated high quality data for the Hugoniot, bulk sound speeds, and longitudinal sound speeds. This data provides a tight constraint on the pressure for the onset of shock melting of beryllium and intriguing information on the solid phase prior to melt. The results of the QMD calculations and the experimental results will be compared, and implications for the HCP and BCC phase boundaries of beryllium will be presented.
Adding quantum effects to the semi-classical molecular dynamics simulations
Yang, Siyang
2011-01-01
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using trajectories have achieved great successes in the computer simulations of various systems, but it is difficult to incorporate quantum effects in a robust way. Therefore, improving quantum wavepacket dynamics and incorporating nonadiabatic transitions and quantum effects into classical and semi-classical molecular dynamics is critical as well as challenging. In this paper, we present a MD scheme in which a new set of equations of motion (EOM) are proposed to effectively propagate nuclear trajectories while conserving quantum mechanical energy which is critical for describing quantum effects like tunneling. The new quantum EOM is tested on a one-state one-dimensional and a two-state two-dimensional model nonadiabatic systems. The global quantum force experienced by each trajecto...
Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture
Feng, Wei; Li, Xin-Qi; Fang, Weihai; Yan, YiJing
2013-01-01
Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.
Quantum molecular dynamics of methyl rotors in peptide links
Del Mar, J
2002-01-01
A particles wavefunction extends beyond the classically accessible regions of the potential energy surface. Quantum mechanical tunnelling is the result of this partial delocalisation, which enables the surpassing of classically inaccessible potential barriers. A particles mass is an important aspect, reflecting the tunnelling probability; a consequence of this is that a proton is ideally suited to this behaviour. Symmetrical molecular rotors such as Ch sub 3 provide a clear example of quantum mechanical tunnelling, seen in their motional spectrum. The advantage of the methyl rotor is that it's found in a wide range of organic compounds, giving a wide range in hindering potentials. It is effectively a proton rotor, and is easily observed using techniques such as Nuclear Magnetic Resonance (NMR), and Inelastic Neutron Scattering (INS). Both NMR and INS techniques are sensitive to molecular motion, and as they measure the tunnel frequencies in different energy windows, are complementary. Of central importance to...
Hasegawa, Taisuke
2016-11-07
We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.
Hasegawa, Taisuke
2016-11-01
We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.
Ishiyama, Tatsuya; Takahashi, Hideaki; Morita, Akihiro
2012-03-28
A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.
Molecular excitation dynamics and relaxation quantum theory and spectroscopy
Valkunas, Leonas; Mancal, Tomas
2013-01-01
Meeting the need for a work that brings together quantum theory and spectroscopy to convey excitation processes to advanced students and specialists wishing to conduct research and understand the entire field rather than just single aspects.Written by an experienced author and recognized authority in the field, this text covers numerous applications and offers examples taken from different disciplines. As a result, spectroscopists, molecular physicists, physical chemists, and biophysicists will all find this a must-have for their research. Also suitable as supplementary reading in graduate
Krajewski, Florian R.; Müser, Martin H.
2005-07-01
The spectral density of quantum mechanical Frenkel Kontorova chains moving in disordered, external potentials is investigated by means of path-integral molecular dynamics. If the second moment of the embedding potential is well defined (roughness exponent H=0), there is one regime in which the chain is pinned (large masses m of chain particles) and one in which it is unpinned (small m). If the embedding potential can be classified as a random walk on large length scales ( H=1/2), then the chain is always pinned irrespective of the value of m. For H=1/2, two phonon-like branches appear in the spectra.
Quantum tunneling splittings from path-integral molecular dynamics
Mátyus, Edit; Wales, David J.; Althorpe, Stuart C.
2016-03-01
We illustrate how path-integral molecular dynamics can be used to calculate ground-state tunnelling splittings in molecules or clusters. The method obtains the splittings from ratios of density matrix elements between the degenerate wells connected by the tunnelling. We propose a simple thermodynamic integration scheme for evaluating these elements. Numerical tests on fully dimensional malonaldehyde yield tunnelling splittings in good overall agreement with the results of diffusion Monte Carlo calculations.
Indian Academy of Sciences (India)
Shubin Liu
2005-09-01
Dynamic behaviors of chemical concepts in density functional theory such as frontier orbitals (HOMO/LUMO), chemical potential, hardness, and electrophilicity index have been investigated in this work in the context of Bohn-Oppenheimer quantum molecular dynamics in association with molecular conformation changes. Exemplary molecular systems like CH$^{+}_{5}$ , Cl- (H2O)30 and Ca2+ (H2O)15 are studied at 300 K in the gas phase, demonstrating that HOMO is more dynamic than LUMO, chemical potential and hardness often fluctuate concurrently. It is argued that DFT concepts and indices may serve as a good framework to understand molecular conformation changes as well as other dynamic phenomena.
Dynamical signatures of molecular symmetries in nonequilibrium quantum transport
Thingna, Juzar; Manzano, Daniel; Cao, Jianshu
2016-06-01
Symmetries play a crucial role in ubiquitous systems found in Nature. In this work, we propose an elegant approach to detect symmetries by measuring quantum currents. Our detection scheme relies on initiating the system in an anti-symmetric initial condition, with respect to the symmetric sites, and using a probe that acts like a local noise. Depending on the position of the probe the currents exhibit unique signatures such as a quasi-stationary plateau indicating the presence of metastability and multi-exponential decays in case of multiple symmetries. The signatures are sensitive to the characteristics of the probe and vanish completely when the timescale of the coherent system dynamics is much longer than the timescale of the probe. These results are demonstrated using a 4-site model and an archetypal example of the para-benzene ring and are shown to be robust under a weak disorder.
Dynamical signatures of molecular symmetries in nonequilibrium quantum transport.
Thingna, Juzar; Manzano, Daniel; Cao, Jianshu
2016-06-17
Symmetries play a crucial role in ubiquitous systems found in Nature. In this work, we propose an elegant approach to detect symmetries by measuring quantum currents. Our detection scheme relies on initiating the system in an anti-symmetric initial condition, with respect to the symmetric sites, and using a probe that acts like a local noise. Depending on the position of the probe the currents exhibit unique signatures such as a quasi-stationary plateau indicating the presence of metastability and multi-exponential decays in case of multiple symmetries. The signatures are sensitive to the characteristics of the probe and vanish completely when the timescale of the coherent system dynamics is much longer than the timescale of the probe. These results are demonstrated using a 4-site model and an archetypal example of the para-benzene ring and are shown to be robust under a weak disorder.
Hele, Timothy J H
2015-01-01
We obtain thermostatted ring polymer molecular dynamics (TRPMD) from exact quantum dynamics via Matsubara dynamics, a recently-derived form of linearization which conserves the quantum Boltzmann distribution. Performing a contour integral in the complex quantum Boltzmann distribution of Matsubara dynamics, replacement of the imaginary Liouvillian which results with a Fokker-Planck term gives TRPMD. We thereby provide error terms between TRPMD and quantum dynamics and predict the systems in which they are likely to be small. Using a harmonic analysis we show that careful addition of friction causes the correct oscillation frequency of the higher ring-polymer normal modes in a harmonic well, which we illustrate with calculation of the position-squared autocorrelation function. However, no physical friction parameter will produce the correct fluctuation dynamics for a parabolic barrier. The results in this paper are consistent with previous numerical studies and advise the use of TRPMD for the computation of spe...
Quantum-Accurate Molecular Dynamics Potential for Tungsten
Energy Technology Data Exchange (ETDEWEB)
Wood, Mitchell; Thompson, Aidan P.
2017-03-01
The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-He binary system.
Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems
Energy Technology Data Exchange (ETDEWEB)
Miller, William H.
2006-04-27
The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.
Molecular internal dynamics studied by quantum path interferences in high order harmonic generation
Energy Technology Data Exchange (ETDEWEB)
Zaïr, Amelle, E-mail: azair@imperial.ac.uk [Imperial College London, Department of Physics, Blackett Laboratory Laser Consortium, London SW7 2AZ (United Kingdom); Siegel, Thomas; Sukiasyan, Suren; Risoud, Francois; Brugnera, Leonardo; Hutchison, Christopher [Imperial College London, Department of Physics, Blackett Laboratory Laser Consortium, London SW7 2AZ (United Kingdom); Diveki, Zsolt; Auguste, Thierry [Service des Photons, Atomes et Molécules, CEA-Saclay, 91191 Gif-sur-Yvette (France); Tisch, John W.G. [Imperial College London, Department of Physics, Blackett Laboratory Laser Consortium, London SW7 2AZ (United Kingdom); Salières, Pascal [Service des Photons, Atomes et Molécules, CEA-Saclay, 91191 Gif-sur-Yvette (France); Ivanov, Misha Y.; Marangos, Jonathan P. [Imperial College London, Department of Physics, Blackett Laboratory Laser Consortium, London SW7 2AZ (United Kingdom)
2013-03-12
Highlights: ► Electronic trajectories in high order harmonic generation encodes attosecond and femtosecond molecular dynamical information. ► The observation of these quantum paths allows us to follow nuclear motion after ionization. ► Quantum paths interference encodes a signature of superposition of ionization channels. ► Quantum paths interference encodes a signature of transfer of population between channels due to laser coupling. ► Quantum paths interference is a promising technique to resolve ultra-fast dynamical processes after ionization. - Abstract: We investigate how short and long electron trajectory contributions to high harmonic emission and their interferences give access to information about intra-molecular dynamics. In the case of unaligned molecules, we show experimental evidence that the long trajectory contribution is more dependent upon the molecular species than the short one, providing a high sensitivity to cation nuclear dynamics from 100’s of as to a few fs after ionisation. Using theoretical approaches based on the strong field approximation and numerical integration of the time dependent Schrödinger equation, we examine how quantum path interferences encode electronic motion when the molecules are aligned. We show that the interferences are dependent upon which ionisation channels are involved and any superposition between them. In particular, quantum path interferences can encode signatures of electron dynamics if the laser field drives a coupling between the channels. Hence, molecular quantum path interferences are a promising method for attosecond spectroscopy, allowing the resolution of ultra-fast charge migration in molecules after ionisation in a self-referenced manner.
Molecular dynamics simulation of thermal conductivity of GaN/AlN quantum dot superlattices
Energy Technology Data Exchange (ETDEWEB)
Kawamura, Takahiro [Graduate School of Engineering, Kyushu University, 6-1, Kasuga-Koen, Kasuga, Fukuoka 816-8580 (Japan); Kangawa, Yoshihiro; Kakimoto, Koichi [Research Institute for Applied Mechanics, Kyushu University, 6-1, Kasuga-Koen, Kasuga, Fukuoka 816-8580 (Japan)
2007-06-15
We calculated thermal conductivity of GaN/AlN quantum dot superlattices by molecular dynamics simulation. The results of investigation of the effect of quantum dots on thermal conductivity as a function of superlattice period are presented in this paper. An empirical potential function of Stillinger-Weber potential was used for simulations. Thermal conductivity was obtained by Green-Kubo's equation. The results show that the values of thermal conductivity parallel to the wetting layers decreased due to the effect of quantum dots. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Coupled electron-phonon transport from molecular dynamics with quantum baths
DEFF Research Database (Denmark)
Lu, Jing Tao; Wang, J. S.
2009-01-01
Based on generalized quantum Langevin equations for the tight-binding wavefunction amplitudes and lattice displacements, electron and phonon quantum transport are obtained exactly using molecular dynamics (MD) in the ballistic regime. The electron-phonon interactions can be handled with a quasi......-classical approximation. Both charge and energy transport and their interplay can be studied. We compare the MD results with those of a fully quantum mechanical nonequilibrium Green's function (NEGF) approach for the electron currents. We find a ballistic to diffusive transition of the electron conduction in one...
Classical and quantum dynamics of a model for atomic-molecular Bose--Einstein condensates
Santos Filho, Gilberto Nascimento; Tonel, Arlei Prestes; Foerster, Angela; Links, Jon(Centre for Mathematical Physics, School of Mathematics and Physics, The University of Queensland, 4072, Australia)
2005-01-01
We study a model for a two-mode atomic-molecular Bose--Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the coupling parameter space into four regions. The different regions give rise to qualitatively different dynamics. We then show that this classification holds true for the quantum dynamics.
Fast Quantum Molecular Dynamics Simulations of Simple Organic Liquids under Shock Compression
Cawkwell, Marc; Niklasson, Anders; Manner, Virginia; McGrane, Shawn; Dattelbaum, Dana
2013-06-01
The responses of liquid formic acid, acrylonitrile, and nitromethane to shock compression have been studied using quantum-based molecular dynamics simulations with the self-consistent tight-binding code LATTE. Microcanonical Born-Oppenheimer trajectories with precise energy conservation were computed without relying on an iterative self-consistent field optimization of the electronic degrees of freedom at each time step via the Fast Quantum Mechanical Molecular Dynamics formalism. The input shock pressures required to initiate chemistry in our simulations agree very well with recent laser- and flyer-plate-driven shock compression experiments. On-the-fly analysis of the electronic structure of the liquids over hundreds of picoseconds after dynamic compression revealed that their reactivity is strongly correlated with the temperature and pressure dependence of their HOMO-LUMO gap.
The quantum nature of the hydrogen bond: insight from path-integral molecular dynamics
Walker, Brent; Li, Xin-Zheng; Michaelides, Angelos
2011-03-01
Hydrogen (H) bonds are weak, generally intermolecular bonds, that hold together much of soft matter, the condensed phases of water, network liquids, and many ferroelectric crystals. The small mass of H means H-bonds are inherently quantum mechanical; effects such as zero point motion and tunneling should be considered, although often are not. In particular, a consistent picture of quantum nuclear effects on the strength of H-bonds and consequently the structure of H-bonded systems is still absent. Here, we report ab initio path-integral molecular dynamics studies on the quantum nature of the H-bond. Systematic examination of a range of H-bonded systems shows that quantum nuclei weaken weak H-bonds but strengthen relatively strong ones. This correlation arises from a competition between anharmonic intermolecular bond bending and intramolecular bond stretching. A simple rule of thumb enables predictions to be made for H-bonded bonded materials in general with merely classical knowledge (e.g. H-bond strength or H-bond length). Our work rationalizes the contrasting influence of quantum nuclear dynamics on a wide variety of materials, including liquid water and HF, and highlights the need for flexible molecules in force-field based studies of quantum nuclear dynamics.
Dynamical signatures of molecular symmetries in nonequilibrium quantum transport
2016-01-01
Symmetries play a crucial role in ubiquitous systems found in Nature. In this work, we propose an elegant approach to detect symmetries by measuring quantum currents. Our detection scheme relies on initiating the system in an anti-symmetric initial condition, with respect to the symmetric sites, and using a probe that acts like a local noise. Depending on the position of the probe the currents exhibit unique signatures such as a quasi-stationary plateau indicating the presence of metastabilit...
Saleh, Muhammad; Hofer, Thomas S.
2016-09-01
An investigation of structural and dynamical properties of Ni2+ in liquid ammonia has been carried out via Quantum Mechanical Charge Field Molecular Dynamics. By extending the quantum mechanical region to include first and second solvation shell, a more realistic representation of the system was achieved yielding improved results on present computational facilities. The structural results obtained from the 16 ps trajectory agree well with experimental investigations for various nitrogen-containing Ni2+ systems. Detailed analysis of mean residence time and vibrational properties highlights a rather flexible structure of the first and second shells compared to Ni2+ in aqueous solution.
Craig, Ian R; Manolopoulos, David E
2004-08-22
We propose an approximate method for calculating Kubo-transformed real-time correlation functions involving position-dependent operators, based on path integral (Parrinello-Rahman) molecular dynamics. The method gives the exact quantum mechanical correlation function at time zero, exactly satisfies the quantum mechanical detailed balance condition, and for correlation functions of the form C(Ax)(t) and C(xB)(t) it gives the exact result for a harmonic potential. It also works reasonably well at short times for more general potentials and correlation functions, as we illustrate with some example calculations. The method provides a consistent improvement over purely classical molecular dynamics that is most apparent in the low-temperature regime.
Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
Equation of State of Al Based on Quantum Molecular Dynamics Calculations
Minakov, Dmitry V.; Levashov, Pavel R.; Khishchenko, Konstantin V.
2011-06-01
In this work, we present quantum molecular dynamics calculations of the shock Hugoniots of solid and porous samples as well as release isentropes and values of isentropic sound velocity behind the shock front for aluminum. We use the VASP code with an ultrasoft pseudopotential and GGA exchange-correlation functional. Up to 108 particles have been used in calculations. For the Hugoniots of Al we solve the Hugoniot equation numerically. To calculate release isentropes, we use Zel'dovich's approach and integrate an ordinary differential equation for the temperature thus restoring all thermodynamic parameters. Isentropic sound velocity is calculated by differentiation along isentropes. The results of our calculations are in good agreement with experimental data. Thus, quantum molecular dynamics results can be effectively used for verification or calibration of semiempirical equations of state under conditions of lack of experimental information at high energy densities. This work is supported by RFBR, grants 09-08-01129 and 11-08-01225.
NATO Advanced Research Workshop on Time-Dependent Quantum Molecular Dynamics : Theory and Experiment
Lathouwers, L
1992-01-01
From March 30th to April 3rd, 1992, a NATO Advanced Research workshop entitled "Time Dependent Quantum Molecular Dynamics: Theory and Experiment" was held at Snowbird, Utah. The organizing committee consisted of J. BROECKHOVE (Antwerp, Belgium), L. CEDERBAUM (Heidelberg, Germany), L. LATHOUWERS (Antwerp, Belgium), N. OHRN (Gainesville, Florida) and J. SIMONS (Salt Lake City, Utah). Fifty-two participants from eleven different countries attended the meeting at which thirty-three talks and one poster session were held. Twenty-eight participants submitted contributions to the proceedings of the meeting, which are reproduced in this volume. The workshop brought together experts in different areas 0 f molecular quantum dynamics, all adhering to the time dependent approach. The aim was to discuss and compare methods and applications. The ~amiliarityo~ the aUdience with the concepts o~ time dependent approaches greatly facilitated topical discussions and probing towards new applications. A broad area of subject matt...
Alvarez, Gonzalo A
2007-01-01
The control of open quantum systems has a fundamental relevance for fields ranging from quantum information processing to nanotechnology. Typically, the system whose coherent dynamics one wants to manipulate, interacts with an environment that smoothly degrades its quantum dynamics. Thus, a precise understanding of the inner mechanisms of this process, called "decoherence", is critical to develop strategies to control the quantum dynamics. In this thesis we solved the generalized Liouville-von Neumann quantum master equation to obtain the dynamics of many-spin systems interacting with a spin bath. We also solve the spin dynamics within the Keldysh formalism. Both methods lead to identical solutions and together gave us the possibility to obtain numerous physical predictions that contrast well with Nuclear Magnetic Resonance experiments. We applied these tools for molecular characterizations, development of new numerical methodologies and the control of quantum dynamics in experimental implementations. But, mo...
Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields.
Curioni, Alessandro; Mordasini, Tiziana; Andreoni, Wanda
2004-12-01
A methodology aimed at improving the accuracy of current docking-scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.
Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng
2006-12-28
Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.
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.
John, Chris; Habershon, Scott; Kühne, Thomas D
2015-01-01
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. This development permits to routinely include nuclear quantum effects in ab-initio molecular dynamics simulations.
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.
Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics
Buin, Andrei
2015-06-18
© 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.
Energy Technology Data Exchange (ETDEWEB)
Luo, Ye, E-mail: xw111luoye@gmail.com; Sorella, Sandro, E-mail: sorella@sissa.it [International School for Advanced Studies (SISSA), and CRS Democritos, CNR-INFM, Via Bonomea 265, I-34136 Trieste (Italy); Zen, Andrea, E-mail: zen.andrea.x@gmail.com [Dipartimento di Fisica, Università di Roma “La Sapienza,” Piazzale Aldo Moro 2, I-00185 Rome (Italy)
2014-11-21
We present a systematic study of a recently developed ab initio simulation scheme based on molecular dynamics and quantum Monte Carlo. In this approach, a damped Langevin molecular dynamics is employed by using a statistical evaluation of the forces acting on each atom by means of quantum Monte Carlo. This allows the use of an highly correlated wave function parametrized by several variational parameters and describing quite accurately the Born-Oppenheimer energy surface, as long as these parameters are determined at the minimum energy condition. However, in a statistical method both the minimization method and the evaluation of the atomic forces are affected by the statistical noise. In this work, we study systematically the accuracy and reliability of this scheme by targeting the vibrational frequencies of simple molecules such as the water monomer, hydrogen sulfide, sulfur dioxide, ammonia, and phosphine. We show that all sources of systematic errors can be controlled and reliable frequencies can be obtained with a reasonable computational effort. This work provides convincing evidence that this molecular dynamics scheme can be safely applied also to realistic systems containing several atoms.
Energy Technology Data Exchange (ETDEWEB)
Miller, J.; Miaskiewicz, K. [Pacific Northwest Lab., Richland, WA (United States); Osman, R. [Mount Sinai School of Medicine, New York, NY (United States). Dept. of Physiology and Biophysics
1993-12-01
Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.
Improved Quantum Molecular Dynamics Model and its Application to Fusion Reaction Near Barrier
Institute of Scientific and Technical Information of China (English)
2001-01-01
An improved quantum molecular dynamics model is proposed. By using this model, the properties of ground state of nuclei from 6Li to 208Pb can be described very well with one set of parameters. The fusion reactions for 40Ca+90Zr, 40Ca+96Zr and 48Ca+90Zr at the energy near the barrier are studied by this model. The experimental data of the fusion cross sections for 40Ca+90,96Zr at the energy near the barrier can be reproduced remarkably well without introducing any new parameters. The mechanism
Study of system- size effects in multi- fragmentation using Quantum Molecular Dynamics model
Singh, J; Aichelin, Jörg; Singh, Jaivir; Puri, Rajeev K.
2001-01-01
We report, for the first time, the dependence of the multiplicity of different fragments on the system size employing a quantum molecular dynamics model. This dependence is extracted from the simulations of symmetric collisions of Ca+Ca, Ni+Ni, Nb+Nb, Xe+Xe, Er+Er, Au+Au and U+U at incident energies between 50 A MeV and 1 A GeV. We find that the multiplicity of different fragments scales with the size of the system which can be parameterized by a simple power law.
Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N
2016-07-12
We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Zen, Andrea, E-mail: a.zen@ucl.ac.uk [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); London Centre for Nanotechnology, University College London, London WC1E 6BT (United Kingdom); Luo, Ye, E-mail: xw111luoye@gmail.com; Mazzola, Guglielmo, E-mail: gmazzola@phys.ethz.ch; Sorella, Sandro, E-mail: sorella@sissa.it [SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste (Italy); Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila (Italy)
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo
Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2014-01-01
Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.
Energy Technology Data Exchange (ETDEWEB)
Yoshikawa, Takehiro; Sugawara, Shuichi [Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takayanagi, Toshiyuki, E-mail: tako@mail.saitama-u.ac.jp [Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Shiga, Motoyuki [Center for Computational Science and E-systems, Japan Atomic Energy Agency, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa City, Chiba 277-8563 (Japan); Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of Nanobioscience, Yokohama-City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027 (Japan)
2012-02-06
Highlights: Black-Right-Pointing-Pointer Double proton transfer mechanisms in porphycene were studied with quantum simulations. Black-Right-Pointing-Pointer Both isotopic substitution and temperature significantly affect the transfer mechanism. Black-Right-Pointing-Pointer Nuclear quantum effects are playing important roles in the transfer mechanism. - Abstract: Path-integral molecular dynamics simulations have been performed for porphycene and its isotopic variants in order to understand the effect of isotopic substitution of inner protons on the double proton transfer mechanism. We have used an on-the-fly direct dynamics technique at the semiempirical PM6 level combined with specific reaction parameterization. Our quantum simulations show that double proton transfer of the unsubstituted porphycene at T = 300 K mainly occurs via a so-called concerted mechanism through the D{sub 2h} second-order saddle point. In addition, we found that both isotopic substitution and temperature significantly affect the double proton transfer mechanism. For example, the contribution of the stepwise mechanism increases with a temperature increase. We have also carried out hypothetical simulations with the porphycene configurations being completely planar. It has been found that out-of-plane vibrational motions significantly decrease the contribution of the concerted proton transfer mechanism.
Fast Quantum Molecular Dynamics Simulations of Shock-induced Chemistry in Organic Liquids
Cawkwell, Marc
2014-03-01
The responses of liquid formic acid and phenylacetylene to shock compression have been investigated via quantum-based molecular dynamics simulations with the self-consistent tight-binding code LATTE. Microcanonical Born-Oppenheimer trajectories with precise conservation of the total energy were computed without relying on an iterative self-consistent field optimization of the electronic degrees of freedom at each time step via the Fast Quantum Mechanical Molecular Dynamics formalism [A. M. N. Niklasson and M. J. Cawkwell, Phys. Rev. B, 86, 174308 (2012)]. The conservation of the total energy in our trajectories was pivotal for the capture of adiabatic shock heating as well as temperature changes arising from endo- or exothermic chemistry. Our self-consistent tight-binding parameterizations yielded very good predictions for the gas-phase geometries of formic acid and phenylacetylene molecules and the principal Hugoniots of the liquids. In accord with recent flyer-plate impact experiments, our simulations revealed i) that formic acid reacts at relatively low impact pressures but with no change in volume between products and reactants, and ii) a two-step polymerization process for phenylacetylene. Furthermore, the evolution of the HOMO-LUMO gap tracked on-the-fly during our simulations could be correlated with changes transient absorption measured during laser-driven shock compression experiments on these liquids.
Systematic study of 16O-induced fusions with the improved quantum molecular dynamics model
Wang, Ning; Li, Zhuxia
2014-01-01
The heavy-ion fusion reactions with 16O bombarding on 62Ni, 65Cu, 74Ge, 148Nd, 180Hf, 186W, 208Pb, 238U are systematically investigated with the improved quantum molecular dynamics (ImQMD) model. The fusion cross sections at energies near and above the Coulomb barriers can be reasonably well reproduced by using this semi-classical microscopic transport model with the parameter sets SkP* and IQ3a. The dynamical nucleus-nucleus potentials and the influence of Fermi constraint on the fusion process are also studied simultaneously. In addition to the mean field, the Fermi constraint also plays a key role for the reliable description of fusion process and for improving the stability of fragments in heavy-ion collisions.
Calculations of Bose-Einstein correlations from Relativistic Quantum Molecular Dynamics
Energy Technology Data Exchange (ETDEWEB)
Sullivan, J.P.; Berenguer, M.; Fields, D.E.; Jacak, B.V.; Sarabura, M.; Simon-Gillo, J.; Sorge, H.; van Hecke, H. [Los Alamos National Lab., NM (United States); Pratt, S. [Michigan State Univ., East Lansing, MI (United States)
1993-10-01
Bose-Einstein correlation functions which are in good agreement with pion data can be calculated from an event generator. Here pion and (preliminary) kaon data from CERN experiment NA44 are compared to the calculations. The dynamics of 200 GeV/nucleon {sup 32}S + Pb collisions are calculated, without correlations due to interference patterns of a many-body wavefunction for identical particles, using the Relativistic Quantum Molecular Dynamics model (RQMD). The model is used to generate the phase-space coordinates of the emitted hadrons at the time they suffer their last strong interaction (freeze-out). Using the freeze-out position and momentum of pairs of randomly selected identical particles, a two-particle symmetrized wave-function is calculated and used to add two-body correlations. Details of the technique have been described previously. The method is similar to that used in the Spacer program.
Yoshikawa, Takehiro; Sugawara, Shuichi; Takayanagi, Toshiyuki; Shiga, Motoyuki; Tachikawa, Masanori
2012-02-01
Path-integral molecular dynamics simulations have been performed for porphycene and its isotopic variants in order to understand the effect of isotopic substitution of inner protons on the double proton transfer mechanism. We have used an on-the-fly direct dynamics technique at the semiempirical PM6 level combined with specific reaction parameterization. Our quantum simulations show that double proton transfer of the unsubstituted porphycene at T = 300 K mainly occurs via a so-called concerted mechanism through the D2h second-order saddle point. In addition, we found that both isotopic substitution and temperature significantly affect the double proton transfer mechanism. For example, the contribution of the stepwise mechanism increases with a temperature increase. We have also carried out hypothetical simulations with the porphycene configurations being completely planar. It has been found that out-of-plane vibrational motions significantly decrease the contribution of the concerted proton transfer mechanism.
Takayanagi, Toshiyuki; Shiga, Motoyuki
2003-04-01
The photodissociation dynamics of Cl 2 embedded in helium clusters is studied by numerical simulation with an emphasis on the effect of quantum character of helium motions. The simulation is based on the hybrid model in which Cl-Cl internuclear dynamics is treated in a wavepacket technique, while the helium motions are described by a path integral centroid molecular dynamics approach. It is found that the cage effect largely decreases when the helium motion is treated quantum mechanically. The mechanism is affected not only by the zero-point vibration in the helium solvation structure, but also by the quantum dynamics of helium.
Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto
Molecular crystal structure prediction has posed a substantial challenge to first-principles methods and requires sophisticated electronic structure methods to determine the stabilities of nearly degenerate polymorphs. In this work, we demonstrate that the anharmonicity from van der Waals interactions is relevant to the finite-temperature structures of pyridine and pyridine-like molecular crystals. Using such an approach, we find that the equilibrium structures are well captured with classical ab initio molecular dynamics (AIMD), despite the presence of light atoms such as hydrogen. Employing path integral AIMD simulations, we demonstrate that the success of classical AIMD results from a separation of nuclear quantum effects between the intermolecular and intramolecular degrees of freedom. In this separation, the quasiclassical and anharmonic intermolecular degrees of freedom determine the equilibrium structure, while the quantum and harmonic intramolecular degrees of freedom are averaging to the correct intramolecular structure. This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.
Sumner, Isaiah; Iyengar, Srinivasan S
2008-08-07
We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this method to include nuclear quantum effects arising from a portion of the system along with a simultaneous description of the electronic structure. The generalizations provided here make the approach a potentially viable alternative for large systems. The quantum wavepacket dynamics is performed on a grid using a banded, sparse, and Toeplitz representation of the discrete free propagator, known as the "distributed approximating functional." Grid-based potential surfaces for wavepacket dynamics are constructed using an empirical valence bond generalization of ONIOM and further computational gains are achieved through the use of our recently introduced time-dependent deterministic sampling technique. The ab initio molecular dynamics is achieved using Born-Oppenheimer dynamics. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics, are harnessed together using a time-dependent Hartree-like procedure. We benchmark the approach through the study of structural and vibrational properties of molecular, hydrogen bonded clusters inclusive of electronic, dynamical, temperature, and critical quantum nuclear effects. The vibrational properties are constructed through a velocity/flux correlation function formalism introduced by us in an earlier publication.
Kawashima, Yukio; Tachikawa, Masanori
2013-05-01
Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.
Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús
2015-01-01
Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.
Molecular dynamics of large systems with quantum corrections for the nuclei
Energy Technology Data Exchange (ETDEWEB)
Gu, Bing; Garashchuk, Sophya, E-mail: garashchuk@sc.edu [Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC 29208 (United States)
2015-12-31
This paper describes an approximate approach to quantum dynamics based on the quantum trajectory formulation of the Schrödinger equation. The quantum-mechanical effects are incorporated through the quantum potential of the mean-field type, acting on a trajectory ensemble in addition to the classical potential. Efficiency for large systems is achieved by using the quantum corrections for selected degrees of freedom and introduction of empirical friction into the ground-state energy calculations. The classical potential, if needed, can be computed on-the-fly using the Density Functional Tight Binding method of electronic structure merged with the quantum trajectory dynamics code. The approach is practical for a few hundred atoms. Applications include a study of adsorption of quantum hydrogen colliding with the graphene model, C{sub 37}H{sub 15} and a calculation of the ground state of solid {sup 4}He simulated by a cell 180-atoms.
Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya
2015-01-14
Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines.
Zero-Point Energy Leakage in Quantum Thermal Bath Molecular Dynamics Simulations.
Brieuc, Fabien; Bronstein, Yael; Dammak, Hichem; Depondt, Philippe; Finocchi, Fabio; Hayoun, Marc
2016-12-13
The quantum thermal bath (QTB) has been presented as an alternative to path-integral-based methods to introduce nuclear quantum effects in molecular dynamics simulations. The method has proved to be efficient, yielding accurate results for various systems. However, the QTB method is prone to zero-point energy leakage (ZPEL) in highly anharmonic systems. This is a well-known problem in methods based on classical trajectories where part of the energy of the high-frequency modes is transferred to the low-frequency modes leading to a wrong energy distribution. In some cases, the ZPEL can have dramatic consequences on the properties of the system. Thus, we investigate the ZPEL by testing the QTB method on selected systems with increasing complexity in order to study the conditions and the parameters that influence the leakage. We also analyze the consequences of the ZPEL on the structural and vibrational properties of the system. We find that the leakage is particularly dependent on the damping coefficient and that increasing its value can reduce and, in some cases, completely remove the ZPEL. When using sufficiently high values for the damping coefficient, the expected energy distribution among the vibrational modes is ensured. In this case, the QTB method gives very encouraging results. In particular, the structural properties are well-reproduced. The dynamical properties should be regarded with caution although valuable information can still be extracted from the vibrational spectrum, even for large values of the damping term.
Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya
2016-05-01
At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision
Application of JAERI quantum molecular dynamics model for collisions of heavy nuclei
Directory of Open Access Journals (Sweden)
Ogawa Tatsuhiko
2016-01-01
Full Text Available The quantum molecular dynamics (QMD model incorporated into the general-purpose radiation transport code PHITS was revised for accurate prediction of fragment yields in peripheral collisions. For more accurate simulation of peripheral collisions, stability of the nuclei at their ground state was improved and the algorithm to reject invalid events was modified. In-medium correction on nucleon-nucleon cross sections was also considered. To clarify the effect of this improvement on fragmentation of heavy nuclei, the new QMD model coupled with a statistical decay model was used to calculate fragment production cross sections of Ag and Au targets and compared with the data of earlier measurement. It is shown that the revised version can predict cross section more accurately.
Pygmy and Giant Dipole Resonances by Coulomb Excitation using a Quantum Molecular Dynamics model
Tao, C; Zhang, G Q; Cao, X G; Wang, D Q Fang H W
2012-01-01
Pygmy and Giant Dipole Resonance (PDR and GDR) in Ni isotopes have been investigated by Coulomb excitation in the framework of the Isospin-dependent Quantum Molecular Dynamics model (IQMD). The spectra of $\\gamma$ rays are calculated and the peak energy, the strength and Full Width at Half Maximum (FWHM) of GDR and PDR have been extracted. Their sensitivities to nuclear equation of state, especially to its symmetry energy term are also explored. By a comparison with the other mean-field calculations, we obtain the reasonable values for symmetry energy and its slope parameter at saturation, which gives an important constrain for IQMD model. In addition, we also studied the neutron excess dependence of GDR and PDR parameters for Ni isotopes and found that the energy-weighted sum rule (EWSR) $PDR_{m_1}/GDR_{m_1}%$ increases linearly with the neutron excess.
Total Reaction Cross Section in an Isospin-Dependent Quantum Molecular Dynamics Model
Institute of Scientific and Technical Information of China (English)
魏义彬; 蔡翔舟; 沈文庆; 马余刚; 张虎勇; 钟晨; 郭威; 陈金根; 马国亮; 王鲲
2003-01-01
The isospin-dependent quantum molecular dynamics (IDQMD) model is used to study the total reaction cross section σR. The energy-dependent Pauli volumes of neutrons and protons have been discussed and introduced into the IDQMD calculation to replace the widely used energy-independent Pauli volumes. The modified IDQMD calculation can reproduce the experimental cr R well for both stable and exotic nuclei induced reactions. Comparisons of the calculated σn induced by 11Li with different initial density distributions have been performed. It is shown that the calculation by using the experimentally deduced density distribution with a long tail can fit the experimental excitation function better than that by using the Skyrme-Hartree-Fock calculated density without long tails. It is also found that σR at high energy is sensitive to the long tail of density distribution.
Nandi, Rana
2016-01-01
We study the effect of isospin-dependent nuclear forces on the pasta phase in the inner crust of neutron stars. To this end we model the crust within the framework of quantum molecular dynamics (QMD). For maximizing the numerical performance, the newly developed code has been implemented on GPU processors. As a first application of the crust studies we investigate the dependence of the particular pasta phases on the slope of the symmetry energy slope L. To isolate the effect of different values of L, we adopt an established QMD Hamiltonian and extend it to include non-linear terms in the isospin-dependent interaction. The strengths of the isospin-dependent forces are used to adjust the asymmetry energy and slope of the matter. Our results indicate that in contrast to earlier studies the phase diagram of the pasta phase is not very sensitive to the value of L.
Isoscaling Behaviour in the Isospin-Dependent Quantum Molecular Dynamics Model
Institute of Scientific and Technical Information of China (English)
TIAN Wen-Dong; SHEN Wen-Qing; WANG Kun; WEI Yi-Bin; YAN Ting-Zhi; ZHONG Chen; ZUO Jia-Xu; MA Yu-Gang; CAI Xiang-Zhou; CHEN Jin-Gen; CHEN Jin-Hui; FANG De-Qing; GUO Wei; MA Chun-Wang; MA Guo-Liang
2005-01-01
@@ The isoscaling behaviour is investigated in a frame of isospin-dependent quantum molecular dynamics models. The isotopic yields ratio Y2/Y1 for reactions 48Ca+48Ca and 40 Ca+ 40 Ca at different entrance channels are simulated and presented, the relationship between the isoscaling parameter and the entrance channel is analysed, the results show that α and β reduce with the rise of incident energies and increase with the impact parameter b, which can be attributed to the temperature varying of the pre-fragments in different entrance channels. The relation of α and symmetry-term coefficient Csym reveals that the chemical potential difference △μ is sensitive to the symmetry-term coefficient Csym, and raises with the increasing Csym.
Quantum molecular dynamics simulations of equation of state of warm dense ethane
Li, Chuan-Ying; Wang, Cong; Li, Yong-Sheng; Li, Da-Fang; Li, Zi; Zhang, Ping
2016-09-01
The equation of state of warm dense ethane is obtained using quantum molecular dynamics simulations based on finite-temperature density functional theory for densities from 0.1 g / cm 3 to 3.1 g / cm 3 and temperatures from 0.1 eV to 5.17 eV. The calculated pressure and internal energy are fitted with cubic polynomials in terms of density and temperature. Specific density-temperature-pressure tracks such as the principal and double shock Hugoniot curves along with release isentropes are predicted which are fundamental for the analysis and interpretation of high-pressure experiments. The principal and double shock Hugoniot curves are in agreement with the experimental data from the Sandia Z-Machine [Magyar et al., Phys. Rev. B 91, 134109 (2015)].
Liu, Wenyuan; Wang, Chao; Li, Yanbin; Lao, Yuyang; Han, Yongjian; Guo, Guang-Can; Zhao, Yong-Hua; He, Lixin
2015-03-01
Tensor network states (TNS) methods combined with the Monte Carlo (MC) technique have been proven a powerful algorithm for simulating quantum many-body systems. However, because the ground state energy is a highly non-linear function of the tensors, it is easy to get stuck in local minima when optimizing the TNS of the simulated physical systems. To overcome this difficulty, we introduce a replica-exchange molecular dynamics optimization algorithm to obtain the TNS ground state, based on the MC sampling technique, by mapping the energy function of the TNS to that of a classical mechanical system. The method is expected to effectively avoid local minima. We make benchmark tests on a 1D Hubbard model based on matrix product states (MPS) and a Heisenberg J1-J2 model on square lattice based on string bond states (SBS). The results show that the optimization method is robust and efficient compared to the existing results.
Krajewski, Florian R.; Müser, Martin H.
2005-03-01
The commensurate Frenkel Kontorova (FK) model is studied using path-integral molecular dynamics (PIMD). We focus on the highly discrete case, in which the embedding potential has a much greater maximum curvature than the harmonic potential connecting two particles in the FK chain. When efficient sampling methods are used, the dynamical interpretation of adiabatic PIMD appears to represent quite accurately the true time correlation functions of this highly correlated many-body system. We have found that the discrete, quantum FK model shows different behavior than its continuum version. The spectral density does not show the characteristic ω-2Θ(ω-ωc) cusp of the continuum solution in the pinned phase (m>mc). We also identify a dynamical quantum hysteresis in addition to the regular classical hysteresis when an external force is applied to the FK chain. In the unpinned phase (m⩽mc), we find a linear response damping coefficient which is finite and only weakly dependent on temperature T at small values of T.
Quantum molecular dynamics simulations of transport properties in liquid and dense-plasma plutonium
Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.
2011-02-01
We have calculated the viscosity and self-diffusion coefficients of plutonium in the liquid phase using quantum molecular dynamics (QMD) and in the dense-plasma phase using orbital-free molecular dynamics (OFMD), as well as in the intermediate warm dense matter regime with both methods. Our liquid metal results for viscosity are about 40% lower than measured experimentally, whereas a previous calculation using an empirical interatomic potential (modified embedded-atom method) obtained results 3-4 times larger than the experiment. The QMD and OFMD results agree well at the intermediate temperatures. The calculations in the dense-plasma regime for temperatures from 50 to 5000 eV and densities about 1-5 times ambient are compared with the one-component plasma (OCP) model, using effective charges given by the average-atom code inferno. The inferno-OCP model results agree with the OFMD to within about a factor of 2, except for the viscosity at temperatures less than about 100 eV, where the disagreement is greater. A Stokes-Einstein relationship of the viscosities and diffusion coefficients is found to hold fairly well separately in both the liquid and dense-plasma regimes.
Sheng, Chunyang; Nomura, Kenichi; Kalia, Rajiv; Nakano, Aiichiro; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya; Department of Physics, Kumamoto University Collaboration; CACS USC Collaboration
High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid, thermal protection of space vehicles, to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. In the validation process Small nSiC in oxygen environment is chosen to perform QMD simulation, then the QMD results provide the number of Si-O and C-O bonds as a function of time and high temperature, Same RMD simulation is simultaneously performed. We compare the time evolution of different bonds, and observe the condensation of large number of C-cluster nuclei into larger carbon clusters. We further provide the QMD simulation results as an input to a genetic algorithm, which trains the RMD force field parameters, the output force field produce results that are closer to the ground truth QMD simulation results. This research was supported by the Department of Energy (DOE).
Quantum molecular dynamics simulations of transport properties in liquid and dense-plasma plutonium.
Kress, J D; Cohen, James S; Kilcrease, D P; Horner, D A; Collins, L A
2011-02-01
We have calculated the viscosity and self-diffusion coefficients of plutonium in the liquid phase using quantum molecular dynamics (QMD) and in the dense-plasma phase using orbital-free molecular dynamics (OFMD), as well as in the intermediate warm dense matter regime with both methods. Our liquid metal results for viscosity are about 40% lower than measured experimentally, whereas a previous calculation using an empirical interatomic potential (modified embedded-atom method) obtained results 3-4 times larger than the experiment. The QMD and OFMD results agree well at the intermediate temperatures. The calculations in the dense-plasma regime for temperatures from 50 to 5000 eV and densities about 1-5 times ambient are compared with the one-component plasma (OCP) model, using effective charges given by the average-atom code INFERNO. The INFERNO-OCP model results agree with the OFMD to within about a factor of 2, except for the viscosity at temperatures less than about 100 eV, where the disagreement is greater. A Stokes-Einstein relationship of the viscosities and diffusion coefficients is found to hold fairly well separately in both the liquid and dense-plasma regimes.
Indian Academy of Sciences (India)
Sanjeev Kumar; Suneel Kumar
2010-05-01
We aim to understand the role of NN cross-sections, equation of state as well as different model ingredients such as width of Gaussian, clusterization range and different clusterization algorithms in multifragmentation using quantum molecular dynamics model. We notice that all model ingredients have sizable effect on the fragment pattern.
Li, Ying; Kalia, Rajiv K; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya
2016-05-14
At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.
Energy Technology Data Exchange (ETDEWEB)
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: paul.tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)
2015-03-14
Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10{sup 3}-10{sup 5} molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.
Energy Technology Data Exchange (ETDEWEB)
Ladd, A.J.C.
1988-08-01
The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.
Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li
2015-03-01
It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-Methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al. We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C =C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.
Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds
Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang
2016-01-01
The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).
Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya
2014-05-01
We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 106-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques
Energy Technology Data Exchange (ETDEWEB)
Shimojo, Fuyuki; Hattori, Shinnosuke [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Kunaseth, Manaschai [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); National Nanotechnology Center, Pathumthani 12120 (Thailand); Ohmura, Satoshi [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Shimamura, Kohei [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka 819-0395 (Japan)
2014-05-14
We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of
Bergstra, J.A.; Bethke, I.
2002-01-01
Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model
Ruderman, A; Santos, E; Pastawski, H M
2015-01-01
In this work we show that the molecular chemical bond formation and dissociation in presence of the d-band of a metal catalyst can be described as a Quantum Dynamical Phase Transition (QDPT). This agree with DFT calculations that predict sudden jumps in some observables as the molecule breaks. According to our model this phenomenon emerges because the catalyst provides for a non- Hermitian Hamiltonian. We show that when the molecule approaches the surface, as occurs in the Heyrovsky reaction of H 2, the bonding H 2 orbital has a smooth crossover into a bonding molecular orbital built with the closest H orbital and the surface metal d-states. The same occurs for the antibonding state. Meanwhile, two resonances appear within the continuous spectrum of the d- band which are associated with bonding and antibonding orbitals between the furthest H atom and the d-states at the second metallic layer. These move towards the band center where they collapse into a pure metallic resonance and an almost isolated H orbital...
Ruderman, A.; Dente, A. D.; Santos, E.; Pastawski, H. M.
2015-08-01
In this work we show that molecular chemical bond formation and dissociation in the presence of the d-band of a metal catalyst can be described as a quantum dynamical phase transition (QDPT). This agrees with DFT calculations that predict sudden jumps in some observables as the molecule breaks. According to our model this phenomenon emerges because the catalyst provides for a non-Hermitian Hamiltonian. We show that when the molecule approaches the surface, as occurs in the Heyrovsky reaction of H2, the bonding H2 orbital has a smooth crossover into a bonding molecular orbital built with the closest H orbital and the surface metal d-states. The same occurs for the antibonding state. Meanwhile, two resonances appear within the continuous spectrum of the d-band, which are associated with bonding and antibonding orbitals between the furthest H atom and the d-states at the second metallic layer. These move toward the band center, where they collapse into a pure metallic resonance and an almost isolated H orbital. This phenomenon constitutes a striking example of the non-trivial physics enabled when one deals with non-Hermitian Hamiltonian beyond the usual wide band approximation.
Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Rode, Bernd M
2010-06-01
An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree-Fock level in conjunction with Dunning double-zeta plus polarization function basis sets. The simulation predicts an average H-Cl bond distance of 1.28 A, which is in good agreement with the experimental value. The H(HCl)...O(w) and Cl(HCl)...H(w) distances of 1.84 and 3.51 A were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure-making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. Copyright 2009 Wiley Periodicals, Inc.
Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.
Moin, Syed Tarique; Hofer, Thomas S
2014-12-21
This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.
Tong, Chinghang; Blanco, Mario; Goddard, William A; Seinfeld, John H
2004-07-15
Ambient particulate matter contains polar multifunctional oxygenates that partition between the vapor and aerosol phases. Vapor pressure predictions are required to determine the gas-particle partitioning of such organic compounds. We present here a method based on atomistic simulations combined with the Clausius-Clapeyron equation to predict the liquid vapor pressure, enthalpies of vaporization, and heats of sublimation of atmospheric organic compounds. The resulting temperature-dependent vapor pressure equation is a function of the heat of vaporization at the normal boiling point [deltaHvap(Tb)], normal boiling point (Tb), and the change in heat capacity (liquid to gas) of the compound upon phase change [deltaCp(Tb)]. We show that heats of vaporization can be estimated from calculated cohesive energy densities (CED) of the pure compound obtained from multiple sampling molecular dynamics. The simulation method (CED) uses a generic force field (Dreiding) and molecular models with atomic charges determined from quantum mechanics. The heats of vaporization of five dicarboxylic acids [malonic (C3), succinic (C4), glutaric (C5), adipic (C6), and pimelic (C7)] are calculated at 500 K. Results are in agreement with experimental values with an averaged error of about 4%. The corresponding heats of sublimation at 298 K are also predicted using molecular simulations. Vapor pressures of the five dicarboxylic acids are also predicted using the derived Clausius-Clapeyron equation. Predicted liquid vapor pressures agree well with available literature data with an averaged error of 29%, while the predicted solid vapor pressures at ambient temperature differ considerably from a recent study by Bilde et al. (Environ. Sci. Technol. 2003, 37, 1371-1378) (an average of 70%). The difference is attributed to the linear dependence assumption thatwe used in the derived Clausius-Clapeyron equation.
Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M
2011-04-18
An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.
Billeter, S R
1998-01-01
This thesis describes the methodology of quantum dynamical (QD) simulation of proton transfers in aqueous solutions, its implementation in the simulation program QDGROMOS and its application to protonated water and aqueous solutions of acetic acid. QDGROMOS is based on the GROMOS96 molecular dynamics (MD) program package. Many of the solutions to partial problems such as the representation of the quantum state, the solution of the time-dependent Schrodinger equation, the forces from the quantum subsystem, the time-ordering of the propagations and the correlations between the subsystems, are complementary. In chapter 1, various numerical propagation algorithms for solving the time-dependent Schrodinger equation under the influence of a constant Hamilton operator are compared against each other, mainly in one dimension. A Chebysheff series expansion and the expansion in terms of eigenstates of the Hamilton operator were found to be most stable. Chapter 2 describes the theory, the methods and the algorithms of Q...
Tao, C; Zhang, G Q; Cao, X G; Fang, D Q; Wang, H W; Xu, J
2013-01-01
The isoscalar giant monopole resonance (ISGMR) in Sn isotopes and other nuclei has been investigated by Coulomb excitations in the framework of the isospin-dependent quantum molecular dynamics (IQMD) model. The spectrum of GMR has been calculated by taking the root-mean-square (RMS) radius of a nucleus as its monopole moment. The peak energy, the full width at half maximum (FWHM), and the strength of GMR extracted by a Gaussian fit to the spectrum have been studied. The GMR peak energies for Sn isotopes from the calculations using a mass-number dependent Gaussian wave-packet width $\\sigma_r$ for nucleons are found to be overestimated and show a weak dependence on the mass number compared with the experimental data. However, it has been found that experimental data of the GMR peak energies for $^{40}$Ca, $^{56}$Ni, $^{90}$Zr and $^{208}$Pb as well as Sn isotopes can be nicely reproduced after taking into account the isospin dependence in isotope chains in addition to the mass number dependence of $\\sigma_r$ fo...
Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik
2003-01-01
The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...
Li, Zhi-Guo; Cheng, Yan; Chen, Qi-Feng; Chen, Xiang-Rong
2016-05-01
The equation of state, self-diffusion, and viscosity coefficients of helium have been investigated by quantum molecular dynamics (QMD) simulations in the warm dense matter regime. Our simulations are validated through the comparison with the reliable experimental data. The calculated principal and reshock Hugoniots of liquid helium are in good agreement with the gas-gun data. On this basis, we revisit the issue for helium, i.e., the possibility of the instabilities predicted by chemical models at around 2000 GPa and 10 g/cm3 along the pressure isotherms of 6309, 15 849, and 31 623 K. Our calculations show no indications of instability in this pressure-temperature region, which reconfirm the predictions of previous QMD simulations. The self-diffusion and viscosity coefficients of warm dense helium have been systematically investigated by the QMD simulations. We carefully test the finite-size effects and convergences of statistics, and obtain numerically converged self-diffusion and viscosity coefficients by using the Kubo-Green formulas. The present results have been used to evaluate the existing one component plasma models. Finally, the validation of the Stokes-Einstein relationship for helium in the warm dense regime is discussed.
Quantum molecular dynamics simulations of uranium at high pressure and temperature
Energy Technology Data Exchange (ETDEWEB)
Hood, R Q; Yang, L H; Moriarty, J A
2008-01-22
Constant-volume quantum molecular dynamics (QMD) simulations of uranium (U) have been carried out over a range of pressures and temperatures that span the experimentally observed solid orthorhombic {alpha}-U, body-centered cubic (bcc), and liquid phases, using an ab initio plane-wave pseudopotential method within the generalized gradient approximation of density functional theory. A robust U pseudopotential has been constructed for these simulations that treats the 14 valence and outer-core electrons per atom necessary to calculate accurate structural and thermodynamic properties up to 100 GPa. Its validity has been checked by comparing low-temperature results with experimental data and all-electron full-potential linear-muffin-tin-orbital calculations of several different uranium solid structures. Calculated QMD energies and pressures for the equation of state of uranium in the solid and liquid phases are given, along with results for the Grueneisen parameter and the specific heat. We also present results for the radial distribution function, bond-angle distribution function, electronic density of states, and liquid diffusion coefficient, as well as evidence for short-range order in the liquid.
Li, Dafang; Liu, Haitao; Zeng, Siliang; Wang, Cong; Wu, Zeqing; Zhang, Ping; Yan, Jun
2014-07-31
By performing quantum molecular dynamics (QMD) simulations, we investigate the equation of states, electrical and optical properties of the expanded beryllium at densities two to one-hundred lower than the normal solid density, and temperatures ranging from 5000 to 30000 K. With decreasing the density of Be, the optical response evolves from the one characteristic of a simple metal to the one of an atomic fluid. By fitting the optical conductivity spectra with the Drude-Smith model, it is found that the conducting electrons become localized at lower densities. In addition, the negative derivative of the electrical resistivity on temperature at density about eight lower than the normal solid density demonstrates that the metal to nonmetal transition takes place in the expanded Be. To interpret this transition, the electronic density of states is analyzed systematically. Furthermore, a direct comparison of the Rosseland opacity obtained by using QMD and the standard opacity code demonstrates that QMD provides a powerful tool to validate plasma models used in atomic physics approaches in the warm dense matter regime.
Wang, Cong; Long, Yao; Tian, Ming-Feng; He, Xian-Tu; Zhang, Ping
2013-04-01
We have calculated the equations of state, the viscosity and self-diffusion coefficients, and electronic transport coefficients of beryllium in the warm dense regime for densities from 4.0 to 6.0 g/cm(3) and temperatures from 1.0 to 10.0 eV by using quantum molecular dynamics simulations. The principal Hugoniot curve is in agreement with underground nuclear explosive and high-power laser experimental results up to ~20 Mbar. The calculated viscosity and self-diffusion coefficients are compared with the one-component plasma model, using effective charges given by the average-atom model. The Stokes-Einstein relationship, which connects viscosity and self-diffusion coefficients, is found to hold fairly well in the strong coupling regime. The Lorenz number, which is the ratio between thermal and electrical conductivities, is computed via Kubo-Greenwood formula and compared to the well-known Wiedemann-Franz law in the warm dense region.
Molecular dynamics simulation and quantum mechanical calculations on α-D-N-acetylneuraminic acid.
Priyadarzini, Thanu R K; Subashini, Balakrishnan; Selvin, Jeyasigamani F A; Veluraja, Kasinadar
2012-04-01
N-Acetylneuraminic acid is a sugar molecule of biological significance due to its pivotal role in molecular recognition processes. The three dimensional structure and conformation of α-Neu5Ac in biological environments can be clearly observed by molecular dynamics (MD) simulation and quantum mechanical (QM) calculations. A 10ns MD simulation on α-Neu5Ac yields two conformational models which are stabilized by water mediated hydrogen bond between O-8/O-9 hydroxyl oxygen and carbonyl of carboxylate group. The average life time of the conformers and the residual time of water which mediates the hydrogen bonding interactions are computed. Based on the amphiprotic nature of water, water mediation of each conformer is divided into two different modes, one donor-one acceptor mode and two donor modes. According to the analysis of simulation trajectories, the preferred mode of water mediation for conformers is the one donor-one acceptor mode. The energy and geometry of the MD derived conformational models of α-Neu5Ac are optimized using HF/6-31G(∗) basis set of Gaussian03. QM calculations also resulted that α-Neu5Ac is preferentially stabilized by water mediated hydrogen bonding between O-8 hydroxyl and the carboxylate group where the mediation is one donor-one acceptor type. The optimized geometry of α-Neu5Ac which is in good agreement with the crystal structure of α-D-N-acetyl-1-O-methylneuraminic acid methyl ester is deposited in the public domain database 3DSDSCAR (http://3dsdscar.org). This optimized structure can be used by biotechnologists, biophysicists and glycobiologists for modelling the sialylglycans and also to design drugs using sialic acid analog inhibitors. Copyright © 2012 Elsevier Ltd. All rights reserved.
Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Hofer, Thomas S; Rode, Bernd M
2008-09-25
The novel ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level has been employed to investigate hydration structure and dynamics of hydrogen fluoride in aqueous solution. The average H-F bond length of 0.93 A obtained from the QMCF MD simulation is in good agreement with the experimental data. The HHF...Ow distance of 1.62 A was evaluated for the first hydration shell, and 2.00 A was observed for the FHF...Hw distance. The stability of hydrogen bonding is more pronounced in the hydrogen site of hydrogen fluoride, with a single water molecule in this part of the first hydration shell. A wide range of coordination numbers between 3 and 9 with an average value of 5.6 was obtained for the fluorine site. The force constants of 819.1 and 5.9 N/m were obtained for the HHF-FHF and HHF...Ow interactions, respectively, proving the stability of the nondissociated form of hydrogen fluoride in aqueous solution. The mean residence times of 2.1 and 2.5 ps were determined for ligand exchange processes in the neighborhood of fluorine and hydrogen atoms of hydrogen fluoride, respectively, indicating a weak structure-making effect of hydrogen fluoride in water. The corresponding H-bond lifetimes attribute this effect to the H atom site of HF.
Marsalek, Ondrej; Markland, Thomas E
2016-02-07
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
2015-01-01
Colloidal quantum dots (QDs) exhibit highly desirable size- and shape-dependent properties for applications from electronic devices to imaging. Indium phosphide QDs have emerged as a primary candidate to replace the more toxic CdSe QDs, but production of InP QDs with the desired properties lags behind other QD materials due to a poor understanding of how to tune the growth process. Using high-temperature ab initio molecular dynamics (AIMD) simulations, we report the first direct observation o...
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice.
Waheed, Qaiser; Edholm, Olle
2011-09-13
Classical simulations of simple water models reproduce many properties of the liquid and ice but overestimate the heat capacity by about 65% at ordinary temperatures and much more for low temperature ice. This is due to the fact that the atomic vibrations are quantum mechanical. The application of harmonic quantum corrections to the molecular motion results in good heat capacities for the liquid and for ice at low temperatures but a successively growing positive deviation from experimental results for ice above 200 K that reaches 15% just below melting. We suggest that this deviation is due to the lack of quantum corrections to the anharmonic motions. For the liquid, the anharmonicities are even larger but also softer and thus in less need of quantum correction. Therefore, harmonic quantum corrections to the classically calculated liquid heat capacities result in agreement with the experimental values. The classical model underestimates the heat of melting by 15%, while the application of quantum corrections produces fair agreement. On the other hand, the heat of vaporization is overestimated by 10% in the harmonically corrected classical model.
Anticipatory dynamics of biological systems: from molecular quantum states to evolution
Igamberdiev, Abir U.
2015-08-01
Living systems possess anticipatory behaviour that is based on the flexibility of internal models generated by the system's embedded description. The idea was suggested by Aristotle and is explicitly introduced to theoretical biology by Rosen. The possibility of holding the embedded internal model is grounded in the principle of stable non-equilibrium (Bauer). From the quantum mechanical view, this principle aims to minimize energy dissipation in expense of long relaxation times. The ideas of stable non-equilibrium were developed by Liberman who viewed living systems as subdivided into the quantum regulator and the molecular computer supporting coherence of the regulator's internal quantum state. The computational power of the cell molecular computer is based on the possibility of molecular rearrangements according to molecular addresses. In evolution, the anticipatory strategies are realized both as a precession of phylogenesis by ontogenesis (Berg) and as the anticipatory search of genetic fixation of adaptive changes that incorporates them into the internal model of genetic system. We discuss how the fundamental ideas of anticipation can be introduced into the basic foundations of theoretical biology.
Efficient molecular quantum dynamics in coordinate and phase space using pruned bases
Larsson, Henrik R; Tannor, David J
2016-01-01
We present an efficient implementation of dynamically pruned quantum dynamics, both in coordinate space and in phase space. We combine the ideas behind the biorthogonal von Neumann basis (PvB) with the orthogonalized momentum-symmetrized Gaussians (Weylets) to create a new basis, projected Weylets, that takes the best from both methods. We benchmark pruned dynamics using phase-space-localized PvB, projected Weylets, and coordinate-space-localized DVR bases, with real-world examples in up to six dimensions. We show that coordinate-space localization is most important for efficient pruning and that pruned dynamics is much faster compared to unpruned, exact dynamics. Phase-space localization is useful for more demanding dynamics where many basis functions are required. There, projected Weylets offer a more compact representation than pruned DVR bases.
Efficient molecular quantum dynamics in coordinate and phase space using pruned bases
Larsson, H. R.; Hartke, B.; Tannor, D. J.
2016-11-01
We present an efficient implementation of dynamically pruned quantum dynamics, both in coordinate space and in phase space. We combine the ideas behind the biorthogonal von Neumann basis (PvB) with the orthogonalized momentum-symmetrized Gaussians (Weylets) to create a new basis, projected Weylets, that takes the best from both methods. We benchmark pruned time-dependent dynamics using phase-space-localized PvB, projected Weylets, and coordinate-space-localized DVR bases, with real-world examples in up to six dimensions. For the examples studied, coordinate-space localization is the most important factor for efficient pruning and the pruned dynamics is much faster than the unpruned, exact dynamics. Phase-space localization is useful for more demanding dynamics where many basis functions are required. There, projected Weylets offer a more compact representation than pruned DVR bases.
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2000-12-01
We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.
Quantum molecular master equations
Brechet, Sylvain D.; Reuse, Francois A.; Maschke, Klaus; Ansermet, Jean-Philippe
2016-10-01
We present the quantum master equations for midsize molecules in the presence of an external magnetic field. The Hamiltonian describing the dynamics of a molecule accounts for the molecular deformation and orientation properties, as well as for the electronic properties. In order to establish the master equations governing the relaxation of free-standing molecules, we have to split the molecule into two weakly interacting parts, a bath and a bathed system. The adequate choice of these systems depends on the specific physical system under consideration. Here we consider a first system consisting of the molecular deformation and orientation properties and the electronic spin properties and a second system composed of the remaining electronic spatial properties. If the characteristic time scale associated with the second system is small with respect to that of the first, the second may be considered as a bath for the first. Assuming that both systems are weakly coupled and initially weakly correlated, we obtain the corresponding master equations. They describe notably the relaxation of magnetic properties of midsize molecules, where the change of the statistical properties of the electronic orbitals is expected to be slow with respect to the evolution time scale of the bathed system.
Grimme, Stefan; Bauer, Christopher Alexander
2015-01-01
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira
The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.
Walker, Brent; Michaelides, Angelos
2010-11-01
The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)2 is about 30% weaker when quantum nuclear effects are included, while that in (H2O)2 is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation.
Non-adiabatic molecular dynamics with complex quantum trajectories. I. The diabatic representation.
Zamstein, Noa; Tannor, David J
2012-12-14
We extend a recently developed quantum trajectory method [Y. Goldfarb, I. Degani, and D. J. Tannor, J. Chem. Phys. 125, 231103 (2006)] to treat non-adiabatic transitions. Each trajectory evolves on a single surface according to Newton's laws with complex positions and momenta. The transfer of amplitude between surfaces stems naturally from the equations of motion, without the need for surface hopping. In this paper we derive the equations of motion and show results in the diabatic representation, which is rarely used in trajectory methods for calculating non-adiabatic dynamics. We apply our method to the first two benchmark models introduced by Tully [J. Chem. Phys. 93, 1061 (1990)]. Besides giving the probability branching ratios between the surfaces, the method also allows the reconstruction of the time-dependent wavepacket. Our results are in quantitative agreement with converged quantum mechanical calculations.
Kishimoto, Tatsunori; Maezawa, Yasuyo; Kudoh, Suguru N.; Taguchi, Takahisa; Hosokawa, Chie
2017-04-01
Molecular dynamics of glutamate receptor, which is major neurotransmitter receptor at excitatory synapse located on neuron, is essential for synaptic plasticity in the complex neuronal networks. Here we studied molecular dynamics in an optical trap of AMPA-type glutamate receptor (AMPAR) labeled with quantum-dot (QD) on living neuronal cells with fluorescence imaging and fluorescence correlation spectroscopy (FCS). When a 1064-nm laser beam for optical trapping was focused on QD-AMPARs located on neuronal cells, the fluorescence intensity of QD-AMPARs gradually increased at the focal spot. Using single-particle tracking of QD-AMPARs on neurons, the average diffusion coefficient decreased in an optical trap. Moreover, the decay time obtained from FCS analysis increased with the laser power and the initial assembling state of AMPARs depended on culturing day, suggesting that the motion of QD-AMPAR was constrained in an optical trap.
Marsalek, Ondrej
2015-01-01
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive pro...
Rosnik, Andreana M; Curutchet, Carles
2015-12-08
Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.
Agarwal, Animesh
2015-01-01
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however computationally this technique is very demanding. The abovementioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One possible solution to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this ...
Menzeleev, Artur R; Ananth, Nandini; Miller, Thomas F
2011-08-21
The use of ring polymer molecular dynamics (RPMD) for the direct simulation of electron transfer (ET) reaction dynamics is analyzed in the context of Marcus theory, semiclassical instanton theory, and exact quantum dynamics approaches. For both fully atomistic and system-bath representations of condensed-phase ET, we demonstrate that RPMD accurately predicts both ET reaction rates and mechanisms throughout the normal and activationless regimes of the thermodynamic driving force. Analysis of the ensemble of reactive RPMD trajectories reveals the solvent reorganization mechanism for ET that is anticipated in the Marcus rate theory, and the accuracy of the RPMD rate calculation is understood in terms of its exact description of statistical fluctuations and its formal connection to semiclassical instanton theory for deep-tunneling processes. In the inverted regime of the thermodynamic driving force, neither RPMD nor a related formulation of semiclassical instanton theory capture the characteristic turnover in the reaction rate; comparison with exact quantum dynamics simulations reveals that these methods provide inadequate quantization of the real-time electronic-state dynamics in the inverted regime.
Quantum molecular dynamics approach to estimate spallation yield from + 208Pb reaction at 800 MeV
Indian Academy of Sciences (India)
P K Sarkar; Maitreyee Nandy
2003-10-01
The spallation yield of neutrons and other mass fragments produced in 800 MeV proton induced reaction on 208Pb have been calculated in the framework of quantum molecular dynamics (QMD) model. The energy spectra and angular distribution have been calculated. Also, multiplicity distributions of the emitted neutrons and kinetic energy carried away by them have been estimated and compared with the available experimental data. The agreement is satisfactory. A major contribution to the neutron emission comes from statistical decay of the fragments. For mass and charge distributions of spallation productsthe QMD process gives rise to target-like and projectile-like fragments only.
Shekaari, Ashkan; Abolhassani, Mohammad Reza
2017-06-01
First-principles molecular dynamics has been applied to inquire into the melting behaviors of n-atom (n = 6, 10) graphene quantum dots (GQD6 and zigzag GQD10) within the temperature range of T = 0-500 K. The temperature dependence of the geometry of each quantum dot is thoroughly evaluated via calculating the related shape deformation parameters and the eigenvalues of the quadrupole tensors. Examining the variations of some phase-transition indicators such as root-mean-square bond length fluctuations and mean square displacements broadly proposes the value of Tm = 70 K for the melting point of GQD6 while a continuous, two-stage phase transition has been concluded for zigzag GQD10.
Energy Technology Data Exchange (ETDEWEB)
Suzuki, Kimichi, E-mail: ki-suzuki@aist.go.jp [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Kayanuma, Megumi [Institut de Chimie, UMR 7177 CNRS/Universite de Strasbourg, 4 rue Blaise Pascal 67000, Strasbourg (France); Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of Science, Yokohama-city University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027 (Japan); Ogawa, Hiroshi [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Nishihara, Hirotomo; Kyotani, Takashi [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Nagashima, Umpei [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568 (Japan)
2011-09-15
Research highlights: > The stable hydrogen adsorption sites on C{sub 36}H{sub 12} were evaluated at 300 K using path integral molecular dynamics. > In the static MO calculation and conventional MD simulation, five stable adsorption sites of hydrogen atom were found. > In path integral simulation, only four stable adsorption sites were obtained. > The thermal and nuclear quantum effects are key role to settle the hydrogen adsorption sites on carbon materials. - Abstract: To settle the hydrogen adsorption sites on buckybowl C{sub 36}H{sub 12}, which is picked up from zeolite-templated carbon (ZTC), we have performed path integral molecular dynamics (PIMD) simulation including thermal and nuclear quantum fluctuations under semi-empirical PM3 method. In the static PM3 calculation and classical simulation the five stable adsorption sites of hydrogen atom are optimized inside a buckybowl C{sub 36}H{sub 12}, which are labeled as {alpha}-, {beta}{sub 1}-, {beta}{sub 2}-, {gamma}-, and {delta}-carbons from edge to innermost carbon. In PIMD simulation, meanwhile, stable adsorption site is not appeared on {delta}-carbon, but on only {alpha}-, {beta}{sub 1}-, {beta}{sub 2}-, and {gamma}-carbons. This result is due to the fact that the adsorbed hydrogen atom can easily go over the barrier for hydrogen transferring from {delta}- to {beta}{sub 1}-carbons by thermal and nuclear quantum fluctuations. The thermal and nuclear quantum effects are key role to settle the hydrogen adsorption sites on carbon materials.
Bayse, Craig A; Merz, Kenneth M
2014-08-05
Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.
Shiga, Motoyuki; Takayanagi, Toshiyuki
2003-09-01
The equilibrium structure of the negatively charged water dimer (H 2O) 2- has been studied using the path-integral molecular dynamics simulation. All the atomic motions as well as the excess electron were treated quantum mechanically, employing a semi-empirical model combining a water-water interatomic potential with an electron-water pseudopotential. It is demonstrated that the molecular structure of (H 2O) 2- is more flexible than that of (H 2O) 2; both the donor switching and donor-acceptor interchange can more effectively occur in (H 2O) 2- than in (H 2O) 2. We conclude that this floppy character is a result of the breakdown of the adiabatic Born-Oppenheimer picture.
2014-01-01
Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...
Energy Technology Data Exchange (ETDEWEB)
Chiba, Satoshi; Iwamoto, Osamu; Fukahori, Tokio; Niita, Koji; Maruyama, Toshiki; Maruyama, Tomoyuki; Iwamoto, Akira [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment
1997-03-01
The production cross sections of various fragments from proton-induced reactions on {sup 56}Fe and {sup 27}Al have been analyzed by the Quantum Molecular Dynamics (QMD) plus Statistical Decay Model (SDM). It was found that the mass and charge distributions calculated with and without the statistical decay have very different shapes. These results also depend strongly on the impact parameter, showing an importance of the dynamical treatment as realized by the QMD approach. The calculated results were compared with experimental data in the energy region from 50 MeV to 5 GeV. The QMD+SDM calculation could reproduce the production cross sections of the light clusters and intermediate-mass to heavy fragments in a good accuracy. The production cross section of {sup 7}Be was, however, underpredicted by approximately 2 orders of magnitude, showing the necessity of another reaction mechanism not taken into account in the present model. (author)
Symmetry of intramolecular quantum dynamics
Burenin, Alexander V
2012-01-01
The main goal of this book is to give a systematic description of intramolecular quantum dynamics on the basis of only the symmetry principles. In this respect, the book has no analogs in the world literature. The obtained models lead to a simple, purely algebraic, scheme of calculation and are rigorous in the sense that their correctness is limited only to the correct choice of symmetry of the internal dynamics. The book is basically intended for scientists working in the field of molecular spectroscopy, quantum and structural chemistry.
Nanomechanics of Carbon and CxByNz Nanotubes: Via a Quantum Molecular Dynamics Method
Srivastava, Deepak; Menon, M.; Cho, Kyeong Jae; Saini, Subhash (Technical Monitor)
1999-01-01
Nanomechanics of single-wall C, BN and BC$_3$ and B doped C nanotubes under axial compression and tension are investigated through a generalized tight-binding molecular dynamics (GTBMD) and {\\it ab-initio} electronic structure methods. The dynamic strength of BN, BC$_3$ and B doped C nanotubes for small axial strain are comparable to each other. The main difference is in the critical strain at which structural collapse occurs. For example, even a shallow doping with B lowers the value of critical strain for C nanotubes. The critical strain for BN nanotube is found to be more than that for the similar C nanotube. Once the structural collapse starts to occur we find that carbon nanotubes irreversibly go into plastic deformation regime via the formation of tetrahedral (four-fold coordinated) bonds at the location of sharp pinches or kinks. This finding is considerably different from the classical MD (molecular dynamics) simulation results known so far. The energetics and electronic densities of states of the collapsed structures, investigated with {\\it ab-initio) methods, will also be discussed.
Wen, Kai; Sakata, Fumihiko; Li, Zhu-Xia; Wu, Xi-Zhen; Zhang, Ying-Xun; Zhou, Shan-Gui
2013-07-05
Macroscopic parameters as well as precise information on the random force characterizing the Langevin-type description of the nuclear fusion process around the Coulomb barrier are extracted from the microscopic dynamics of individual nucleons by exploiting the numerical simulation of the improved quantum molecular dynamics. It turns out that the dissipation dynamics of the relative motion between two fusing nuclei is caused by a non-Gaussian distribution of the random force. We find that the friction coefficient as well as the time correlation function of the random force takes particularly large values in a region a little bit inside of the Coulomb barrier. A clear non-Markovian effect is observed in the time correlation function of the random force. It is further shown that an emergent dynamics of the fusion process can be described by the generalized Langevin equation with memory effects by appropriately incorporating the microscopic information of individual nucleons through the random force and its time correlation function.
Zheng, Guishan; Irle, Stephan; Morokuma, Keiji
2006-05-01
We are presenting the first quantum chemical molecular dynamics (QM/MD) model simulations for iron catalyzed single-walled carbon nanotube (SWNT) growth based on the density functional tight binding (DFTB) quantum chemical potential. As model systems, open-ended (10,10) armchair tube fragments were selected with 0, 10, and 20 Fe atoms attached in 1,4-positions on the open rims, and ensembles of randomly oriented C2 molecules were included to simulate carbon plasma feedstock molecules. Isokinetic trajectories at 1500 K to 3000 K show that divalent Fe increases the number of coordination partners with carbon and/or Fe, depending on the Fe concentration. Fe/C interactions weaken the tube sidewall due to electron transfer from Fe into antibonding carbon orbitals, and C2 addition occurs mainly in an Fe-C2-Fe bridge addition mechanism, while growth of polyyne chains characteristic for high-temperature carbon systems is suppressed in the presence of Fe on the rims of the growing SWNT. Our findings are the first quantum chemical evidence for the importance of intermetallic interactions during SWNT growth.
Lill, Markus A.; Helms, Volkhard
2001-11-01
A very efficient scheme is presented to simulate proton transport by classical molecular dynamics simulation coupled with quantum mechanically derived proton hopping. Simulated proton transfer rates and proton diffusion constants for an excess proton in a box of water molecules are in good agreement with experimental data and with previous simulations that employed empirical valence bond (EVB) theory. For the first time, the proton occupancy of an aspartic acid residue in water was computed directly by MD simulations. Locally enhanced sampling or multi copy techniques were used to facilitate proton release in simulations of an imidazole ring in a solvent box. Summarizing, a quasiclassical description of proton transfer dynamics has been able to capture important kinetic and thermodynamic features of these systems at less than 50% computational overhead compared to standard molecular dynamics simulations. The method can be easily generalized to simulate the protonation equilibria of a large number of titratable sites. This should make it an attractive method to study proton transport in large biological systems.
Wallrapp, Frank H; Voityuk, Alexander A; Guallar, Victor
2010-10-12
We report a quantum chemistry and molecular dynamics study on the temperature dependence of electronic coupling in two short model oligopeptides. Ten nanoseconds replica exchange molecular dynamics was performed on Trp-(Pro)3-Trp and Trp-(Pro)6-Trp peptides in the gas phase in combination with computation of the energy and electronic coupling for thermal hole transfer between Trp residues. The electron transfer parameters were estimated by using the semiempirical INDO/S method together with the charge fragment difference scheme. Conformational analysis of the derived trajectories revealed that the electronic coupling becomes temperature dependent when incorporating structural dynamics of the system. We demonstrate that Trp-(Pro)3-Trp, having only few degrees of freedom, results in relatively weak couplings at low and high temperature and a strong peak at 144 K, whereas the more flexible system Trp-(Pro)6-Trp shows monotonically decreased coupling. Only a few conformations with strong donor-acceptor couplings are shown to be crucial for the overall ET rates. Our results introduce the question whether the T dependence of ET coupling can also be found in large biological systems.
State-Dependent Molecular Dynamics
Directory of Open Access Journals (Sweden)
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Mirsakiyeva, Amina; Hugosson, Håkan W.; Crispin, Xavier; Delin, Anna
2016-12-01
We present simulation results, computed with the Car-Parrinello molecular dynamics method, at zero and ambient temperature (300 K) for poly(3,4-ethylenedioxythiophene) [PEDOT] and its selenium and tellurium derivatives PEDOS and PEDOTe, represented as 12-oligomer chains. In particular, we focus on structural parameters such as the dihedral rotation angle distribution, as well as how the charge distribution is affected by temperature. We find that for PEDOT, the dihedral angle distribution shows two distinct local maxima whereas for PEDOS and PEDOTe, the distributions only have one clear maximum. The twisting stiffness at ambient temperature appears to be larger the lighter the heteroatom (S, Se, Te) is, in contrast to the case at 0 K. As regards point charge distributions, they suggest that aromaticity increases with temperature, and also that aromaticity becomes more pronounced the lighter the heteroatom is, both at 0 K and ambient temperature. Our results agree well with previous results, where available. The bond lengths are consistent with substantial aromatic character both at 0 K and at ambient temperature. Our calculations also reproduce the expected trend of diminishing gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital with increasing atomic number of the heteroatom.
Cwiklik, Lukasz; Aquino, Adelia J A; Vazdar, Mario; Jurkiewicz, Piotr; Pittner, Jiří; Hof, Martin; Lischka, Hans
2011-10-20
Absorption and fluorescence spectra of PRODAN (6-propionyl-2-dimethylaminonaphthalene) were studied by means of the time-dependent density functional theory and the algebraic diagrammatic construction method. The influence of environment, a phosphatidylcholine lipid bilayer and water, was taken into account employing a combination of quantum chemical calculations with empirical force-field molecular dynamics simulations. Additionally, experimental absorption and emission spectra of PRODAN were measured in cyclohexane, water, and lipid vesicles. Both planar and twisted configurations of the first excited state of PRODAN were taken into account. The twisted structure is stabilized in both water and a lipid bilayer, and should be considered as an emitting state in polar environments. Orientation of the excited dye in the lipid bilayer significantly depends on configuration. In the bilayer, the fluorescence spectrum can be regarded as a combination of emission from both planar and twisted structures.
Wohlert, Jakob
2014-05-22
In this paper, we report the calculation of the enthalpy of sublimation, Δ(sub)H, as a function of temperature of crystalline β-cellobiose from molecular dynamics (MD) simulations, using two popular carbohydrate force fields. Together with the entropy difference between the solid and the vapor, ΔS, evaluated at atmospheric pressure, Δ(sub)H gives the vapor pressure of cellobiose over the solid phase as a function of T. It is found that when quantum mechanical corrections to the enthalpy calculated from the distribution of normal modes is applied both force fields give Δ(sub)H close to experiments. The entropy change, ΔS, which is calculated within a harmonic approximation becomes too small, leading to vapor pressures that are too low. These findings are relevant to MD simulations of crystalline carbohydrates in general, e.g., native cellulose.
Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.
Energy Technology Data Exchange (ETDEWEB)
Lee Chong Young.
1990-01-01
The author introduces two different techniques to investigate the high-Tc superconductor BaKBiO{sub 3}. The first one is the rigid-ion molecular dynamics model to calculate classical properties of the crystal. This method provides the ionic anisotropic vibrational spectra. It is found that the oxygen modes dominate the vibrational spectrum from 150 up to 820 cm{sup {minus}1}. An increase in the number of substituted K around an oxygen favors high frequency vibrational modes. Also determined by experiment was an IR spectrum, with absorption peaks between 380 to 880 cm{sup {minus}1}. Experimental and computational data are in good agreement in the high frequency region. The second technique used is based on quantum path integral molecular dynamics. It is applied for the first time to the determination of electron-phonon interaction energy. The electron-phonon coupling constant is estimated at about 1.34. This value represents a weak to moderate electron-phonon coupling in Ba{sub 1(minus)x}K{sub x}BiO{sub 3} in agreement with current views of this pairing mechanism in this material.
Cawkwell, Marc; Sanville, Edward; Coe, Joshua; Niklasson, Anders
2012-02-01
Shock-induced reactions in liquid hydrocarbons have been studied using quantum-based, self-consistent tight-binding (SC-TB) molecular dynamics simulations with an accurate and transferable model for interatomic bonding. Our SC-TB code LATTE enables explicit simulations of shock compression using the universal liquid Hugoniot. Furthermore, the effects of adiabatic shock heating are captured precisely using Niklasson's energy conserving extended Lagrangian Born-Oppenheimer Molecular Dynamics formalism. We have been able to perform relatively large-scale SC-TB simulations by either taking advantage of the sparsity of the density matrix to achieve O(N) performance or by using graphics processing units to accelerate O(N^3) algorithms. We have developed the capability for the on-the-fly computation of Raman spectra from the Fourier transform of the polarizability autocorrelation function via the density matrix perturbation theory of Niklasson and Challacombe. These time-resolved Raman spectra enable us compare the results of our simulations with identical diagnostics collected experimentally. We will illustrate these capabilities with a series of simulations of shock-induced reaction paths in a number of simple molecules.
Energy Technology Data Exchange (ETDEWEB)
Lee, C.Y. (Dept. of Physics, Univ. of Arizona, Tucson (United States)); Deymier, P.A. (Dept. of Materials Science and Engineering, Univ. of Arizona, Tucson (United States))
1992-01-01
We calculated the electron-phonon interaction energy and estimated the electron-phonon coupling constant in Ba{sub 0.6}K{sub 0.4}BiO{sub 3} using a quantum path integral molecular dynamics. We determined the electron-phonon coupling constant at room temperature to be about 1.34. (orig.).
Sardar, Subhankar; Paul, Amit Kumar; Mondal, Padmabati; Sarkar, Biplab; Adhikari, Satrajit
2008-11-14
We are investigating the molecular dynamics of the butatriene cation after excitation from the ground state (X(2)B(2g)) to the first excited electronic state (A(2)B(2u)) by using the time-dependent discrete variable representation (TDDVR) method. The investigation is being carried out with a realistic 18-mode model Hamiltonian consisting of all the vibrational degrees of freedom of the butatriene molecule. First, we perform the simulation on a basic five mode model, and then by including additional thirteen modes as bath on the basic model. This sequential inclusion of bath modes demonstrates the effect of so called weak modes on the subsystem, where the calculations of energy and population transfer from the basic model to the bath quantify the same effect. The spectral profile obtained by using the TDDVR approach shows reasonably good agreement with the results calculated by the quantum mechanical approach/experimental measurement. It appears that the TDDVR approach for those large systems where quantum mechanical description is needed in a restricted region, is a good compromise between accuracy and speed.
Energy Technology Data Exchange (ETDEWEB)
Dardi, P.S.
1984-11-01
Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.
Arrighi, Pablo
2016-01-01
Consider a graph having quantum systems lying at each node. Suppose that the whole thing evolves in discrete time steps, according to a global, unitary causal operator. By causal we mean that information can only propagate at a bounded speed, with respect to the distance given by the graph. Suppose, moreover, that the graph itself is subject to the evolution, and may be driven to be in a quantum superposition of graphs---in accordance to the superposition principle. We show that these unitary causal operators must decompose as a finite-depth circuit of local unitary gates. This unifies a result on Quantum Cellular Automata with another on Reversible Causal Graph Dynamics. Along the way we formalize a notion of causality which is valid in the context of quantum superpositions of time-varying graphs, and has a number of good properties. Keywords: Quantum Lattice Gas Automata, Block-representation, Curtis-Hedlund-Lyndon, No-signalling, Localizability, Quantum Gravity, Quantum Graphity, Causal Dynamical Triangula...
Quantum Mechanics and First-Principles Molecular Dynamics Selection of Polymer Sensing Materials
Blanco, Mario; Shevade, Abhijit V.; Ryan, Margaret A.
We present two first-principles methods, density functional theory (DFT) and a molecular dynamics (MD) computer simulation protocol, as computational means for the selection of polymer sensing materials. The DFT methods can yield binding energies of polymer moieties to specific vapor bound compounds, quantities that were found useful in materials selection for sensing of organic and inorganic compounds for designing sensors for the electronic nose (ENose) that flew on the International Space Station (ISS) in 2008-2009. Similarly, we present an MD protocol that offers high consistency in the estimation of Hildebrand and Hansen solubility parameters (HSP) for vapor bound compounds and amorphous polymers. HSP are useful for fitting measured polymer sensor responses with physically rooted analytical models. We apply the method to the JPL electronic nose (ENose), an array of sensors with conducting leads connected through thin film polymers loaded with carbon black. Detection relies on a change in electric resistivity of the polymer film as function of the amount of swelling caused by the presence of the analyte chemical compound. The amount of swelling depends upon the chemical composition of the polymer and the analyte molecule. The pattern is unique and it unambiguously identifies the compound. Experimentally determined changes in relative resistivity of fifteen polymer sensor materials upon exposure to ten vapors were modeled with the first-principles HSP model.
Lim, Len Herald V; Bhattacharjee, Anirban; Asam, S Sikander; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M
2010-03-01
An ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation was performed to investigate the behavior of the Sb(3+) ion in aqueous solution. The simulation reveals a significant influence of the residual valence shell electron density on the solvation structure and dynamics of Sb(3+). A strong hemidirectional behavior of the ligand binding pattern is observed for the first hydration shell extending up to the second hydration layer. The apparent domain partitioned structural behavior was probed by solvent reorientational kinetics and three-body distribution functions. The three-dimensional hydration space was conveniently segmented such that domains having different properties were properly resolved. The approach afforded a fair isolation of localized solvent structural and dynamical motifs that Sb(3+) seems to induce to a remarkable degree. Most intriguing is the apparent impact of the lone pair electrons on the second hydration shell, which offers insight into the mechanistic aspects of hydrogen bonding networks in water. Such electronic effects observed in the hydration of Sb(3+) can only be studied by applying a suitable quantum mechanical treatment including first and second hydration shell as provided by the QMCF ansatz.
Energy Technology Data Exchange (ETDEWEB)
Dong Cunku [Department of Chemistry, Harbin Institute of Technology, Harbin 150090 (China); Li Xin, E-mail: lixin@hit.edu.cn [Department of Chemistry, Harbin Institute of Technology, Harbin 150090 (China); Guo Zechong [School of Municipal Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Qi Jingyao, E-mail: jyq@hit.edu.cn [School of Municipal Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China)
2009-08-04
A new rational approach for the preparation of molecularly imprinted polymer (MIP) based on the combination of molecular dynamics (MD) simulations and quantum mechanics (QM) calculations is described in this work. Before performing molecular modeling, a virtual library of functional monomers was created containing forty frequently used monomers. The MD simulations were first conducted to screen the top three monomers from virtual library in each porogen-acetonitrile, chloroform and carbon tetrachloride. QM simulations were then performed with an aim to select the optimum monomer and progen solvent in which the QM simulations were carried out; the monomers giving the highest binding energies were chosen as the candidate to prepare MIP in its corresponding solvent. The acetochlor, a widely used herbicide, was chosen as the target analyte. According to the theoretical calculation results, the MIP with acetochlor as template was prepared by emulsion polymerization method using N,N-methylene bisacrylamide (MBAAM) as functional monomer and divinylbenzene (DVB) as cross-linker in chloroform. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the acetochlor. Mulliken charge distribution and {sup 1}H NMR spectroscopy of the synthesized MIP provided insight on the nature of recognition during the imprinting process probing the governing interactions for selective binding site formation at a molecular level. We think the computer simulation method first proposed in this paper is a novel and reliable method for the design and synthesis of MIP.
Duster, Adam W; Lin, Hai
2017-09-14
Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. The results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.
Electronic absorption and resonance Raman spectroscopy from ab initio quantum molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Ben-Nun, M.; Martinez, T.J.
1999-12-09
The absorption and resonance Raman excitation profiles of ethylene following {pi} {yields} {pi}* excitation and taking full account of anharmonicity and Duschinsky rotation effects are calculated from first principles molecular dynamics using the ab initio multiple spawning (AIMS) method and a correlation function approach. The AIMS method solves the nuclear and electronic Schroedinger equations simultaneously and it associates a unique nuclear wave function with each electronic state. The compound absorption spectrum has a full width at half maximum of 9,800 and 1,300 cm{sup {minus}1} (in agreement with the experimental value, 9,500 cm{sup {minus}1}) and a high-frequency structure spaced by 800 and 10 cm{sup {minus}1}, attributed to C{double{underscore}bond}C stretching. The resonance Raman excitation profile exhibits fundamental activity in all totally symmetric modes with the C{double{underscore}bond}C stretching mode being the most dominant. In addition, overtone activity is observed in the torsional motion, out-of-plane wagging motions and the out-of-plane rocking motions. The activity is consistent with the observation that the first excited state is twisted and one of the CH{sub 2} groups is pyramidalized. The coordinate dependence of the electronic transition dipole is investigated, and they find that it depends very strongly on the torsional coordinate and less so on the pyramidalization and C{double{underscore}bond}C stretching coordinates. However, within the approximations used in this paper this dependence does not influence the spectra significantly and the Condon approximation is quite accurate.
Theoretical Concepts in Molecular Photodissociation Dynamics
DEFF Research Database (Denmark)
Henriksen, Niels Engholm
1995-01-01
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
Dynamics of complex quantum systems
Akulin, Vladimir M
2014-01-01
This book gathers together a range of similar problems that can be encountered in different fields of modern quantum physics and that have common features with regard to multilevel quantum systems. The main motivation was to examine from a uniform standpoint various models and approaches that have been developed in atomic, molecular, condensed matter, chemical, laser and nuclear physics in various contexts. The book should help senior-level undergraduate, graduate students and researchers putting particular problems in these fields into a broader scientific context and thereby taking advantage of well-established techniques used in adjacent fields. This second edition has been expanded to include substantial new material (e.g. new sections on Dynamic Localization and on Euclidean Random Matrices and new chapters on Entanglement, Open Quantum Systems, and Coherence Protection). It is based on the author’s lectures at the Moscow Institute of Physics and Technology, at the CNRS Aimé Cotton Laboratory, and on ...
Kishi, Ryohei; Fujii, Hiroaki; Kishimoto, Shingo; Murata, Yusuke; Ito, Soichi; Okuno, Katsuki; Shigeta, Yasuteru; Nakano, Masayoshi
2012-05-03
We develop novel calculation and analysis methods for the dynamic first hyperpolarizabilities β [the second-order nonlinear optical (NLO) properties at the molecular level] in the second-harmonic generation based on the quantum master equation method combined with the ab initio molecular orbital (MO) configuration interaction method. As examples, we have evaluated off-resonant dynamic β values of donor (NH(2))- and/or acceptor (NO(2))-substituted benzenes using these methods, which are shown to reproduce those by the conventional summation-over-states method well. The spatial contributions of electrons to the dynamic β of these systems are also analyzed using the dynamic β density and its partition into the MO contributions. The present results demonstrate the advantage of these methods in unraveling the mechanism of dynamic NLO properties and in building the structure-dynamic NLO property relationships of real molecules.
Hanson, David E.; Martin, Richard L.
2010-08-01
We investigate the thermodynamic consequences of the distribution of rotational conformations of polyisoprene on the elastic response of a network chain. In contrast to the classical theory of rubber elasticity, which associates the elastic force with the distribution of end-to-end distances, we find that the distribution of chain contour lengths provides a simple mechanism for an elastic force. Entropic force constants were determined for small contour length extensions of chains constructed as a series of localized kinks, with each kink containing between one and five cis-1,4-isoprene units. The probability distributions for the kink end-to-end distances were computed by two methods: (1) by constructing a Boltzmann distribution from the lengths corresponding to the minimum energy dihedral rotational conformations, obtained by optimizing isoprene using first principles density functional theory, and (2) by sampling the trajectories of molecular dynamics simulations of an isolated molecule composed of five isoprene units. Analogous to the well-known tube model of elasticity, we make the assumption that, for small strains, the chain is constrained by its surrounding tube, and can only move, by a process of reptation, along the primitive path of the contour. Assuming that the chain entropy is Boltzmann's constant times the logarithm of the contour length distribution, we compute the tensile force constants for chain contour length extension as the change in entropy times the temperature. For a chain length typical of moderately crosslinked rubber networks (78 isoprene units), the force constants range between 0.004 and 0.033 N/m, depending on the kink size. For a cross-linked network, these force constants predict an initial tensile modulus of between 3 and 8 MPa, which is comparable to the experimental value of 1 MPa. This mechanism is also consistent with other thermodynamic phenomenology.
Coherent Dynamics of Complex Quantum Systems
Akulin, Vladimir M
2006-01-01
A large number of modern problems in physics, chemistry, and quantum electronics require a consideration of population dynamics in complex multilevel quantum systems. The purpose of this book is to provide a systematic treatment of these questions and to present a number of exactly solvable problems. It considers the different dynamical problems frequently encountered in different areas of physics from the same perspective, based mainly on the fundamental ideas of group theory and on the idea of ensemble average. Also treated are concepts of complete quantum control and correction of decoherence induced errors that are complementary to the idea of ensemble average. "Coherent Dynamics of Complex Quantum Systems" is aimed at senior-level undergraduate students in the areas of Atomic, Molecular, and Laser Physics, Physical Chemistry, Quantum Optics and Quantum Informatics. It should help them put particular problems in these fields into a broader scientific context and thereby take advantage of the well-elabora...
Zhou, C L; Fang, D Q; Zhang, G Q
2013-01-01
Thermodynamic and transport properties of nuclear fireball created in the central region of heavy-ion collisions below 200 MeV/nucleon are investigated within the isospin-dependent quantum molecular dynamic (IQMD) model. These properties include time evolutions of the density, temperature, chemical potential, entropy density ($s$) and shear viscosity ($\\eta$) as well as density and temperature dependencies of the ratio of shear viscosity over entropy density ($\\eta/s$) etc. Based on the shear viscosity parametrization developed by Danilewicz and entropy density which is obtained by a generalized hot Thomas Fermi formalism, the ratio of shear viscosity over entropy density is calculated in the whole collision process as well as in the freeze-out stage. With the collision goes on, a transient minimal $\\eta/s$ with the value around 5/$4\\pi$ occurs in the largest compression stage. While, the relationship of $\\eta/s$ to tempertaure ($T$) in the freeze-out stage displays a local minimum which is about 9-10 times $...
Distasio, Robert A., Jr.; Santra, Biswajit; Ko, Hsin-Yu; Car, Roberto
2014-03-01
In this work, we report highly accurate ab initio path-integral molecular dynamics (AI-PIMD) simulations on liquid water at ambient conditions utilizing the recently developed PBE0+vdW(SC) exchange-correlation functional, which accounts for exact exchange and a self-consistent pairwise treatment of van der Waals (vdW) or dispersion interactions, combined with nuclear quantum effects (via the colored-noise generalized Langevin equation). The importance of each of these effects in the theoretical prediction of the structure of liquid water will be demonstrated by a detailed comparative analysis of the predicted and experimental oxygen-oxygen (O-O), oxygen-hydrogen (O-H), and hydrogen-hydrogen (H-H) radial distribution functions as well as other structural properties. In addition, we will discuss the theoretically obtained proton momentum distribution, computed using the recently developed Feynman path formulation, in light of the experimental deep inelastic neutron scattering (DINS) measurements. DOE: DE-SC0008626, DOE: DE-SC0005180.
Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S
2014-06-10
We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good
Energy Technology Data Exchange (ETDEWEB)
Pask, J E; Sukumar, N; Guney, M; Hu, W
2011-02-28
completely general, applicable to any crystal symmetry and to both metals and insulators alike. We have developed and implemented a full self-consistent Kohn-Sham method, including both total energies and forces for molecular dynamics, and developed a full MPI parallel implementation for large-scale calculations. We have applied the method to the gamut of physical systems, from simple insulating systems with light atoms to complex d- and f-electron systems, requiring large numbers of atomic-orbital enrichments. In every case, the new PU FE method attained the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the current state-of-the-art PW method. Finally, our initial MPI implementation has shown excellent parallel scaling of the most time-critical parts of the code up to 1728 processors, with clear indications of what will be required to achieve comparable scaling for the rest. Having shown that the key remaining disadvantage of real-space methods can in fact be overcome, the work has attracted significant attention: with sixteen invited talks, both domestic and international, so far; two papers published and another in preparation; and three new university and/or national laboratory collaborations, securing external funding to pursue a number of related research directions. Having demonstrated the proof of principle, work now centers on the necessary extensions and optimizations required to bring the prototype method and code delivered here to production applications.
Directory of Open Access Journals (Sweden)
James W. Gauld
2012-10-01
Full Text Available Ornithine cyclodeaminase (OCD is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD and a hybrid quantum mechanics/molecular mechanics (QM/MM method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2+ Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.
Danel, J-F; Kazandjian, L
2015-01-01
We test two isothermal-isobaric mixing rules, respectively based on excess-pressure and total-pressure equilibration, applied to the equation of state of a dense plasma. While the equation of state is generally known for pure species, that of arbitrary mixtures is not available so that the validation of accurate mixing rules, that implies resorting to first-principles simulations, is very useful. Here we consider the case of a plastic with composition C(2)H(3) and we implement two complementary ab initio approaches adapted to the dense plasma domain: quantum molecular dynamics, limited to low temperature by its computational cost, and orbital-free molecular dynamics, that can be implemented at high temperature. The temperature and density range considered is 1-10 eV and 0.6-10 g/cm(3) for quantum molecular dynamics, and 5-1000 eV and 1-10 g/cm(3) for orbital-free molecular dynamics. Simulations for the full C(2)H(3) mixture are the benchmark against which to assess the mixing rules, and both pressure and internal energy are compared. We find that the mixing rule based on excess-pressure equilibration is overall more accurate than that based on total-pressure equilibration; except for quantum molecular dynamics and a thermodynamic domain characterized by very low or negative excess pressures, it gives pressures which are generally within statistical error or within 1% of the exact ones. Besides, its superiority is amplified in the calculation of a principal Hugoniot.
Quantum mechanics of molecular structures
Yamanouchi, Kaoru
2012-01-01
At a level accessible to advanced undergraduates, this textbook explains the fundamental role of quantum mechanics in determining the structure, dynamics, and other properties of molecules. Readers will come to understand the quantum-mechanical basis for harmonic oscillators, angular momenta and scattering processes. Exercises are provided to help readers deepen their grasp of the essential phenomena.
Jones, N
2002-01-01
The wavefunction of a particle extends into the classically forbidden barrier region of the potential energy surface. The consequence of this partial delocalisation is the phenomenon of quantum tunnelling, an effect which enables a particle to penetrate a potential barrier of magnitude greater than the energy of the particle. The tunnelling probability is an exponential function of the particle mass. The effect is therefore an important contribution to the behaviour of light atoms, in particular the proton. The hydrogen bond has long been appreciated to be an essential component of many biological and chemical systems, and the proton transfer reaction in the hydrogen bond is fundamental to many of these processes. The proton behaviour in the hydrogen bonds of benzoic acid, acetylacetone and calix-4-arene has been studied. A variety of techniques, both experimental and computational, were adopted for the study of the three hydrogen bonded systems. The complementary spectroscopic techniques of inelastic neutron...
Carelli, Fabio
2012-01-01
For decades astronomers and astrophysicists believed that only positively charged ions were worthy of relevance in drawing the networks for possible chemical reactions in the interstellar medium, as well as in modeling the physical conditions in most of astrophysical environments. Thus, molecular negative ions received minor attention until their possible existence was observationally confirmed (discovery of the first interstellar anion, C6H-), about thirty years after the first physically reasonable proposal on their actual detection was theoretically surmised by E.Herbst. In an astrophysical context, their role should be then found in their involvement in the charge balance as well as in the chemical evolution of the considered environment: depending on their amount and on the global gas density, in fact, the possible evolutive scenario could be susceptible of marked variations on the estimated time needed for reaching the steady state, their presence having thus also important repercussions on the final ch...
Molecular quantum electrodynamics
Craig, D P
1998-01-01
This systematic introduction to quantum electrodynamics focuses on the interaction of radiation with outer electrons and nuclei of atoms and molecules, answering the long-standing need of chemists and physicists for a comprehensive text on this highly specialized subject.Geared toward postgraduate students in the chemical sciences who require an understanding of quantum electrodynamics as applied to the interpretation of optical experiments on atoms and molecules, the text offers a detailed explanation of the quantum theory of electromagnetic radiation and its interaction with matter. It feat
Femtosecond quantum dynamics and laser-cooling in thermal molecular systems
Warmuth, C
2000-01-01
of thermal trans-stilbene upon excitation at the omega sub 0 frequency. The experimental results are in good agreement with theoretical analysis. This work deals with coherent and incoherent vibrational phenomena in thermal systems, wave packet motion and laser-cooling. In the first part, the principle of COIN (Coherence Observation by Interference Noise) has been applied as a new approach to measuring wave packet motion. In the experiment pairs of phase-randomized femtosecond pulses with relative delay-time tau prepare interference fluctuations in the excited state population, so the variance of the correlated fluorescence intensity directly mimics the dynamics of the propagating wave packet. The scheme is demonstrated by measuring the vibrational coherence of wave packet-motion in the B-state of gaseous iodine. The COIN-interferograms obtained recover propagation, recurrences, spreading, and revivals as the typical signature of wave packets. Due to the disharmony of the B-state-potential, fractional revival...
Hele, Timothy J H; Althorpe, Stuart C
2013-02-28
Surprisingly, there exists a quantum flux-side time-correlation function which has a non-zero t → 0+ limit and thus yields a rigorous quantum generalization of classical transition-state theory (TST). In this Part I of two articles, we introduce the new time-correlation function and derive its t → 0+ limit. The new ingredient is a generalized Kubo transform which allows the flux and side dividing surfaces to be the same function of path-integral space. Choosing this function to be a single point gives a t → 0+ limit which is identical to an expression introduced on heuristic grounds by Wigner in 1932; however, this expression does not give positive-definite quantum statistics, causing it to fail while still in the shallow-tunnelling regime. Positive-definite quantum statistics is obtained only if the dividing surface is invariant to imaginary-time translation, in which case the t → 0+ limit is identical to ring-polymer molecular dynamics (RPMD) TST. The RPMD-TST rate is not a strict upper bound to the exact quantum rate, but is a good approximation to one if real-time coherence effects are small. Part II will show that the RPMD-TST rate is equal to the exact quantum rate in the absence of recrossing.
Lo, Rabindranath; Chandar, Nellore Bhanu; Ghosh, Shibaji; Ganguly, Bishwajit
2016-04-01
A highly toxic nerve agent, tabun, can inhibit acetylcholinesterase (AChE) at cholinergic sites, which leads to serious cardiovascular complications, respiratory compromise and death. We have examined the structural features of the tabun-conjugated AChE complex with an oxime reactivator, Ortho-7, to provide a strategy for designing new and efficient reactivators. Mutation of mAChE within the choline binding site by Y337A and F338A and its interaction with Ortho-7 has been investigated using steered molecular dynamics (SMD) and quantum chemical methods. The overall study shows that after mutagenesis (Y337A), the reactivator can approach more freely towards the phosphorylated active site of serine without any significant steric hindrance in the presence of tabun compared to the wild type and double mutant. Furthermore, the poor binding of Ortho-7 with the peripheral residues of mAChE in the case of the single mutant compared to that of the wild-type and double mutant (Y337A/F338A) can contribute to better efficacy in the former case. Ortho-7 has formed a greater number of hydrogen bonds with the active site surrounding residues His447 and Phe295 in the case of the single mutant (Y337A), and that stabilizes the drug molecule for an effective reactivation process. The DFT M05-2X/6-31+G(d) level of theory shows that the binding energy of Ortho-7 with the single mutant (Y337A) is energetically more preferred (-19.8 kcal mol(-1)) than the wild-type (-8.1 kcal mol(-1)) and double mutant (Y337A/F338A) (-16.0 kcal mol(-1)). The study reveals that both the orientation of the oxime reactivator for nucleophilic attack and the stabilization of the reactivator at the active site would be crucial for the design of an efficient reactivator.
Dynamic quantum molecular sieving separation of D2 from H2-D2 mixture with nanoporous materials.
Niimura, Subaru; Fujimori, Toshihiko; Minami, Daiki; Hattori, Yoshiyuki; Abrams, Lloyd; Corbin, Dave; Hata, Kenji; Kaneko, Katsumi
2012-11-14
Quantum molecular sieving separability of D(2) from an H(2)-D(2) mixture was measured at 77 K for activated carbon fiber, carbon molecular sieve, zeolite and single wall carbon nanotube using a flow method. The amount of adsorbed D(2) was evidently larger than H(2) for all samples. The maximum adsorption ratio difference between D(2) and H(2) was 40% for zeolite (MS13X), yielding a selectivity for D(2) with respect to H(2) of 3.05.
Aage Poulsen, Jens; Nyman, Gunnar; Rossky, Peter J.
2005-05-01
Structure, transport properties, and IR spectra including quantum effects are calculated for a flexible simple point charge model of liquid water. A recently introduced combination of a variational local harmonic description of the liquid potential surface and the classical Wigner approximation for the dynamics is used. The potential energy and interatomic radial distribution functions are in good agreement with accurate results from the literature and are significantly closer to experiment than predictions found from classical theory. The oxygen and hydrogen velocity correlation functions are also calculated, and the corresponding molecular diffusion coefficient is in good accord with existing theoretical estimates including quantum effects. Of most interest, an ab initio quantum correction factor is obtained to correct the far IR spectrum of water. When corrected, a spectrum based on a classical simulation yields results that agree well with experiment. Combined with internal tests of consistency, these observations indicate that this quite flexible approach will be effective for a variety of molecular problems involving the dynamics of light nuclei. computer simulation | liquid dynamics
Murugan, N. Arul; Jha, Prakash Chandra; Rinkevicius, Z.; Ruud, Kenneth; Ågren, Hans
2010-06-01
The present work addresses the solvatochromic shift of phenol blue (PB) dye. For this purpose the results of Car-Parrinello molecular dynamics (CPMD) simulations for PB in gas phase are compared with results obtained for PB in water from CPMD hybrid quantum mechanics-molecular mechanics (CPMD-QM/MM) calculations. The absorption spectra were obtained using the intermediate neglect of differential overlap/spectroscopic-configuration interaction (INDO/CIS) method and were calculated for a multitude of configurations of the trajectory. The calculated λmax for PB in gas phase was found to be about 535 nm, which is considerably lower than the λmax reported for PB in nonpolar solvents. Different solvation shells for PB in water have been defined based on the solute-all-atoms and solvent center of mass radial distribution function (g(rX-O)). The electronic excitation energies for PB computed in the presence of solvent molecules in an increasing number of solvation shells were calculated in a systematic way to evaluate their contributions to the solvatochrmic shift. The inclusion of solvent molecules in the hydration shell yields a λmax of 640 nm, which contributes to almost 78% of the solvatochromic shift. The inclusion of solvent molecules up to 10 Å in the g(rX-O) rdf yields a λmax of 670 nm which is in good agreement with the experimentally reported value of 654-684 nm. Overall, the present study suggests that the combined CPMD-QM/MM and INDO-CIS approach can be used successfully to model solvatochromic shifts of organic dye molecules.
Dynamics of quantum entanglement
Zyczkowski, K; Horodecki, M; Horodecki, R; Zyczkowski, Karol; Horodecki, Pawel; Horodecki, Michal; Horodecki, Ryszard
2002-01-01
A model of discrete dynamics of entanglement of bipartite quantum state is considered. It involves a global unitary dynamics of the system and periodic actions of local bistochastic or decaying channel. For initially pure states the decay of entanglement is accompanied with an increase of von Neumann entropy of the system. We observe and discuss revivals of entanglement due to unitary interaction of both subsystems. For some mixed states having different marginal entropies of both subsystems (one larger than the global entropy and one smaller) we find an asymmetry in speed of entanglement decay. The entanglement of these states decreases faster, if the depolarizing channel acts on the "classical" subsystem, characterized by smaller marginal entropy.
Coarse Grained Quantum Dynamics
Agon, Cesar; Kasko, Skyler; Lawrence, Albion
2014-01-01
We consider coarse graining a quantum system divided between short distance and long distance degrees of freedom, which are coupled by the Hamiltonian. Observations using purely long distance observables can be described by the reduced density matrix that arises from tracing out the short-distance observables. The dynamics of this density matrix is that of an open quantum system, and is nonlocal in time, on the order of some short time scale. We describe these dynamics in a model system with a simple hierarchy of energy gaps $\\Delta E_{UV} > \\Delta E_{IR}$, in which the coupling between high-and low-energy degrees of freedom is treated to second order in perturbation theory. We then describe the equations of motion under suitable time averaging, reflecting the limited time resolution of actual experiments, and find an expansion of the master equation in powers of $\\Delta E_{IR}/\\Delta E_{UV}$, in which the failure of the system to be Hamiltonian or even Markovian appears at higher orders in this ratio. We com...
Quantum dynamic imaging theoretical and numerical methods
Ivanov, Misha
2011-01-01
Studying and using light or "photons" to image and then to control and transmit molecular information is among the most challenging and significant research fields to emerge in recent years. One of the fastest growing areas involves research in the temporal imaging of quantum phenomena, ranging from molecular dynamics in the femto (10-15s) time regime for atomic motion to the atto (10-18s) time scale of electron motion. In fact, the attosecond "revolution" is now recognized as one of the most important recent breakthroughs and innovations in the science of the 21st century. A major participant in the development of ultrafast femto and attosecond temporal imaging of molecular quantum phenomena has been theory and numerical simulation of the nonlinear, non-perturbative response of atoms and molecules to ultrashort laser pulses. Therefore, imaging quantum dynamics is a new frontier of science requiring advanced mathematical approaches for analyzing and solving spatial and temporal multidimensional partial differ...
Poulsen, Jens Aage; Nyman, Gunnar; Rossky, Peter J
2006-11-01
The Feynman-Kleinert Linearized Path Integral (FK-LPI) representation of quantum correlation functions is extended in applications and algorithms. Diffusion including quantum effects for a flexible simple point charge model of liquid water is explored, including new tests of internal consistency. An ab initio quantum correction factor (QCF) is also obtained to correct the far-infrared spectrum of water. After correction, a spectrum based on a classical simulation is in good agreement with the experiment. The FK-LPI QCF is shown to be superior to the so-called harmonic QCF. New computational algorithms are introduced so that the quantum Boltzmann Wigner phase-space density, the central object in the implementation, can be obtained for arbitrary potentials. One scheme requires only that the standard classical force routine be replaced when turning from one molecular problem to another. The new algorithms are applied to the calculation of the Van Hove spectrum of liquid He(4) at 27 K. The spectrum moments are in very good agreement with the experiment. These observations indicate that the FK-LPI approach can be broadly effective for molecular problems involving the dynamics of light nuclei.
Energy Technology Data Exchange (ETDEWEB)
Pham, V.T. [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Tavernelli, I. [Ecole Polytechnique Federale de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Milne, C.J.; van der Veen, R.M. [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); D' Angelo, P. [Dipartimento di Chimica, Universita di Roma ' La Sapienza' , Ple A. Moro 5, 00185 Roma (Italy); Bressler, Ch. [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland); Chergui, M., E-mail: Majed.Chergui@epfl.ch [Ecole Polytechnique Federale de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne (Switzerland)
2010-05-25
Graphical abstract: The L{sub 3}-edge EXAFS spectra of aqueous iodide are compared to classical, QM/MM and DFT-based molecular dynamics simulations. The QM/MM simulations reproduce best the experimental data. An anisotropy of the solvation shell is also identified. - Abstract: The L{sub 3} X-ray absorption spectrum of aqueous iodide is reported, and its EXAFS is compared to theoretical spectra reconstructed from the radial distribution function of the iodide hydration obtained from classical, hybrid Quantum Mechanics Molecular Mechanics, (QM/MM) and full quantum (density functional theory, DFT) molecular dynamics simulations. Since EXAFS is mainly sensitive to short distances around the iodide ion, it is a direct probe of the local solvation structure. The comparison shows that QM/MM simulations deliver a satisfactory description of the EXAFS signal, while nonpolarizable classical simulations are somewhat less satisfactory and DFT-based simulations perform poorly. We also identify a weak anisotropy of the water solvation shell around iodide, which may be of importance in electron photoejection experiments.
Ufimtsev, Ivan S; Martinez, Todd J
2009-10-13
We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.
Wang, Qi; Suzuki, Kimichi; Nagashima, Umpei; Tachikawa, Masanori; Yan, Shiwei
2013-06-01
The nuclear quantum effect, which plays important roles on ionic hydrogen bonded structures of Cl-(H2O)n (n = 1-4) clusters, was explored by carrying out path integral molecular dynamic simulations. An outer shell coordinate rl(Cl⋯O) is selected to display the rearrangement of single and multi hydration shell cluster structures. By incorporating the nuclear quantum effect, it is shown that the probability for single shell structures is decreased while the probability for multi shell structures is increased. On the other hand, the correlations between changing of bonded H∗ atom to Cl- (defined as δ) and other cluster vibration coordinates are studied. We have found that δ strongly correlates with proton transfer motion while it has little correlation with ion-water stretching motion. Contrary to θ(H-O-H∗) coordinate, the correlations between δ and other coordinates are decreased by inclusion of nuclear quantum effect. The results indicate that the water-water hydrogen bond interactions are encouraged by quantum simulations.
Quantum dynamical semigroups and applications
Energy Technology Data Exchange (ETDEWEB)
Alicki, R. [Gdansk Univ. (Poland). Inst. of Theoretical Physics and Astrophysics; Lendi, K. [Zuerich Univ. (Switzerland). Inst. of Physical Chemistry
2007-07-01
Reinvigorated by advances and insights, in particular from the active fields of quantum information and computing, the quantum theory of irreversible processes has recently attracted growing attention. This volume introduces the very basic concepts of semigroup dynamics of open quantum systems and reviews a variety of modern applications. The present book, originally published as Vol. 286 (1987) in Lecture in Physics, has been newly typeset, revised and corrected and also expanded to include a review on recent developments. (orig.)
Dynamic molecular graphs: "hopping" structures.
Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María
2014-05-05
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Energy Technology Data Exchange (ETDEWEB)
Ghatee, Mohammad Hadi, E-mail: ghatee@susc.ac.ir; Sedghamiz, Tahereh
2014-12-05
Highlights: • Enantiomeric recognition of Propranolol studied by β-Cyclodextrin complexations. • Complexes characterized by PM3 and molecular dynamics (MD) simulation methods. • Results support more stability of R-enantiomer complex in gas and in aqueous solution phases. • Gas phase complexes are unlikely free-energy-wise, though solution phase’s are more likely. • Higher molecular diffusion in aqueous solution phase is inherent to S-enantiomer. - Abstract: Enantiomeric recognition of Propranolol by complexation with β-Cyclodextrin was studied by PM3 method and molecular dynamics (MD) simulation. Gas phase results show that the R-enantiomer complex is more stable than the S-enantiomer complex by 8.54 kJ/mol (Hartree–Fock energy). Using polarized continuum model, solution phase of R-enantiomer complex was found to be more stable than S-enantiomer complex by 25.95 kJ/mol. Both complexes hardly occur at room temperature free-energy-wise, though, complexation with R-enantiomer is more favorable than with S-enantiomer enthalpy-wise. Also, complexes were studied by molecular dynamics simulation in gas and solution phases. More stability of R-enantiomer complex in gas phase is confirmed by MD van der Waals energy (5.04 kJ/mol) and closely by the counterpart PM3 binding energy (8.54 kJ/mol). Simulation in solution phase indicates more stability of R-enantiomer complex. Finally, simulated transport property provides insight into the high anisotropic atoms motion according to which S-Propranolol found possessing significantly higher dynamics.
Goldstein, Sheldon; Struyve, Ward
2015-01-01
Non-relativistic de Broglie-Bohm theory describes particles moving under the guidance of the wave function. In de Broglie's original formulation, the particle dynamics is given by a first-order differential equation. In Bohm's reformulation, it is given by Newton's law of motion with an extra potential that depends on the wave function—the quantum potential—together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm's formulation of the de Broglie-Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint.
Quantum logic with molecular ions
Wolf, Fabian; Heip, Jan C; Gebert, Florian; Shi, Chunyan; Schmidt, Piet O
2015-01-01
Laser spectroscopy of cold and trapped molecular ions is a powerful tool for fundamental physics, including the determination of fundamental constants, the laboratory test for their possible variation, and the search for a possible electric dipole moment of the electron. Optical clocks based on molecular ions sensitive to some of these effects are expected to achieve uncertainties approaching the $10^{-18}$ level. While the complexity of molecular structure facilitates these applications, the absence of cycling transitions poses a challenge for direct laser cooling, quantum state control, and detection. Previously employed state detection techniques based on photo-dissociation or chemical reactions are destructive and therefore inefficient. Here we experimentally demonstrate non-destructive state detection of a single trapped molecular ion through its strong Coulomb coupling to a well-controlled co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force(ODF) changes the internal state...
Aidas, Kęstutis; Ågren, Hans; Kongsted, Jacob; Laaksonen, Aatto; Mocci, Francesca
2013-02-07
The (23)Na quadrupolar coupling constant of the Na(+) ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na(+) ions in solution are found to differ significantly.
Ito, Hiroshi; Kuwahara, Takuya; Kawaguchi, Kentaro; Higuchi, Yuji; Ozawa, Nobuki; Kubo, Momoji
2016-03-21
We used our etching simulator [H. Ito et al., J. Phys. Chem. C, 2014, 118, 21580-21588] based on tight-binding quantum chemical molecular dynamics (TB-QCMD) to elucidate SiC etching mechanisms. First, the SiC surface is irradiated with SF5 radicals, which are the dominant etchant species in experiments, with the irradiation energy of 300 eV. After SF5 radicals bombard the SiC surface, Si-C bonds dissociate, generating Si-F, C-F, Si-S, and C-S bonds. Then, etching products, such as SiS, CS, SiFx, and CFx (x = 1-4) molecules, are generated and evaporated. In particular, SiFx is the main generated species, and Si atoms are more likely to vaporize than C atoms. The remaining C atoms on SiC generate C-C bonds that may decrease the etching rate. Interestingly, far fewer Si-Si bonds than C-C bonds are generated. We also simulated SiC etching with SF3 radicals. Although the chemical reaction dynamics are similar to etching with SF5 radicals, the etching rate is lower. Next, to clarify the effect of O atom addition on the etching mechanism, we also simulated SiC etching with SF5 and O radicals/atoms. After bombardment with SF5 radicals, Si-C bonds dissociate in a similar way to the etching without O atoms. In addition, O atoms generate many C-O bonds and COy (y = 1-2) molecules, inhibiting the generation of C-C bonds. This indicates that O atom addition improves the removal of C atoms from SiC. However, for a high O concentration, many C-C and Si-Si bonds are generated. When the O atoms dissociate the Si-C bonds and generate dangling bonds, the O atoms terminate only one or two dangling bonds. Moreover, at high O concentrations there are fewer S and F atoms to terminate the dangling bonds than at low O concentration. Therefore, few dangling bonds of dissociated Si and C atoms are terminated, and they form many Si-Si and C-C bonds. Furthermore, we propose that the optimal O concentration is 50-60% because both Si and C atoms generate many etching products producing fewer C
Li, Yongle; Suleimanov, Yury V; Green, William H; Guo, Hua
2014-03-20
Thermal rate coefficients and kinetic isotope effect have been calculated for prototypical heavy-light-heavy polyatomic bimolecular reactions Cl + CH4/CD4 → HCl/DCl + CH3/CD3, using a recently proposed quantum dynamics approach: ring polymer molecular dynamics (RPMD). Agreement with experimental rate coefficients, which are quite scattered, is satisfactory. However, differences up to 50% have been found between the RPMD results and those obtained from the harmonic variational transition-state theory on one of the two full-dimensional potential energy surfaces used in the calculations. Possible reasons for such discrepancy are discussed. The present work is an important step in a series of benchmark studies aimed at assessing accuracy for RPMD for chemical reaction rates, which demonstrates that this novel method is a quite reliable alternative to previously developed techniques based on transition-state theory.
Kishi, Ryohei; Nakano, Masayoshi
2011-04-21
A novel method for the calculation of the dynamic polarizability (α) of open-shell molecular systems is developed based on the quantum master equation combined with the broken-symmetry (BS) time-dependent density functional theory within the Tamm-Dancoff approximation, referred to as the BS-DFTQME method. We investigate the dynamic α density distribution obtained from BS-DFTQME calculations in order to analyze the spatial contributions of electrons to the field-induced polarization and clarify the contributions of the frontier orbital pair to α and its density. To demonstrate the performance of this method, we examine the real part of dynamic α of singlet 1,3-dipole systems having a variety of diradical characters (y). The frequency dispersion of α, in particular in the resonant region, is shown to strongly depend on the exchange-correlation functional as well as on the diradical character. Under sufficiently off-resonant condition, the dynamic α is found to decrease with increasing y and/or the fraction of Hartree-Fock exchange in the exchange-correlation functional, which enhances the spin polarization, due to the decrease in the delocalization effects of π-diradical electrons in the frontier orbital pair. The BS-DFTQME method with the BHandHLYP exchange-correlation functional also turns out to semiquantitatively reproduce the α spectra calculated by a strongly correlated ab initio molecular orbital method, i.e., the spin-unrestricted coupled-cluster singles and doubles.
Ghatee, Mohammad Hadi; Sedghamiz, Tahereh
2014-12-01
Enantiomeric recognition of Propranolol by complexation with β-Cyclodextrin was studied by PM3 method and molecular dynamics (MD) simulation. Gas phase results show that the R-enantiomer complex is more stable than the S-enantiomer complex by 8.54 kJ/mol (Hartree-Fock energy). Using polarized continuum model, solution phase of R-enantiomer complex was found to be more stable than S-enantiomer complex by 25.95 kJ/mol. Both complexes hardly occur at room temperature free-energy-wise, though, complexation with R-enantiomer is more favorable than with S-enantiomer enthalpy-wise. Also, complexes were studied by molecular dynamics simulation in gas and solution phases. More stability of R-enantiomer complex in gas phase is confirmed by MD van der Waals energy (5.04 kJ/mol) and closely by the counterpart PM3 binding energy (8.54 kJ/mol). Simulation in solution phase indicates more stability of R-enantiomer complex. Finally, simulated transport property provides insight into the high anisotropic atoms motion according to which S-Propranolol found possessing significantly higher dynamics.
Dissipative Dynamics of Quantum Fluctuations
Benatti, F; Floreanini, R
2015-01-01
One way to look for complex behaviours in many-body quantum systems is to let the number $N$ of degrees of freedom become large and focus upon collective observables. Mean-field quantities scaling as $1/N$ tend to commute, whence complexity at the quantum level can only be inherited from complexity at the classical level. Instead, fluctuations of microscopic observables scale as $1/\\sqrt{N}$ and exhibit collective Bosonic features, typical of a mesoscopic regime half-way between the quantum one at the microscopic level and the classical one at the level of macroscopic averages. Here, we consider the mesoscopic behaviour emerging from an infinite quantum spin chain undergoing a microscopic dissipative, irreversible dynamics and from global states without long-range correlations and invariant under lattice translations and dynamics. We show that, from the fluctuations of one site spin observables whose linear span is mapped into itself by the dynamics, there emerge bosonic operators obeying a mesoscopic dissipa...
DEFF Research Database (Denmark)
Aidas, Kestutis; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob
2013-01-01
Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores—acridine yellow and proflavin—located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site....... The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted...
Nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
Quantum Control of Molecular Processes
Shapiro, Moshe
2012-01-01
Written by two of the world's leading researchers in the field, this is a systematic introduction to the fundamental principles of coherent control, and to the underlying physics and chemistry.This fully updated second edition is enhanced by 80% and covers the latest techniques and applications, including nanostructures, attosecond processes, optical control of chirality, and weak and strong field quantum control. Developments and challenges in decoherence-sensitive condensed phase control as well as in bimolecular control are clearly described.Indispensable for atomic, molecular and chemical
Dynamical evaporation of quantum horizons
Pranzetti, Daniele
2013-01-01
We describe the black hole evaporation process driven by the dynamical evolution of the quantum gravitational degrees of freedom resident at the horizon, as identified by the Loop Quantum Gravity kinematics. Using a parallel with the Brownian motion, we interpret the first law of quantum dynamical horizon in terms of a fluctuation-dissipation relation applied to this fundamental discrete structure. In this way, the horizon evolution is described in terms of relaxation to an equilibrium state balanced by the excitation of Planck scale constituents of the horizon. We investigate the final stage of the evaporation process and show how, from this setting, the emergence of several conservative scenarios for the information paradox can be microscopically derived. Namely, the leakage of part of the horizon quantum geometry information prior to the Planckian phase and the stabilization of the hole surface shrinkage forming a massive remnant, which can eventually decay, are described.
Khavani, Mohammad; Izadyar, Mohammad; Housaindokht, Mohammad Reza
2015-10-14
In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.
Energy Technology Data Exchange (ETDEWEB)
Chiba, Satoshi; Niita, Koji; Fukahori, Tokio; Maruyama, Tomoyuki; Maruyama, Toshiki; Iwamoto, Akira [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment
1997-05-01
Energy dependence of the ratio of the isovector and isoscalar strengths in the imaginary part of the nucleon optical model potential at the medium energy range was extracted from an analysis of proton and neutron induced total reaction cross sections on {sup 11}Li with a theoretical framework called quantum molecular dynamics (QMD). The isovector/isoscalar ratio was found to be about 0.8 at 100 MeV, and decreased almost linearly in log(E) to 0 at several hundred MeV. This result was consistent with an estimate at lower energy, and was also in good accord with the values used by Kozack and Madland for the analysis of nucleon + {sup 208}Pb reactions. (author)
Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad
2015-02-15
The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported.
Polymer friction Molecular Dynamics
DEFF Research Database (Denmark)
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....
Nonlinear Dynamics In Quantum Physics -- Quantum Chaos and Quantum Instantons
Kröger, H.
2003-01-01
We discuss the recently proposed quantum action - its interpretation, its motivation, its mathematical properties and its use in physics: quantum mechanical tunneling, quantum instantons and quantum chaos.
Nonlinear Dynamics In Quantum Physics -- Quantum Chaos and Quantum Instantons
Kröger, H.
2003-01-01
We discuss the recently proposed quantum action - its interpretation, its motivation, its mathematical properties and its use in physics: quantum mechanical tunneling, quantum instantons and quantum chaos.
Quantum Computation and Quantum Spin Dynamics
Raedt, Hans De; Michielsen, Kristel; Hams, Anthony; Miyashita, Seiji; Saito, Keiji
2001-01-01
We analyze the stability of quantum computations on physically realizable quantum computers by simulating quantum spin models representing quantum computer hardware. Examples of logically identical implementations of the controlled-NOT operation are used to demonstrate that the results of a quantum
Quantum Computation and Quantum Spin Dynamics
Raedt, Hans De; Michielsen, Kristel; Hams, Anthony; Miyashita, Seiji; Saito, Keiji
2001-01-01
We analyze the stability of quantum computations on physically realizable quantum computers by simulating quantum spin models representing quantum computer hardware. Examples of logically identical implementations of the controlled-NOT operation are used to demonstrate that the results of a quantum
Dundas, Daniel
2012-05-21
A mixed quantum-classical approach is introduced which allows the dynamical response of molecules driven far from equilibrium to be modeled. This method is applied to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations are possible. The approach is applied to the study of high harmonic generation in N(2) and benzene using linearly polarized laser pulses and, to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N(2) an enhancement of the cut-off harmonics is observed whenever the laser polarization is aligned perpendicular to the molecular axis. This enhancement is attributed to the symmetry properties of the Kohn-Sham orbital that responds predominantly to the pulse. In benzene we predict that a suppression in the cut-off harmonics occurs whenever the laser polarization is aligned parallel to the molecular plane. We attribute this suppression to the symmetry-induced response of the highest-occupied molecular orbital.
Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J
2016-03-21
We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.
Izadyar, Mohammad; Khavani, Mohammad; Housaindokht, Mohammad Reza
2015-05-07
Molecular dynamic simulations were performed to investigate the stability of heterocyclic peptide nanotubes composed of 1,4-disubstituted-1,2,3-triazol ε-amino acid. 45 ns MD simulations were conducted on the cyclic peptide nanotube (CPNT) and cyclic peptide dimer in methanol, chloroform, and water and revealed that these structures are more stable in nonpolar solvents. MM-PBSA and MM-GBSA calculations were employed to analyze the solvent effect on the stability and length of the CPNT. These calculations showed that CPNT in chloroform was more stable and longer as compared to other solvents. In addition, the effect of the guest molecule (ethanol) inside the dimer and CPNT was investigated. The obtained results confirmed that guest molecule(s) stabilized the dimer and CPNT in all solvents. Quantum chemistry calculations on the cyclic peptide dimer were performed at the M06-2X/6-31G(d) level in the gas phase and three solvents. The obtained results from the quantum chemistry study were in good agreement with the MD simulation results. DFT calculations showed that the guest molecule stabilized the dimer structure and electrostatically interacted with the cyclic peptide dimer. Finally, for investigation of the solvent effects on the hydrogen bonds of the cyclic peptide dimer, NBO and AIM analysis were performed.
Dynamical quantum phase transitions (Review Article)
Zvyagin, A. A.
2016-11-01
During recent years the interest to dynamics of quantum systems has grown considerably. Quantum many body systems out of equilibrium often manifest behavior, different from the one predicted by standard statistical mechanics and thermodynamics in equilibrium. Since the dynamics of a many-body quantum system typically involve many excited eigenstates, with a non-thermal distribution, the time evolution of such a system provides an unique way for investigation of non-equilibrium quantum statistical mechanics. Last decade such new subjects like quantum quenches, thermalization, pre-thermalization, equilibration, generalized Gibbs ensemble, etc. are among the most attractive topics of investigation in modern quantum physics. One of the most interesting themes in the study of dynamics of quantum many-body systems out of equilibrium is connected with the recently proposed important concept of dynamical quantum phase transitions. During the last few years a great progress has been achieved in studying of those singularities in the time dependence of characteristics of quantum mechanical systems, in particular, in understanding how the quantum critical points of equilibrium thermodynamics affect their dynamical properties. Dynamical quantum phase transitions reveal universality, scaling, connection to the topology, and many other interesting features. Here we review the recent achievements of this quickly developing part of low-temperature quantum physics. The study of dynamical quantum phase transitions is especially important in context of their connection to the problem of the modern theory of quantum information, where namely non-equilibrium dynamics of many-body quantum system plays the major role.
Substructured multibody molecular dynamics.
Energy Technology Data Exchange (ETDEWEB)
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Aseev, Oleg; Perez, Marta A S; Rothlisberger, Ursula; Rizzo, Thomas R
2015-07-02
Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) sequence. Some of these fragments may experience a "head-to-tail" cyclization, which after proton migration, can lead to the cyclic structure opening in a different place than the initially formed bond. This process leads to AA sequence scrambling that may hinder sequencing of the initial peptide. Here we combine cryogenic ion spectroscopy and ab initio molecular dynamics simulations to isolate and characterize the precise structures of key intermediates in the scrambling process. The most stable peptide fragments show intriguing symmetric cyclic structures in which the proton is situated on a C2 symmetry axis and forms exceptionally short H-bonds (1.20 Å) with two backbone oxygens. Other nonsymmetric cyclic structures also exist, one of which is protonated on the amide nitrogen, where ring opening is likely to occur.
Molecular Dynamics for Dense Matter
Maruyama, Toshiki; Chiba, Satoshi
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...
Dynamical quantum teleportation
Energy Technology Data Exchange (ETDEWEB)
Muschik, Christine [ICFO-Institut de Ciencies Fotoniques (Spain); Polzik, Eugene [Niels Bohr Institute (Denmark); Cirac, Ignacio [Max-Planck-Institute (Germany)
2013-07-01
We introduce two protocols for inducing non-local dynamics between two separate parties. The first scheme allows for the engineering of an interaction between the two remote systems, while the second protocol induces a dynamics in one of the parties, which is controlled by the other one. Both schemes apply to continuous variable systems, run continuously in time and are based on instantaneous feedback.
Quantum Phase Analysis of Field-Free Molecular Alignment
Yun, Sang Jae; Lee, Jongmin; Nam, Chang Hee
2015-01-01
We present quantum mechanical explanations for unresolved phenomena observed in field-free molecular alignment by a femtosecond laser pulse. Quantum phase analysis of molecular rotational states reveals the physical origin of the following phenomena: strong alignment peaks appear periodically, and the temporal shape of each alignment peak changes in an orderly fashion depending on molecular species; the strongest alignment is not achieved at the first peak; the transition between aligned and anti-aligned states is very fast compared to the time scale of rotational dynamics. These features are understood in a unified way analogous to that describing a carrier-envelope-phase-stabilized mode-locked laser.
Simulated Quantum Computation of Molecular Energies
Aspuru-Guzik, A; Love, P J; Head-Gordon, M; Aspuru-Guzik, Al\\'an; Dutoi, Anthony D.; Love, Peter J.; Head-Gordon, Martin
2005-01-01
The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical interest using modest numbers of quantum bits. Calculations of the water and lithium hydride molecular ground-state energies have been carried out on a quantum computer simulator using a recursive phase-estimation algorithm. The recursive algorithm reduces the number of quantum bits required for the readout register from about 20 to 4. Mappings of the molecular wave function to the quantum bits are described. An adiabatic method for the preparation of a good approximate ground-state wave function is described and demonstrated for a stretched hydrogen molecule. The number of quantum bits required scales linearly with the number of basis functions, and the number of gates required grows polynomially with the number of quantum bits.
A quantum spin-probe molecular microscope
Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L.C.L.
2016-01-01
Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy. PMID:27725630
A quantum spin-probe molecular microscope
Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.
2016-10-01
Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.
Shkrob, I A; Larsen, R E; Schwartz, B J; Glover, William J.; Larsen, Ross E.; Schwartz, Benjamin J.; Shkrob, Ilya A.
2006-01-01
Adiabatic mixed quantum/classical molecular dynamics simulations were used to generate snapshots of the hydrated electron (e-) in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the e- were extracted from these simulations and embedded in a matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory and single-excitation configuration interaction methods were then applied to these embedded clusters. The salient feature of these hybrid calculations is significant transfer (ca. 0.18) of the excess electron's charge density into the O 2p orbitals in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfc) tensors, and the IR and Raman spectra of the e-. The calculated hfc tensors were used to compute the EPR and ESEEM spectra for the ...
Quantum dynamics in open quantum-classical systems.
Kapral, Raymond
2015-02-25
Often quantum systems are not isolated and interactions with their environments must be taken into account. In such open quantum systems these environmental interactions can lead to decoherence and dissipation, which have a marked influence on the properties of the quantum system. In many instances the environment is well-approximated by classical mechanics, so that one is led to consider the dynamics of open quantum-classical systems. Since a full quantum dynamical description of large many-body systems is not currently feasible, mixed quantum-classical methods can provide accurate and computationally tractable ways to follow the dynamics of both the system and its environment. This review focuses on quantum-classical Liouville dynamics, one of several quantum-classical descriptions, and discusses the problems that arise when one attempts to combine quantum and classical mechanics, coherence and decoherence in quantum-classical systems, nonadiabatic dynamics, surface-hopping and mean-field theories and their relation to quantum-classical Liouville dynamics, as well as methods for simulating the dynamics.
Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi
2017-10-01
Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.
Ohta, Yasuhito; Okamoto, Yoshiko; Page, Alister J; Irle, Stephan; Morokuma, Keiji
2009-11-24
The atomic scale details of single-walled carbon nanotube (SWNT) nucleation on metal catalyst particles are elusive to experimental observations. Computer simulation of metal-catalyzed SWNT nucleation is a challenging topic but potentially of great importance to understand the factors affecting SWNT diameters, chirality, and growth efficiency. In this work, we use nonequilibrium density functional tight-binding molecular dynamics simulations and report nucleation of sp(2)-carbon cap structures on an iron particle consisting of 38 atoms. One C(2) molecule was placed every 1.0 ps around an Fe(38) cluster for 30 ps, after which a further 410 ps of annealing simulation without carbon supply was performed. We find that sp(2)-carbon network nucleation and annealing processes occur in three sequential and repetitive stages: (A) polyyne chains on the metal surface react with each other to evolve into a Y-shaped polyyne junction, which preferentially form a five-membered ring as a nucleus; (B) polyyne chains on the first five-membered ring form an additional fused five- or six-membered ring; and (C) pentagon-to-hexagon self-healing rearrangement takes place with the help of short-lived polyyne chains, stabilized by the mobile metal atoms. The observed nucleation process resembles the formation of a fullerene cage. However, the metal particle plays a key role in differentiating the nucleation process from fullerene cage formation, most importantly by keeping the growing cap structure from closing into a fullerene cage and by keeping the carbon edge "alive" for the addition of new carbon material.
Voityuk, Alexander A.
2008-03-01
The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15ns MD trajectories for several DNA oligomers, we calculate the average coupling squares ⟨V2⟩ and the energies of basepair triplets XG +Y and XA +Y, where X, Y =G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B-DNA structure and show that in several important cases the couplings calculated for the idealized B-DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ˜0.07eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The XG +Y are by 0.5eV more stable than XA +Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA.
Voityuk, Alexander A
2008-03-21
The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the pi stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares V(2) and the energies of basepair triplets XG(+)Y and XA(+)Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15,000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B-DNA structure and show that in several important cases the couplings calculated for the idealized B-DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, approximately 0.07 eV, while the interstrand couplings are quite different. The energies of hole states G(+) and A(+) in the stack depend on the nature of the neighboring pairs. The XG(+)Y are by 0.5 eV more stable than XA(+)Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA.
Dephasing of quantum tunnelling in molecular nanomagnets
Institute of Scientific and Technical Information of China (English)
Zhang Shu-Qun; Chen Zhi-De
2008-01-01
Dephasing mechanism of quantum tunnelling in molecular magnets has been studied by means of the spin-coherentstate path integral in a mean field approximation. It is found that the fluctuating uncompensated transverse field from the dipolar-dipolar interaction between molecular magnets contributes a random phase to the quantum interference phase. The resulting transition rate is determined by the average tunnel splitting over the random phase. Such a dephasing process leads to the suppression of quenching due to the quantum phase interference, and to the steps due to odd resonances in hysteresis loop survived, which is in good agreement with experimental observations in molecular nanomagnets Fee and Mn12.
Logical entropy of quantum dynamical systems
Directory of Open Access Journals (Sweden)
Ebrahimzadeh Abolfazl
2016-01-01
Full Text Available This paper introduces the concepts of logical entropy and conditional logical entropy of hnite partitions on a quantum logic. Some of their ergodic properties are presented. Also logical entropy of a quantum dynamical system is dehned and ergodic properties of dynamical systems on a quantum logic are investigated. Finally, the version of Kolmogorov-Sinai theorem is proved.
Theory of controlled quantum dynamics
De Martino, S; Illuminati, F; Martino, Salvatore De; Siena, Silvio De; Illuminati, Fabrizio
1997-01-01
We introduce a general formalism, based on the stochastic formulation of quantum mechanics, to obtain localized quasi-classical wave packets as dynamically controlled systems, for arbitrary anharmonic potentials. The control is in general linear, and it amounts to introduce additional quadratic and linear time-dependent terms to the given potential. In this way one can construct for general systems either coherent packets moving with constant dispersion, or dynamically squeezed packets whose spreading remains bounded for all times. In the standard operatorial framework our scheme corresponds to a suitable generalization of the displacement and scaling operators that generate the coherent and squeezed states of the harmonic oscillator.
Scalable Quantum Simulation of Molecular Energies
O'Malley, P J J; Kivlichan, I D; Romero, J; McClean, J R; Barends, R; Kelly, J; Roushan, P; Tranter, A; Ding, N; Campbell, B; Chen, Y; Chen, Z; Chiaro, B; Dunsworth, A; Fowler, A G; Jeffrey, E; Megrant, A; Mutus, J Y; Neill, C; Quintana, C; Sank, D; Vainsencher, A; Wenner, J; White, T C; Coveney, P V; Love, P J; Neven, H; Aspuru-Guzik, A; Martinis, J M
2015-01-01
We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. We use a programmable array of superconducting qubits to compute the energy surface of molecular hydrogen using two distinct quantum algorithms. First, we experimentally execute the unitary coupled cluster method using the variational quantum eigensolver. Our efficient implementation predicts the correct dissociation energy to within chemical accuracy of the numerically exact result. Next, we experimentally demonstrate the canonical quantum algorithm for chemistry, which consists of Trotterization and quantum phase estimation. We compare the experimental performance of these approaches to show clear evidence that the variational quantum eigensolver is robust to certain errors, inspiring hope that quantum simulation of classically intractable molecules may be viable in the near future.
Dynamical memory effects in correlated quantum channels
Addis, Carole; Karpat, Göktuǧ; Macchiavello, Chiara; Maniscalco, Sabrina
2016-09-01
Memory effects play a fundamental role in the study of the dynamics of open quantum systems. There exist two conceptually distinct notions of memory discussed for quantum channels in the literature. In quantum information theory quantum channels with memory are characterized by the existence of correlations between successive applications of the channel on a sequence of quantum systems. In open quantum systems theory memory effects arise dynamically during the time evolution of quantum systems and define non-Markovian dynamics. Here we relate and combine these two different concepts of memory. In particular, we study the interplay between correlations between multiple uses of quantum channels and non-Markovianity as nondivisibility of the t -parametrized family of channels defining the dynamical map.
Quantum dynamics as a physical resource
Nielsen, M A; Dodd, J L; Gilchrist, A; Mortimer, D; Osborne, T J; Bremner, M J; Harrow, A W; Hines, A; Nielsen, Michael A.; Dawson, Christopher M.; Dodd, Jennifer L.; Gilchrist, Alexei; Mortimer, Duncan; Osborne, Tobias J.; Bremner, Michael J.; Harrow, Aram W.; Hines, Andrew
2003-01-01
How useful is a quantum dynamical operation for quantum information processing? Motivated by this question we investigate several strength measures quantifying the resources intrinsic to a quantum operation. We develop a general theory of such strength measures, based on axiomatic considerations independent of state-based resources. The power of this theory is demonstrated with applications to quantum communication complexity, quantum computational complexity, and entanglement generation by unitary operations.
State-to-state dynamics of molecular energy transfer
Energy Technology Data Exchange (ETDEWEB)
Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)
1993-12-01
The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.
Ferrara, Ph; Curioni, A; Vangrevelinghe, E; Meyer, T; Mordasini, T; Andreoni, W; Acklin, P; Jacoby, E
2006-01-01
A recently introduced new methodology based on ultrashort (50-100 ps) molecular dynamics simulations with a quantum-refined force-field (QRFF-MD) is here evaluated in its ability both to predict protein-ligand binding affinities and to discriminate active compounds from inactive ones. Physically based scoring functions are derived from this approach, and their performance is compared to that of several standard knowledge-based scoring functions. About 40 inhibitors of cyclin-dependent kinase 2 (CDK2) representing a broad chemical diversity were considered. The QRFF-MD method achieves a correlation coefficient, R(2), of 0.55, which is significantly better than that obtained by a number of traditional approaches in virtual screening but only slightly better than that obtained by consensus scoring (R(2) = 0.50). Compounds from the Available Chemical Directory, along with the known active compounds, were docked into the ATP binding site of CDK2 using the program Glide, and the 650 ligands from the top scored poses were considered for a QRFF-MD analysis. Combined with structural information extracted from the simulations, the QRFF-MD methodology results in similar enrichment of known actives compared to consensus scoring. Moreover, a new scoring function is introduced that combines a QRFF-MD based scoring function with consensus scoring, which results in substantial improvement on the enrichment profile.
Indian Academy of Sciences (India)
ALEXANDER M ANDRIANOV; IVAN A KASHYN; VIKTOR M ANDRIANOV; MAKSIM B SHUNDALAU; ANTON V HLINISTY; SERGEY V GAPONENKO; ELENA V SHABUNYA -KLYACHKOVSKAYA; ANNA MATSUKOVICH; ABDUL-MALEK S AL- TAMIMI; ALI A EL- EMAM
2016-12-01
The molecular dynamics simulations of the structure of the N'-(adamantan-2-ylidene)benzohydrazide followed by the quantum chemical calculations at the DFT level of theory have identified four stable conformers of this potential antibacterial agent in solution: one “central” cis- and three (“central”, “left” and “right”) trans-conformers. The UV-Vis absorption spectrum in the 220–320 nm region in the ethanol solution reveals two bands that can be primarily explained based on the ab initio calculations of the spectral characteristics of the “side” trans-conformers at the MRPT level of theory. However, the close energy values for thecalculated cis- S₁ ← S₀ and “side” trans- S₂ ← S₀ transitions cannot exclude the presence of cis-conformer in solution. Therefore, the data obtained show that the coexistence of both trans-conformers and cis-conformer should be taken into consideration when studying the pharmaceutical properties of the title molecule.
Simulation and understanding of atomic and molecular quantum crystals
Cazorla, Claudio; Boronat, Jordi
2017-07-01
Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.
Quantum Interactomics and Cancer Molecular Mechanisms: I. Report Outline
Baianu, I C
2004-01-01
Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quant...
Bead-Fourier path integral molecular dynamics
Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto
2003-06-01
Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.
Quantum dynamics in dual spaces
Energy Technology Data Exchange (ETDEWEB)
Sudarshan, E.C.G.
1993-12-31
Quantum mechanics gives us information about spectra of dynamical variables and transition rates including scattering cross sections. They can be exhibited as spectral information in analytically continued spaces and their duals. Quantum mechanics formulated in these generalized spaces is used to study scattering and time evolution. It is shown that the usual asymptotic condition is inadequate to deal with scattering of composite or unstable particles. Scattering theory needs amendment when the interacting system is not isospectral with the free Hamiltonian, and the amendment is formulated. Perturbation theory in generalized spaces is developed and used to study the deletion and augmentation of the spectrum of the Hamiltonian. A complete set of algebraically independent constants for an interacting system is obtained. The question of the breaking of time symmetry is discussed.
Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun
2011-05-14
We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.
Dynamical quenching of tunneling in molecular magnets
Energy Technology Data Exchange (ETDEWEB)
José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)
2015-12-15
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.
In the crystal structure of cellulose Ibeta, disordered hydrogen (H) bonding can be represented by the average of two mutually exclusive H bonding schemes that have been designated A and B. An unanswered question is whether A and B interconvert dynamically, or whether they are static but present in ...
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano
2016-09-13
We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.
Quantum electron-vibrational dynamics at finite temperature: Thermo field dynamics approach
Borrelli, Raffaele; Gelin, Maxim F.
2016-12-01
Quantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on the thermo field dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. A comparison with the theoretically equivalent density matrix formulation shows the key numerical advantages of the present approach. The solution of thermo field dynamics equations with a novel technique for the propagation of tensor trains (matrix product states) is discussed. Numerical applications to model spin-boson systems show that the present approach is a promising tool for the description of quantum dynamics of complex molecular systems at finite temperature.
Theory of controlled quantum dynamics
Energy Technology Data Exchange (ETDEWEB)
De Martino, Salvatore; De Siena, Silvio; Illuminati, Fabrizio [Dipartimento di Fisica, Universita di Salerno, and INFN, Sezione di Napoli, Gruppo collegato di Salerno, Baronissi (Italy)
1997-06-07
We introduce a general formalism to obtain localized quantum wavepackets as dynamically controlled systems, in the framework of Nelson stochastic quantization. We show that in general the control is linear, and it amounts to introducing additional time-dependent terms in the potential. In this way one can construct for general systems either coherent packets following classical motion with constant dispersion, or coherent packets following classical motion whose time-dependent dispersion remains bounded for all times. We show that in the operatorial language our scheme amounts to introducing a suitable generalization to arbitrary potentials of the displacement and scaling operators that generate the coherent and squeezed states of the harmonic oscillator. (author)
Classical Dynamics of Quantum Entanglement
Casati, Giulio; Reslen, Jose
2011-01-01
We numerically analyze the dynamical generation of quantum entanglement in a system of 2 interacting particles, started in a coherent separable state, for decreasing values of $\\hbar$. As $\\hbar\\to 0$ the entanglement entropy, computed at any finite time, converges to a finite nonzero value, that can be reproduced by purely classical computations. The limiting classical law which rules the time dependence of entropy is different in the integrable and in the chaotic case, and its general qualitative and quantitative features may be explained by simple heuristic arguments.
Quantum Transport Through Tunable Molecular Diodes
Obodo, Joshua Tobechukwu
2017-07-31
Employing self-interaction corrected density functional theory combined with the non-equilibrium Green\\'s function method, we study the quantum transport through molecules with different numbers of phenyl (donor) and pyrimidinyl (acceptor) rings in order to evaluate the effects of the molecular composition on the transport properties. Excellent agreement with the results of recent experiments addressing the rectification behavior of molecular junctions is obtained, which demonstrates the potential of quantum transport simulations for designing high performance junctions by tuning the molecular specifications.
Quantum coherence in the dynamical Casimir effect
Samos-Sáenz de Buruaga, D. N.; Sabín, Carlos
2017-02-01
We propose to use quantum coherence as the ultimate proof of the quantum nature of the radiation that appears by means of the dynamical Casimir effect in experiments with superconducting microwave waveguides. We show that, unlike previously considered measurements such as entanglement and discord, quantum coherence does not require a threshold value of the external pump amplitude and is highly robust to thermal noise.
Model dynamics for quantum computing
Tabakin, Frank
2017-08-01
A model master equation suitable for quantum computing dynamics is presented. In an ideal quantum computer (QC), a system of qubits evolves in time unitarily and, by virtue of their entanglement, interfere quantum mechanically to solve otherwise intractable problems. In the real situation, a QC is subject to decoherence and attenuation effects due to interaction with an environment and with possible short-term random disturbances and gate deficiencies. The stability of a QC under such attacks is a key issue for the development of realistic devices. We assume that the influence of the environment can be incorporated by a master equation that includes unitary evolution with gates, supplemented by a Lindblad term. Lindblad operators of various types are explored; namely, steady, pulsed, gate friction, and measurement operators. In the master equation, we use the Lindblad term to describe short time intrusions by random Lindblad pulses. The phenomenological master equation is then extended to include a nonlinear Beretta term that describes the evolution of a closed system with increasing entropy. An external Bath environment is stipulated by a fixed temperature in two different ways. Here we explore the case of a simple one-qubit system in preparation for generalization to multi-qubit, qutrit and hybrid qubit-qutrit systems. This model master equation can be used to test the stability of memory and the efficacy of quantum gates. The properties of such hybrid master equations are explored, with emphasis on the role of thermal equilibrium and entropy constraints. Several significant properties of time-dependent qubit evolution are revealed by this simple study.
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Quantum emitters dynamically coupled to a quantum field
Energy Technology Data Exchange (ETDEWEB)
Acevedo, O. L.; Quiroga, L.; Rodríguez, F. J. [Departamento de Física, Universidad de los Andes, A.A. 4976, Bogotá (Colombia); Johnson, N. F. [Department of Physics, University of Miami, Coral Gables, Miami, FL 33124 (United States)
2013-12-04
We study theoretically the dynamical response of a set of solid-state quantum emitters arbitrarily coupled to a single-mode microcavity system. Ramping the matter-field coupling strength in round trips, we quantify the hysteresis or irreversible quantum dynamics. The matter-field system is modeled as a finite-size Dicke model which has previously been used to describe equilibrium (including quantum phase transition) properties of systems such as quantum dots in a microcavity. Here we extend this model to address non-equilibrium situations. Analyzing the system’s quantum fidelity, we find that the near-adiabatic regime exhibits the richest phenomena, with a strong asymmetry in the internal collective dynamics depending on which phase is chosen as the starting point. We also explore signatures of the crossing of the critical points on the radiation subsystem by monitoring its Wigner function; then, the subsystem can exhibit the emergence of non-classicality and complexity.
Quantum emitters dynamically coupled to a quantum field
Acevedo, O. L.; Quiroga, L.; Rodríguez, F. J.; Johnson, N. F.
2013-12-01
We study theoretically the dynamical response of a set of solid-state quantum emitters arbitrarily coupled to a single-mode microcavity system. Ramping the matter-field coupling strength in round trips, we quantify the hysteresis or irreversible quantum dynamics. The matter-field system is modeled as a finite-size Dicke model which has previously been used to describe equilibrium (including quantum phase transition) properties of systems such as quantum dots in a microcavity. Here we extend this model to address non-equilibrium situations. Analyzing the system's quantum fidelity, we find that the near-adiabatic regime exhibits the richest phenomena, with a strong asymmetry in the internal collective dynamics depending on which phase is chosen as the starting point. We also explore signatures of the crossing of the critical points on the radiation subsystem by monitoring its Wigner function; then, the subsystem can exhibit the emergence of non-classicality and complexity.
Liouville-von Neumann molecular dynamics
Jakowski, Jacek; Morokuma, Keiji
2009-06-01
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.
Macroscopic Quantum Coherence in Antiferromagnetic Molecular Magnets
Institute of Scientific and Technical Information of China (English)
HU Hui; LO Rong; ZHU Jia-Lin; XIONG Jia-Jiong
2001-01-01
The macroscopic quantum coherence in a biaxial antiferromagnetic molecular magnet in the presence of magnetic field acting parallel to its hard anisotropy axis is studied within the two-sublattice model. On the basis of instanton technique in the spin-coherent-state path-integral representation, both the rigorous Wentzel-Kramers-Brillouin exponent and pre-exponential factor for the ground-state tunnel splitting are obtained. We find that the quantum fluctuations around the classical paths can not only induce a new quantum phase previously reported by Chiolero and Loss (Phys. Rev. Lett. 80 (1998) 169), but also have great influence on the intensity of the ground-state tunnel splitting. Those features clearly have no analogue in the ferromagnetic molecular magnets. We suggest that they may be the universal behaviors in all antiferromagnetic molecular magnets. The analytical results are complemented by exact diagonalization calculation.
Macroscopic Quantum Coherence in Antiferromagnetic Molecular Magnets
Institute of Scientific and Technical Information of China (English)
HUHui; LURong; 等
2001-01-01
The macroscopic quantum coherence in a biaxial antiferromagnetic molecular magnet in the presence of magnetic field acting parallel to its hard anisotropy axis is studied within the two-sublattice model.On the basis of instanton technique in the spin-coherent-state path-integral representation,both the rigorous Wentzel-Kramers-Brillouin exponent and pre-exponential factor for the ground-state tunnel splitting are obtained.We find that the quantum fluctuations around the classical paths can not only induce a new quantum phase previously reported by Chiolero and Loss (Phys.Rev.Lett.80(1998)169),but also have great influence on the intensity of the ground-state tunnel splitting.Those features clearly have no analogue in the ferromagnetic molecular magnets.We suggest that they may be the universal behaviors in all antiferromagnetic molecular magnets.The analytical results are complemented by exact diagonalization calculation.
Molecular Dynamics and Protein Function
National Research Council Canada - National Science Library
M. Karplus; J. Kuriyan; Bruce J. Berne
2005-01-01
.... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...
Shkrob, Ilya A; Glover, William J; Larsen, Ross E; Schwartz, Benjamin J
2007-06-21
Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess
Energy Technology Data Exchange (ETDEWEB)
Shkrob, I. A.; Glover, W. J.; Larsen, R. E.; Schwartz, B. J.; Chemistry; Univ. of California at Los Angeles
2007-06-21
Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Angstrom x 18 Angstrom x 18 Angstrom matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer ({approx}18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not
Recombination Dynamics in Quantum Well Semiconductor Structures
Fouquet, Julie Elizabeth
Time-resolved and time-integrated photoluminescence as a function of excitation energy density have been observed in order to study recombination dynamics in GaAs/Al(,x)Ga(,1 -x)As quantum well structures. The study of room temperature photoluminescence from the molecular beam epitaxy (MBE) -grown multiple quantum well structure and photoluminescence peak energy as a function of tem- perature shows that room temperature recombination at excitation densities above the low 10('16) cm('-3) level is due to free carriers, not excitons. This is the first study of time-resolved photoluminescence of impurities in quantum wells; data taken at different emission wave- lengths at low temperatures shows that the impurity-related states at photon energies lower than the free exciton peaks luminesce much more slowly than the free exciton states. Results from a similar structure grown by metal -organic chemical vapor deposition (MOCVD) are explained by saturation of traps. An unusual increase in decay rate observed tens of nanoseconds after excitation is probably due to carriers falling out of the trap states. Since this is the first study of time-resolved photoluminescence of MOCVD-grown quantum well structures, this unusual behavior may be realted to the MOCVD growth process. Further investigations indi- cate that the traps are not active at low temperatures; they become active at approximately 150 K. The traps are probably associated with the (hetero)interfaces rather than the bulk Al(,x)Ga(,1-x)As material. The 34 K photoluminescence spectrum of this sample revealed a peak shifted down by approximately 36 meV from the main peak. Time-resolved and time-integrated photoluminescence results here show that this peak is not a stimulated phonon emission sideband, but rather is an due to an acceptor impurity, probably carbon. Photo- luminescence for excitation above and below the barrier bandgap shows that carriers are efficiently collected in the wells in both single and multiple
Advances in molecular vibrations and collision dynamics molecular clusters
Bacic, Zatko
1998-01-01
This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...
Quantum speed limits in open system dynamics.
del Campo, A; Egusquiza, I L; Plenio, M B; Huelga, S F
2013-02-01
Bounds to the speed of evolution of a quantum system are of fundamental interest in quantum metrology, quantum chemical dynamics, and quantum computation. We derive a time-energy uncertainty relation for open quantum systems undergoing a general, completely positive, and trace preserving evolution which provides a bound to the quantum speed limit. When the evolution is of the Lindblad form, the bound is analogous to the Mandelstam-Tamm relation which applies in the unitary case, with the role of the Hamiltonian being played by the adjoint of the generator of the dynamical semigroup. The utility of the new bound is exemplified in different scenarios, ranging from the estimation of the passage time to the determination of precision limits for quantum metrology in the presence of dephasing noise.
Quantum entanglement and coherence in molecular magnets
Shiddiq, Muhandis
Quantum computers are predicted to outperform classical computers in certain tasks, such as factoring large numbers and searching databases. The construction of a computer whose operation is based on the principles of quantum mechanics appears extremely challenging. Solid state approaches offer the potential to answer this challenge by tailor-making novel nanomaterials for quantum information processing (QIP). Molecular magnets, which are materials whose energy levels and magnetic quantum states are well defined at the molecular level, have been identified as a class of material with properties that make them attractive for quantum computing purpose. In this dissertation, I explore the possibilities and challenges for molecular magnets to be used in quantum computing architecture. The properties of molecular magnets that are critical for applications in quantum computing, i.e., quantum entanglement and coherence, are comprehensively investigated to probe the feasibility of molecular magnets to be used as quantum bits (qubits). Interactions of qubits with photons are at the core of QIP. Photons can be used to detect and manipulate qubits, after which information can then be transferred over long distances. As a potential candidate for qubits, the interactions between Fe8 single-molecule magnets (SMMs) and cavity photons were studied. An earlier report described that a cavity mode splitting was observed in a spectrum of a cavity filled with a single-crystal of Fe8 SMMs. This splitting was interpreted as a vacuum Rabi splitting (VRS), which is a signature of an entanglement between a large number of SMMs and a cavity photon. However, find that large absorption and dispersion of the magnetic susceptibility are the reasons for this splitting. This finding highlights the fact that an observation of a peak splitting in a cavity transmission spectrum neither represents an unambiguous indication of quantum coherence in a large number of spins, nor a signature of
Computer studies of multiple-quantum spin dynamics
Energy Technology Data Exchange (ETDEWEB)
Murdoch, J.B.
1982-11-01
The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.
Dynamical fermions in lattice quantum chromodynamics
Energy Technology Data Exchange (ETDEWEB)
Szabo, Kalman
2007-07-01
The thesis presentS results in Quantum Chromo Dynamics (QCD) with dynamical lattice fermions. The topological susceptibilty in QCD is determined, the calculations are carried out with dynamical overlap fermions. The most important properties of the quark-gluon plasma phase of QCD are studied, for which dynamical staggered fermions are used. (orig.)
Vepuri, Suresh B.; Devarajegowda, H. C.; Soliman, Mahmoud E.
2016-02-01
Hydrochloride salt formation for Active Pharmaceutical Ingredients (APIs) is the primary choice to impart aqueous solubility and to promote dissolution. Dipyridamole (DIP) is a cardiovascular drug which is practically insoluble in water. We discovered a new form of DIP called as dipyridamole hydrochloride trihydrate (DIPHT), which was prepared by an unusual method of reacting the DIP with hydrated hydrochloric acid (HCl) that was liberated in situ by the reaction of ferric chloride with water. The liberated HCl was consumed as reagent in situ by the scavenger (API) and was converted to a hydrochloride trihydrate. The product was characterized by FTIR, mass spectroscopy, PXRD and DSC. Supramolecular structure of this novel DIPHT was revealed by single crystal XRD. A sustained intramolecular hydrogen bond alliance was found in DIP and the DIPHT. Stability of this hydrogen bond was further evaluated by means of molecular modelling studies. We performed electron calculations using quantum mechanics (QM) on both the base and salt structures to compare their geometry and molecular orbital energy levels. Molecular Dynamics (MD) simulations were also conducted in explicit solvent models to provide more insights into the hydrogen bond strength and conformational preferences of the base and salt structure. Together with QM and MD, we were able to explain the influence of hydrogen bonds on proton uptake activity of DIP and stability of DIP and DIPHT. DIPHT which can dissolve faster than DIP in water may enhance the dissolution and bioavailability of the drug. As the current drug development research is shifting to repurpose the existing drugs in order to subside the untoward risks in new drug development, we believe that DIPHT with its intrinsic aqueous solubility could bring more application for DIP and generate interest within the pharmaceutical industry.
Energy Technology Data Exchange (ETDEWEB)
Gonzalez Giralda, C.
2005-07-01
The main objective of this thesis is to search for points of correspondence between the classic and quantum behavior of the dynamics of non-rigid molecular system HO2 (Hidroperoxil Radix), and too, the study of the manifestation mode as the regularity than the ergodicity from the point of view of the classical and quantum mechanics laws. (Author)
Molecular Dynamics of Lipid Bilayers
1989-08-09
The aim of this work is to study, by molecular dynamics simulations, the properties of lipid bilayers. We have applied the vectorizable, order-N...fast angle-dependent force/potential algorithms to treat angle bending and torsion. Keywords: Molecular dynamics , Lipid bilayers.
Energy Technology Data Exchange (ETDEWEB)
Park, Kwangwook; Ravindran, Sooraj; Ju, Gun Wu; Min, Jung-Wook; Kang, Seokjin; Myoung, NoSoung; Yim, Sang-Youp; Jo, Yong-Ryun; Kim, Bong-Joong; Lee, Yong Tak
2016-12-01
GaAs/GaInAs multiple-quantum-well (MQW) shells having different GaInAs shell width formed on the surface of self-catalyzed GaAs core nanowires (NWs) are grown on (100) Si substrate using molecular beam epitaxy. The photoluminescence emission from GaAs/GaInAs MQW shells and the carrier lifetime could be varied by changing the width of GaInAs shell. Time-resolved photoluminescence measurements showed that the carrier lifetime had a fast and slow decay owing to the mixing of wurtzite and zinc-blende structures of the NWs. Furthermore, strain relaxation caused the carrier lifetime to decrease beyond a certain thickness of GaInAs quantum well shells.
MDplot: Visualise Molecular Dynamics.
Margreitter, Christian; Oostenbrink, Chris
2017-05-10
The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.
Quantum Dynamics of Nonlinear Cavity Systems
Nation, Paul D.
2010-01-01
We investigate the quantum dynamics of three different configurations of nonlinear cavity systems. To begin, we carry out a quantum analysis of a dc superconducting quantum interference device (SQUID) mechanical displacement detector comprised of a SQUID with a mechanically compliant loop segment. The SQUID is approximated by a nonlinear current-dependent inductor, inducing a flux tunable nonlinear Duffing term in the cavity equation of motion. Expressions are derived for the detector signal ...
Chaos in effective classical and quantum dynamics
Casetti, L; Modugno, M; Casetti, Lapo; Gatto, Raoul; Modugno, Michele
1998-01-01
We investigate the dynamics of classical and quantum N-component phi^4 oscillators in presence of an external field. In the large N limit the effective dynamics is described by two-degree-of-freedom classical Hamiltonian systems. In the classical model we observe chaotic orbits for any value of the external field, while in the quantum case chaos is strongly suppressed. A simple explanation of this behaviour is found in the change in the structure of the orbits induced by quantum corrections. Consistently with Heisenberg's principle, quantum fluctuations are forced away from zero, removing in the effective quantum dynamics a hyperbolic fixed point that is a major source of chaos in the classical model.
Acetylcholine molecular arrays enable quantum information processing
Tamulis, Arvydas; Majauskaite, Kristina; Talaikis, Martynas; Zborowski, Krzysztof; Kairys, Visvaldas
2017-09-01
We have found self-assembly of four neurotransmitter acetylcholine (ACh) molecular complexes in a water molecules environment by using geometry optimization with DFT B97d method. These complexes organizes to regular arrays of ACh molecules possessing electronic spins, i.e. quantum information bits. These spin arrays could potentially be controlled by the application of a non-uniform external magnetic field. The proper sequence of resonant electromagnetic pulses would then drive all the spin groups into the 3-spin entangled state and proceed large scale quantum information bits.
Quantum Entanglement Molecular Absorption Spectrum Simulator
Nguyen, Quang-Viet; Kojima, Jun
2006-01-01
Quantum Entanglement Molecular Absorption Spectrum Simulator (QE-MASS) is a computer program for simulating two photon molecular-absorption spectroscopy using quantum-entangled photons. More specifically, QE-MASS simulates the molecular absorption of two quantum-entangled photons generated by the spontaneous parametric down-conversion (SPDC) of a fixed-frequency photon from a laser. The two-photon absorption process is modeled via a combination of rovibrational and electronic single-photon transitions, using a wave-function formalism. A two-photon absorption cross section as a function of the entanglement delay time between the two photons is computed, then subjected to a fast Fourier transform to produce an energy spectrum. The program then detects peaks in the Fourier spectrum and displays the energy levels of very short-lived intermediate quantum states (or virtual states) of the molecule. Such virtual states were only previously accessible using ultra-fast (femtosecond) laser systems. However, with the use of a single-frequency continuous wave laser to produce SPDC photons, and QEMASS program, these short-lived molecular states can now be studied using much simpler laser systems. QE-MASS can also show the dependence of the Fourier spectrum on the tuning range of the entanglement time of any externally introduced optical-path delay time. QE-MASS can be extended to any molecule for which an appropriate spectroscopic database is available. It is a means of performing an a priori parametric analysis of entangled photon spectroscopy for development and implementation of emerging quantum-spectroscopic sensing techniques. QE-MASS is currently implemented using the Mathcad software package.
Lowdin, Per-Olov; Ohrn, N. Y.; Sabin, John R.; Zerner, Michael C.
1993-03-01
The topics covered at the 33rd annual Sanibel Symposium, organized by the faculty and staff of the Quantum Theory Project of the University of Florida, and held March 13 - 20, 1993, include advanced scientific computing, interaction of photons and matter, quantum molecular dynamics, electronic structure methods, polymeric systems, and quantum chemical methods for extended systems.
Robust dynamical decoupling for quantum computing and quantum memory.
Souza, Alexandre M; Alvarez, Gonzalo A; Suter, Dieter
2011-06-17
Dynamical decoupling (DD) is a popular technique for protecting qubits from the environment. However, unless special care is taken, experimental errors in the control pulses used in this technique can destroy the quantum information instead of preserving it. Here, we investigate techniques for making DD sequences robust against different types of experimental errors while retaining good decoupling efficiency in a fluctuating environment. We present experimental data from solid-state nuclear spin qubits and introduce a new DD sequence that is suitable for quantum computing and quantum memory.
Bonizzoni, C; Ghirri, A; Bader, K; van Slageren, J; Perfetti, M; Sorace, L; Lan, Y; Fuhr, O; Ruben, M; Affronte, M
2016-11-14
We present spectroscopic measurements looking for the coherent coupling between molecular magnetic centers and microwave photons. The aim is to find the optimal conditions and the best molecular features to achieve the quantum strong coupling regime, for which coherent dynamics of hybrid photon-spin states take place. To this end, we used a high critical temperature YBCO superconducting planar resonator working at 7.7 GHz and at low temperatures to investigate three molecular mononuclear coordination compounds, namely (PPh4)2[Cu(mnt)2] (where mnt(2-) = maleonitriledithiolate), [ErPc2](-)TBA(+) (where pc(2-) is the phtalocyaninato and TBA(+) is the tetra-n-butylammonium cation) and Dy(trensal) (where H3trensal = 2,2',2''-tris(salicylideneimino)triethylamine). Although the strong coupling regime was not achieved in these preliminary experiments, the results provided several hints on how to design molecular magnetic centers to be integrated into hybrid quantum circuits.
The quantum Rabi model: solution and dynamics
Xie, Qiongtao; Zhong, Honghua; Batchelor, Murray T.; Lee, Chaohong
2017-03-01
This article presents a review of recent developments on various aspects of the quantum Rabi model. Particular emphasis is given on the exact analytic solution obtained in terms of confluent Heun functions. The analytic solutions for various generalisations of the quantum Rabi model are also discussed. Results are also reviewed on the level statistics and the dynamics of the quantum Rabi model. The article concludes with an introductory overview of several experimental realisations of the quantum Rabi model. An outlook towards future developments is also given.
The quantum Rabi model: solution and dynamics
Xie, Qiongtao; Batchelor, Murray T; Lee, Chaohong
2016-01-01
This article presents a review of recent developments on various aspects of the quantum Rabi model. Particular emphasis is given on the exact analytic solution obtained in terms of confluent Heun functions. The analytic solutions for various generalisations of the quantum Rabi model are also discussed. Results are also reviewed on the level statistics and the dynamics of the quantum Rabi model. The article concludes with an introductory overview of several experimental realisations of the quantum Rabi model. An outlook towards future developments is also given.
What is dynamics in quantum gravity?
Małkiewicz, Przemysław
2017-10-01
The appearance of the Hamiltonian constraint in the canonical formalism for general relativity reflects the lack of a fixed external time. The dynamics of general relativistic systems can be expressed with respect to an arbitrarily chosen internal degree of freedom, the so-called internal clock. We investigate the way in which the choice of internal clock determines the quantum dynamics and how much different quantum dynamics induced by different clocks are. We develop our method of comparison by extending the Hamilton–Jacobi theory of contact transformations to include a new type of transformation which transforms both the canonical variables and the internal clock. We employ our method to study the quantum dynamics of the Friedmann–Lemaitre model and obtain semiclassical corrections to the classical dynamics, which depend on the choice of internal clock. For a unique quantisation map we find the abundance of inequivalent semiclassical corrections induced by quantum dynamics taking place in different internal clocks. It follows that the concepts like minimal volume, maximal curvature and the number of quantum bounces, often used to describe quantum effects in cosmological models, depend on the choice of internal clock.
Pérez, Alejandro; Tuckerman, Mark E.; Müser, Martin H.
2009-05-01
The problems of ergodicity and internal consistency in the centroid and ring-polymer molecular dynamics methods are addressed in the context of a comparative study of the two methods. Enhanced sampling in ring-polymer molecular dynamics (RPMD) is achieved by first performing an equilibrium path integral calculation and then launching RPMD trajectories from selected, stochastically independent equilibrium configurations. It is shown that this approach converges more rapidly than periodic resampling of velocities from a single long RPMD run. Dynamical quantities obtained from RPMD and centroid molecular dynamics (CMD) are compared to exact results for a variety of model systems. Fully converged results for correlations functions are presented for several one dimensional systems and para-hydrogen near its triple point using an improved sampling technique. Our results indicate that CMD shows very similar performance to RPMD. The quality of each method is further assessed via a new χ2 descriptor constructed by transforming approximate real-time correlation functions from CMD and RPMD trajectories to imaginary time and comparing these to numerically exact imaginary time correlation functions. For para-hydrogen near its triple point, it is found that adiabatic CMD and RPMD both have similar χ2 error.
What is Dynamics in Quantum Gravity?
Malkiewicz, Przemyslaw
2015-01-01
Dynamics of general relativistic systems is given with respect to internal clocks. We investigate the extent to which the choice of internal clock in quantum description of the gravitational field determines the quantum dynamics. We develop our method by making use of the Hamilton-Jacobi theory, which is extended to include time coordinate transformations. Next, we apply our method to a quantum model of the flat Friedmann universe and compute some clock-induced deviations to semiclassical phase space portrait. Within a fixed quantization we find the abundance of possible semiclassical extensions to general relativity by switching between clocks. It follows that quantities like minimal volume, maximal curvature and even a number of quantum bounces, often used to describe quantum effects in gravity, are ill-defined.
Molecular quantum similarity using conceptual DFT descriptors
Indian Academy of Sciences (India)
Patrick Bultinck; Ramon carbó-dorca
2005-09-01
This paper reports a Molecular Quantum Similarity study for a set of congeneric steroid molecules, using as basic similarity descriptors electron density ρ (r), shape function (r), the Fukui functions +(r) and -(r) and local softness +(r) and -(r). Correlations are investigated between similarity indices for each couple of descriptors used and compared to assess whether these different descriptors sample different information and to investigate what information is revealed by each descriptor.
Macroscopic Quantum Coherence in Magnetic Molecular Clusters
Institute of Scientific and Technical Information of China (English)
JIN Yan-Hong; NIE Yi-Hang; LIANG Jiu-Qing; PU Fu-Cho
2001-01-01
The oscillation of tunnel splitting in Fes molecular clusters is obtained as a function of magnetic field applied along the hard axis by means of the instanton method with both semiclassical treatment and the effective potential field description of the quantum spin system. The theoretical splittings of the instanton method are compared with the numerical result by diagonalization of spin Hamiltonian operators and experimental observations. By taking the appropriate parameters, our theoretical formula yields a result the same as the experimental observation.
Rajput, Nav Nidhi; Qu, Xiaohui; Sa, Niya; Burrell, Anthony K; Persson, Kristin A
2015-03-11
In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg(2+) → Mg(+)), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI(-) exhibits a significant bond weakening while paired with the transient, partially reduced Mg(+). In contrast, BH4(-) and BF4(-) are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.
Rossi, Mariana; Paesani, Francesco; Bowman, Joel; Ceriotti, Michele
2014-01-01
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 (LMon) model and a mixed quantum-classical (MQC) model as representatives of the first family of methods, and centroid molecular dynamics (CMD) and thermostatted ring polymer molecular dynamics (TRPMD) as examples of the latter. We use as benchmarks D$_2$O doped with HOD and pure H$_2$O at three distinc...
Dynamic optical hysteresis in the quantum regime
Rodriguez, S R K; Storme, F; Sagnes, I; Gratiet, L Le; Galopin, E; Lemaitre, A; Amo, A; Ciuti, C; Bloch, J
2016-01-01
For more than 40 years, optical bistability --- the existence of two stable states with different photon numbers for the same driving conditions --- has been experimentally reported. Surprisingly, the quantum theory of a single-mode nonlinear cavity always predicts a unique steady state, i.e. no bistability. To reconcile this apparent contradiction, a tunneling time for bistability has been introduced. This is a timescale over which quantum fluctuations trigger transitions between classically stable states, and which can be astronomically longer than the measurement. While quantum fluctuations ultimately forbid the static hysteresis associated with bistability, it was recently predicted that optical hysteresis should emerge dynamically for finite sweep rates of the driving intensity. This dynamic hysteresis is expected to exhibit a double power-law behavior defining a classical-to-quantum crossover. Here, by measuring the dynamic optical hysteresis of a semiconductor microcavity for various sweep rates of the...
Ardèvol, Albert; Rovira, Carme
2015-06-24
Carbohydrate-active enzymes such as glycoside hydrolases (GHs) and glycosyltransferases (GTs) are of growing importance as drug targets. The development of efficient competitive inhibitors and chaperones to treat diseases related to these enzymes requires a detailed knowledge of their mechanisms of action. In recent years, sophisticated first-principles modeling approaches have significantly advanced in our understanding of the catalytic mechanisms of GHs and GTs, not only the molecular details of chemical reactions but also the significant implications that just the conformational dynamics of a sugar ring can have on these mechanisms. Here we provide an overview of the progress that has been made in the past decade, combining molecular dynamics simulations with density functional theory to solve these sweet mysteries of nature.
Molecular dynamics of silicon indentation
Energy Technology Data Exchange (ETDEWEB)
Kallman, J.S.; Hoover, W.G.; Hoover, C.G.; De Groot, A.J.; Lee, S.M.; Wooten, F. (Department of Applied Science Davis-Livermore, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States))
1993-04-01
We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.
Energy Technology Data Exchange (ETDEWEB)
Musa, Ahmed Y., E-mail: ahmed.musa@ymail.com [Department of Chemical and Process Engineering, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor (Malaysia); Kadhum, Abdul Amir H.; Mohamad, Abu Bakar; Takriff, Mohd Sobri [Department of Chemical and Process Engineering, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor (Malaysia)
2011-09-15
Highlights: {yields} This work deals with a study of chemical additives for corrosion inhibition of mild steel in acidic conditions. {yields} The effects of the additive 4,4-dimethyl-3-thiosemicarbazide (DTS) on mild steel were studied by means of electrochemical techniques. {yields} Quantum chemical calculations and molecular dynamic model were performed to characterize the inhibition mechanism. {yields} The calculations provided information that helps in the analysis/interpretation of the experimental work. - Abstract: The inhibition of mild steel corrosion in a 2.5 M H{sub 2}SO{sub 4} solution by 4,4-dimethyl-3-thiosemicarbazide (DTS) was studied at 30 deg. C using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). Quantum chemical parameters were calculated for DTS using PM3-SCF method. The molecular dynamic method was performed to simulate the adsorption of the DTS molecules on Fe surface. Results showed that DTS performed excellent as inhibitor for mild steel corrosion in a 2.5 M H{sub 2}SO{sub 4} solution and indicated that the inhibition efficiencies increase with the concentration of inhibitor. Theoretical results indicated that DTS could adsorb on the mild steel surface firmly through heteroatoms.
Quantum dot waveguides: ultrafast dynamics and applications
DEFF Research Database (Denmark)
Chen, Yaohui; Mørk, Jesper
2009-01-01
In this paper we analyze, based on numerical simulations, the dynamics of semiconductor devices incorporating quantum dots (QDs). In particular we emphasize the unique ultrafast carrier dynamics occurring between discrete QD bound states, and its influence on QD semiconductor optical amplifiers...... (SOAs). Also the possibility of realizing an all-optical regenerator by incorporating a QD absorber section in an amplifier structure is discussed....
Molecular modelling and molecular dynamics of CFTR.
Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul
2017-01-01
The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.
Energy Technology Data Exchange (ETDEWEB)
Zhang, Yu, E-mail: zhy@yangtze.hku.hk; Chen, GuanHua, E-mail: ghc@everest.hku.hk [Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong (China); Yam, ChiYung [Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong (China); Beijing Computational Science Research Center, Beijing 100084 (China)
2015-04-28
A time-dependent inelastic electron transport theory for strong electron-phonon interaction is established via the equations of motion method combined with the small polaron transformation. In this work, the dissipation via electron-phonon coupling is taken into account in the strong coupling regime, which validates the small polaron transformation. The corresponding equations of motion are developed, which are used to study the quantum interference effect and phonon-induced decoherence dynamics in molecular junctions. Numerical studies show clearly quantum interference effect of the transport electrons through two quasi-degenerate states with different couplings to the leads. We also found that the quantum interference can be suppressed by the electron-phonon interaction where the phase coherence is destroyed by phonon scattering. This indicates the importance of electron-phonon interaction in systems with prominent quantum interference effect.
Zhang, Yu; Yam, ChiYung; Chen, GuanHua
2015-04-28
A time-dependent inelastic electron transport theory for strong electron-phonon interaction is established via the equations of motion method combined with the small polaron transformation. In this work, the dissipation via electron-phonon coupling is taken into account in the strong coupling regime, which validates the small polaron transformation. The corresponding equations of motion are developed, which are used to study the quantum interference effect and phonon-induced decoherence dynamics in molecular junctions. Numerical studies show clearly quantum interference effect of the transport electrons through two quasi-degenerate states with different couplings to the leads. We also found that the quantum interference can be suppressed by the electron-phonon interaction where the phase coherence is destroyed by phonon scattering. This indicates the importance of electron-phonon interaction in systems with prominent quantum interference effect.
Dundas, Daniel
2012-01-01
A mixed quantum-classical approach is introduced which allows the dynamically response of molecules driven far from equilibrium to be modeled. This method is applied here to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations can be performed. The approach is applied to the study of high harmonic generation in N_2 and benzene using linearly-polarized laser pulses and to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N_2 an enhancement ...
Generated dynamics of Markov and quantum processes
Janßen, Martin
2016-01-01
This book presents Markov and quantum processes as two sides of a coin called generated stochastic processes. It deals with quantum processes as reversible stochastic processes generated by one-step unitary operators, while Markov processes are irreversible stochastic processes generated by one-step stochastic operators. The characteristic feature of quantum processes are oscillations, interference, lots of stationary states in bounded systems and possible asymptotic stationary scattering states in open systems, while the characteristic feature of Markov processes are relaxations to a single stationary state. Quantum processes apply to systems where all variables, that control reversibility, are taken as relevant variables, while Markov processes emerge when some of those variables cannot be followed and are thus irrelevant for the dynamic description. Their absence renders the dynamic irreversible. A further aim is to demonstrate that almost any subdiscipline of theoretical physics can conceptually be put in...
Hybrid quantum processors: molecular ensembles as quantum memory for solid state circuits.
Rabl, P; DeMille, D; Doyle, J M; Lukin, M D; Schoelkopf, R J; Zoller, P
2006-07-21
We investigate a hybrid quantum circuit where ensembles of cold polar molecules serve as long-lived quantum memories and optical interfaces for solid state quantum processors. The quantum memory realized by collective spin states (ensemble qubit) is coupled to a high-Q stripline cavity via microwave Raman processes. We show that, for convenient trap-surface distances of a few microm, strong coupling between the cavity and ensemble qubit can be achieved. We discuss basic quantum information protocols, including a swap from the cavity photon bus to the molecular quantum memory, and a deterministic two qubit gate. Finally, we investigate coherence properties of molecular ensemble quantum bits.
Hybrid Quantum Processors: molecular ensembles as quantum memory for solid state circuits
Rabl, P; Doyle, J M; Lukin, M D; Schölkopf, R J; Zoller, P
2006-01-01
We investigate a hybrid quantum circuit where ensembles of cold polar molecules serve as long-lived quantum memories and optical interfaces for solid state quantum processors. The quantum memory realized by collective spin states (ensemble qubit) is coupled to a high-Q stripline cavity via microwave Raman processes. We show that for convenient trap-surface distances of a few $\\mu$m, strong coupling between the cavity and ensemble qubit can be achieved. We discuss basic quantum information protocols, including a swap from the cavity photon bus to the molecular quantum memory, and a deterministic two qubit gate. Finally, we investigate coherence properties of molecular ensemble quantum bits.
Mouhat, Félix; Sorella, Sandro; Vuilleumier, Rodolphe; Saitta, Antonino Marco; Casula, Michele
2017-06-13
We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most-advanced post-Hartree-Fock approaches, and with a favorable scaling with the system size. In order to cope with the intrinsic noise due to the stochastic nature of quantum Monte Carlo methods, we generalize the path integral molecular dynamics using a Langevin thermostat correlated according to the covariance matrix of quantum Monte Carlo nuclear forces. The variational parameters of the quantum Monte Carlo wave function are evolved during the nuclear dynamics, such that the Born-Oppenheimer potential energy surface is unbiased. Statistical errors on the wave function parameters are reduced by resorting to bead grouping average, which we show to be accurate and well-controlled. Our general algorithm relies on a Trotter breakup between the dynamics driven by ionic forces and the one set by the harmonic interbead couplings. The latter is exactly integrated, even in the presence of the Langevin thermostat, thanks to the mapping onto an Ornstein-Uhlenbeck process. This framework turns out to be also very efficient in the case of noiseless (deterministic) ionic forces. The new implementation is validated on the Zundel ion (H5O2(+)) by direct comparison with standard path integral Langevin dynamics calculations made with a coupled cluster potential energy surface. Nuclear quantum effects are confirmed to be dominant over thermal effects well beyond
Dynamical symmetry breaking in quantum field theories
Miransky, Vladimir A
1993-01-01
The phenomenon of dynamical symmetry breaking (DSB) in quantum field theory is discussed in a detailed and comprehensive way. The deep connection between this phenomenon in condensed matter physics and particle physics is emphasized. The realizations of DSB in such realistic theories as quantum chromodynamics and electroweak theory are considered. Issues intimately connected with DSB such as critical phenomenona and effective lagrangian approach are also discussed.
Dynamics of Coupled Quantum-Classical Oscillators
Institute of Scientific and Technical Information of China (English)
HE Wei-Zhong; XU Liu-Su; ZOU Feng-Wu
2004-01-01
@@ The dynamics of systems consisting of coupled quantum-classical oscillators is numerically investigated. It is shown that, under certain conditions, the quantum oscillator exhibits chaos. When the mass of the classical oscillator increases, the chaos will be suppressed; if the energy of the system and/or the coupling strength between the two oscillators increases, chaotic behaviour of the system appears. This result will be helpful to understand the probability of the emergence of quantum chaos and may be applied to explain the spectra of complex atoms qualitatively.
Symmetries, variational principles, and quantum dynamics
Directory of Open Access Journals (Sweden)
A. Sissakian
2004-05-01
Full Text Available We describe the role of symmetries in formation of quantum dynamics. A quantum version of d'Alembert's principle is proposed to take into account the symmetry constrains more exact. It is argued that the time reversibility of quantum process, as the quantum analogy of d'Alembert's principle, makes the measure of the corresponding path integral ÃŽÂ´-like. The argument of this ÃŽÂ´-function is the sum of all classical forces of the problem under consideration plus the random force of quantum excitations. Such measure establishes the one-to-one correspondence with classical mechanics and, for this reason, allows a free choice of the useful dynamical variables. The analysis shows that choosing the action-angle variables, one may get to the free-from-divergences quantum field theory. Moreover, one can try to get an independence from necessity to extract the degrees of freedom constrained by the symmetry. These properties of new quantization scheme are vitally essential for such theories as the non-Abelian Yang-Mills gauge theory and quantum gravity.
Origin of Dynamical Quantum Non-locality
Pachon, Cesar E.; Pachon, Leonardo A.
2014-03-01
Non-locality is one of the hallmarks of quantum mechanics and is responsible for paradigmatic features such as entanglement and the Aharonov-Bohm effect. Non-locality comes in two ``flavours'': a kinematic non-locality- arising from the structure of the Hilbert space- and a dynamical non-locality- arising from the quantum equations of motion-. Kinematic non-locality is unable to induce any change in the probability distributions, so that the ``action-at-a-distance'' cannot manifest. Conversely, dynamical non-locality does create explicit changes in probability, though in a ``causality-preserving'' manner. The origin of non-locality of quantum measurements and its relations to the fundamental postulates of quantum mechanics, such as the uncertainty principle, have been only recently elucidated. Here we trace the origin of dynamical non-locality to the superposition principle. This relation allows us to establish and identify how the uncertainty and the superposition principles determine the non-local character of the outcome of a quantum measurement. Being based on group theoretical and path integral formulations, our formulation admits immediate generalizations and extensions to to, e.g., quantum field theory. This work was supported by the Departamento Administrativo de Ciencia, Tecnologia e Innovacion -COLCIENCIAS- of Colombia under the grant number 111556934912.
Quantum Simulation for Open-System Dynamics
Wang, Dong-Sheng; de Oliveira, Marcos Cesar; Berry, Dominic; Sanders, Barry
2013-03-01
Simulations are essential for predicting and explaining properties of physical and mathematical systems yet so far have been restricted to classical and closed quantum systems. Although forays have been made into open-system quantum simulation, the strict algorithmic aspect has not been explored yet is necessary to account fully for resource consumption to deliver bounded-error answers to computational questions. An open-system quantum simulator would encompass classical and closed-system simulation and also solve outstanding problems concerning, e.g. dynamical phase transitions in non-equilibrium systems, establishing long-range order via dissipation, verifying the simulatability of open-system dynamics on a quantum Turing machine. We construct an efficient autonomous algorithm for designing an efficient quantum circuit to simulate many-body open-system dynamics described by a local Hamiltonian plus decoherence due to separate baths for each particle. The execution time and number of gates for the quantum simulator both scale polynomially with the system size. DSW funded by USARO. MCO funded by AITF and Brazilian agencies CNPq and FAPESP through Instituto Nacional de Ciencia e Tecnologia-Informacao Quantica (INCT-IQ). DWB funded by ARC Future Fellowship (FT100100761). BCS funded by AITF, CIFAR, NSERC and USARO.
Multiscale Reactive Molecular Dynamics
2012-08-15
as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP
Molecular model with quantum mechanical bonding information.
Bohórquez, Hugo J; Boyd, Russell J; Matta, Chérif F
2011-11-17
The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.
General linear dynamics - quantum, classical or hybrid
Elze, H-T; Vallone, F
2011-01-01
We describe our recent proposal of a path integral formulation of classical Hamiltonian dynamics. Which leads us here to a new attempt at hybrid dynamics, which concerns the direct coupling of classical and quantum mechanical degrees of freedom. This is of practical as well as of foundational interest and no fully satisfactory solution of this problem has been established to date. Related aspects will be observed in a general linear ensemble theory, which comprises classical and quantum dynamics in the form of Liouville and von Neumann equations, respectively, as special cases. Considering the simplest object characterized by a two-dimensional state-space, we illustrate how quantum mechanics is special in several respects among possible linear generalizations.
Thermalization Using Quantum Field Dynamics?
Salle, M; Vink, Jeroen C
2001-01-01
We describe a Hartree ensemble method to approximately solve the Heisenberg equations for the \\phi^4 model in 1+1 dimensions. We compute the energies and number densities of the quantum particles described by the \\phi field and find that the particles initially thermalize with a Bose-Einstein distribution for the particle density. Gradually, however, the distribution changes towards classical equipartition. Using suitable initial conditions quantum thermalization is achieved much faster than the onset of this undesirable equipartition. We also show how the numerical efficiency of our method can be significantly improved.
Guo, Xunmin; Liu, Zheyun; Song, Qinhua; Wang, Lijuan; Zhong, Dongping
2015-02-26
Many biomimetic chemical systems for repair of UV-damaged DNA showed very low repair efficiency, and the molecular origin is still unknown. Here, we report our systematic characterization of the repair dynamics of a model compound of indole-thymine dimer adduct in three solvents with different polarity. By resolving all elementary steps including three electron-transfer processes and two bond-breaking and bond-formation dynamics with femtosecond resolution, we observed the slow electron injection in 580 ps in water, 4 ns in acetonitrile, and 1.38 ns in dioxane, the fast back electron transfer without repair in 120, 150, and 180 ps, and the slow bond splitting in 550 ps, 1.9 ns, and 4.5 ns, respectively. The dimer bond cleavage is clearly accelerated by the solvent polarity. By comparing with the biological repair machine photolyase with a slow back electron transfer (2.4 ns) and a fast bond cleavage (90 ps), the low repair efficiency in the biomimetic system is mainly determined by the fast back electron transfer and slow bond breakage. We also found that the model system exists in a dynamic heterogeneous C-clamped conformation, leading to a stretched dynamic behavior. In water, we even identified another stacked form with ultrafast cyclic electron transfer, significantly reducing the repair efficiency. Thus, the comparison of the repair efficiency in different solvents is complicated and should be cautious, and only the dynamics by resolving all elementary steps can finally determine the total repair efficiency. Finally, we use the Marcus electron-transfer theory to analyze all electron-transfer reactions and rationalize all observed electron-transfer dynamics.
Molecular dynamics simulation of pyridine
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
Influence of conformational molecular dynamics on matter wave interferometry
Gring, Michael; Eibenberger, Sandra; Nimmrichter, Stefan; Berrada, Tarik; Arndt, Markus; Ulbricht, Hendrik; Hornberger, Klaus; Müri, Marcel; Mayor, Marcel; Böckmann, Marcus; Doltsinis, Nikos
2014-01-01
We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum object, our experiment demonstrates that the translational quantum phase is sensitive to dynamic conformational state changes inside the diffracted molecules. The structural flexibility of tailor-made hot organic particles is sufficient to admit a mixture of strongly fluctuating dipole moments. These modify the electric susceptibility and through this the quantum interference pattern in the presence of an external electric field. Detailed molecular dynamics simulations combined with density functional theory allow us to quantify the time-dependent structural reconfigurations and to predict the ensemble-averaged square of the dipole moment which is found to be in good agreement with the interferometric result. The experiment thus opens a new perspective on matter wave interfe...
Quantum Dynamics Simulations for Modeling Experimental Pump-Probe Measurements
Pearson, Brett; Nayyar, Sahil; Liss, Kyle; Weinacht, Thomas
2016-05-01
Time-resolved studies of quantum dynamics have benefited greatly from developments in ultrafast table-top and free electron lasers. Advances in computer software and hardware have lowered the barrier for performing calculations such that relatively simple simulations allow for direct comparison with experimental results. We describe here a set of quantum dynamics calculations in low-dimensional molecular systems. The calculations incorporate coupled electronic-nuclear dynamics, including two interactions with an applied field and nuclear wave packet propagation. The simulations were written and carried out by undergraduates as part of a senior research project, with the specific goal of allowing for detailed interpretation of experimental pump-probe data (in additional to the pedagogical value).
Reversible part of a quantum dynamical system
2016-01-01
In this work a quantum dynamical system $(\\mathfrak M,\\Phi, \\varphi)$ is constituted by a von Neumann algebra $\\mathfrak M$, by a unital Schwartz map $\\Phi:\\mathfrak{M\\rightarrow M}$ and by a $\\Phi$-invariant normal faithful state $\\varphi$ on $\\mathfrak M$. The ergodic properties of a quantum dynamical system, depends on its reversible part $(\\mathfrak{D}_\\infty,\\Phi_\\infty, \\varphi_\\infty)$. It is constituted by a von Neumann sub-algebra $\\mathfrak{D}_\\infty$ of $\\mathfrak M$ by an automorp...
DEFF Research Database (Denmark)
Pomogaev, Vladimir; Pomogaeva, Anna; Avramov, Pavel
2011-01-01
Three polycyclic organic molecules in various solvents focused on thermo-dynamical aspects were theoretically investigated using the recently developed statistical quantum mechanical/classical molecular dynamics method for simulating electronic-vibrational spectra. The absorption bands of estradiol...
Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori
2009-10-01
We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.
Nonequilibrium quantum dynamics in optomechanical systems
Patil, Yogesh Sharad; Cheung, Hil F. H.; Shaffer, Airlia; Wang, Ke; Vengalattore, Mukund
2016-05-01
The thermalization dynamics of isolated quantum systems has so far been explored in the context of cold atomic systems containing a large number of particles and modes. Quantum optomechanical systems offer prospects of studying such dynamics in a qualitatively different regime - with few individually addressable modes amenable to continuous quantum measurement and thermalization times that vastly exceed those observed in cold atomic systems. We have experimentally realized a dynamical continuous phase transition in a quantum compatible nondegenerate mechanical parametric oscillator. This system is formally equivalent to the optical parametric amplifiers whose dynamics have been a subject of intense theoretical study. We experimentally verify its phase diagram and observe nonequilibrium behavior that was only theorized, but never directly observed, in the context of optical parametric amplifiers. We discuss prospects of using nonequilibrium protocols such as quenches in optomechanical systems to amplify weak nonclassical correlations and to realize macroscopic nonclassical states. This work was supported by the DARPA QuASAR program through a Grant from the ARO and the ARO MURI on non-equilibrium manybody dynamics.
Geometry from dynamics, classical and quantum
Cariñena, José F; Marmo, Giuseppe; Morandi, Giuseppe
2015-01-01
This book describes, by using elementary techniques, how some geometrical structures widely used today in many areas of physics, like symplectic, Poisson, Lagrangian, Hermitian, etc., emerge from dynamics. It is assumed that what can be accessed in actual experiences when studying a given system is just its dynamical behavior that is described by using a family of variables ("observables" of the system). The book departs from the principle that ''dynamics is first'', and then tries to answer in what sense the sole dynamics determines the geometrical structures that have proved so useful to describe the dynamics in so many important instances. In this vein it is shown that most of the geometrical structures that are used in the standard presentations of classical dynamics (Jacobi, Poisson, symplectic, Hamiltonian, Lagrangian) are determined, though in general not uniquely, by the dynamics alone. The same program is accomplished for the geometrical structures relevant to describe quantum dynamics. Finall...
Dynamics of multipartite quantum correlations under decoherence
Ramzan, M
2012-01-01
Quantum discord is an optimal resource for the quantification of classical and non-classical correlations as compared to other related measures. Geometric measure of quantum discord is another measure of quantum correlations. Recently, the geometric quantum discord for multipartite states has been introduced by Jianwei Xu [arxiv:quant/ph.1205.0330]. Motivated from the recent study [Ann. Phys. 327 (2012) 851] for the bipartite systems, I have investigated global quantum discord (QD) and geometric quantum discord (GQD) under the influence of external environments for different multipartite states. Werner-GHZ type three-qubit and six-qubit states are considered in inertial and non-inertial settings. The dynamics of QD and GQD is investigated under amplitude damping, phase damping, depolarizing and flipping channels. It is seen that the quantum discord vanishes for p>0.75 in case of three-qubit GHZ states and for p>0.5 for six qubit GHZ states. This implies that multipartite states are more fragile to decoherence...
Fractal dynamics in chaotic quantum transport.
Kotimäki, V; Räsänen, E; Hennig, H; Heller, E J
2013-08-01
Despite several experiments on chaotic quantum transport in two-dimensional systems such as semiconductor quantum dots, corresponding quantum simulations within a real-space model have been out of reach so far. Here we carry out quantum transport calculations in real space and real time for a two-dimensional stadium cavity that shows chaotic dynamics. By applying a large set of magnetic fields we obtain a complete picture of magnetoconductance that indicates fractal scaling. In the calculations of the fractality we use detrended fluctuation analysis-a widely used method in time-series analysis-and show its usefulness in the interpretation of the conductance curves. Comparison with a standard method to extract the fractal dimension leads to consistent results that in turn qualitatively agree with the previous experimental data.
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Optical dynamics of molecular aggregates
de Boer, Steven
2006-01-01
The subject of this thesis is the spectroscopy and dynamics of molecular aggregates in amorphous matrices. Aggregates of three different molecules were studied. The molecules are depicted in Fig. (1.1). Supersaturated solutions of these molecules show aggregate formation. Aggregation is a process si
Quantum process tomography quantifies coherence transfer dynamics in vibrational exciton.
Chuntonov, Lev; Ma, Jianqiang
2013-10-31
Quantum coherence has been a subject of great interest in many scientific disciplines. However, detailed characterization of the quantum coherence in molecular systems, especially its transfer and relaxation mechanisms, still remains a major challenge. The difficulties arise in part because the spectroscopic signatures of the coherence transfer are typically overwhelmed by other excitation-relaxation processes. We use quantum process tomography (QPT) via two-dimensional infrared spectroscopy to quantify the rate of the elusive coherence transfer between two vibrational exciton states. QPT retrieves the dynamics of the dissipative quantum system directly from the experimental observables. It thus serves as an experimental alternative to theoretical models of the system-bath interaction and can be used to validate these theories. Our results for coupled carbonyl groups of a diketone molecule in chloroform, used as a benchmark system, reveal the nonsecular nature of the interaction between the exciton and the Markovian bath and open the door for the systematic studies of the dissipative quantum systems dynamics in detail.
Dynamics of quantum trajectories in chaotic systems
Wisniacki, D A; Benito, R M
2003-01-01
Quantum trajectories defined in the de Broglie--Bohm theory provide a causal way to interpret physical phenomena. In this Letter, we use this formalism to analyze the short time dynamics induced by unstable periodic orbits in a classically chaotic system, a situation in which scars are known to play a very important role. We find that the topologies of the quantum orbits are much more complicated than that of the scarring and associated periodic orbits, since the former have quantum interference built in. Thus scar wave functions are necessary to analyze the corresponding dynamics. Moreover, these topologies imply different return routes to the vicinity of the initial positions, and this reflects in the existence of different contributions in each peak of the survival probability function.
An exact factorization perspective on quantum interferences in nonadiabatic dynamics
Curchod, Basile F. E.; Agostini, Federica; Gross, E. K. U.
2016-07-01
Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface—the exact surface on which the nuclear dynamics takes place. We use a one-dimensional exactly solvable model to reproduce different conditions for quantum interferences, whose characteristic features already appear in one-dimension. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrast to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics one of the exact nuclear probability densities.
An Exact Factorization Perspective on Quantum Interferences in Nonadiabatic Dynamics
Curchod, Basile F E; Gross, E K U
2016-01-01
Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface - the exact surface on which the nuclear dynamics takes place - using an exactly-solvable model to reproduce different conditions for quantum interferences. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrast to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics the one of the exact nuclear probability density.
Schmidt, Burkhard; Lorenz, Ulf
2017-04-01
WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. The graphical capabilities allow visualization of quantum dynamics 'on the fly', including Wigner phase space representations. Being easy to use and highly versatile, WavePacket is well suited for the teaching of quantum mechanics as well as for research projects in atomic, molecular and optical physics or in physical or theoretical chemistry. The present Part I deals with the description of closed quantum systems in terms of Schrödinger equations. The emphasis is on discrete variable representations for spatial discretization as well as various techniques for temporal discretization. The upcoming Part II will focus on open quantum systems and dimension reduction; it also describes the codes for optimal control of quantum dynamics. The present work introduces the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge platform, where extensive Wiki-documentation as well as worked-out demonstration examples can be found.
Dynamical Symmetry Breaking in RN Quantum Gravity
Directory of Open Access Journals (Sweden)
A. T. Kotvytskiy
2011-01-01
Full Text Available We show that in the RN gravitation model, there is no dynamical symmetry breaking effect in the formalism of the Schwinger-Dyson equation (in flat background space-time. A general formula for the second variation of the gravitational action is obtained from the quantum corrections hμν (in arbitrary background metrics.
Quantum dynamical entropies in discrete classical chaos
Energy Technology Data Exchange (ETDEWEB)
Benatti, Fabio [Dipartimento di Fisica Teorica, Universita di Trieste, Strada Costiera 11, 34014 Trieste (Italy); Cappellini, Valerio [Dipartimento di Fisica Teorica, Universita di Trieste, Strada Costiera 11, 34014 Trieste (Italy); Zertuche, Federico [Instituto de Matematicas, UNAM, Unidad Cuernavaca, AP 273-3, Admon. 3, 62251 Cuernavaca, Morelos (Mexico)
2004-01-09
We discuss certain analogies between quantization and discretization of classical systems on manifolds. In particular, we will apply the quantum dynamical entropy of Alicki and Fannes to numerically study the footprints of chaos in discretized versions of hyperbolic maps on the torus.
Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander
2012-11-28
Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.
Quantum mechanical force fields for condensed phase molecular simulations
Giese, Timothy J.; York, Darrin M.
2017-09-01
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.
Complex dynamics in diatomic molecules. Part II: Quantum trajectories
Energy Technology Data Exchange (ETDEWEB)
Yang, C.-D. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: cdyang@mail.ncku.edu.tw; Weng, H.-J. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: principlex@yahoo.com.tw
2008-10-15
The second part of this paper deals with quantum trajectories in diatomic molecules, which has not been considered before in the literature. Morse potential serves as a more accurate function than a simple harmonic oscillator for illustrating a realistic picture about the vibration of diatomic molecules. However, if we determine molecular dynamics by integrating the classical force equations derived from a Morse potential, we will find that the resulting trajectories do not consist with the probabilistic prediction of quantum mechanics. On the other hand, the quantum trajectory determined by Bohmian mechanics [Bohm D. A suggested interpretation of the quantum theory in terms of hidden variable. Phys. Rev. 1952;85:166-179] leads to the conclusion that a diatomic molecule is motionless in all its vibrational eigen-states, which also contradicts probabilistic prediction of quantum mechanics. In this paper, we point out that the quantum trajectory of a diatomic molecule completely consistent with quantum mechanics does exist and can be solved from the quantum Hamilton equations of motion derived in Part I, which is based on a complex-space formulation of fractal spacetime [El Naschie MS. A review of E-Infinity theory and the mass spectrum of high energy particle physics. Chaos, Solitons and Fractals 2004;19:209-36; El Naschie MS. E-Infinity theory - some recent results and new interpretations. Chaos, Solitons and Fractals 2006;29:845-853; El Naschie MS. The concepts of E-infinity. An elementary introduction to the cantorian-fractal theory of quantum physics. Chaos, Solitons and Fractals 2004;22:495-511; El Naschie MS. SU(5) grand unification in a transfinite form. Chaos, Solitons and Fractals 2007;32:370-374; Nottale L. Fractal space-time and microphysics: towards a theory of scale relativity. Singapore: World Scientific; 1993; Ord G. Fractal space time and the statistical mechanics of random works. Chaos, Soiltons and Fractals 1996;7:821-843] approach to quantum
Quantum Localization in Laser-Driven Molecular Rotation
Averbukh, Ilya
2016-05-01
Recently we predicted that several celebrated solid state quantum localization phenomena - Anderson localization, Bloch oscillations, and Tamm-Shockley surface states - may manifest themselves in the rotational dynamics of laser-kicked molecules. In this talk, I will present these new rotational effects in a gas of linear molecules subject to a moderately long periodic train of femtosecond laser pulses. A small detuning of the train period from the rotational revival time causes Anderson localization in the angular momentum space above some critical value of J - the Anderson wall. This wall marks an impenetrable border stopping any further rotational excitation. Below the Anderson wall, the rotational excitation oscillates with the number of pulses due to a mechanism similar to Bloch oscillations in crystalline solids. I will present the results of the first experimental observation of the laser-induced rotational Bloch oscillations in molecular nitrogen at ambient conditions (Stanford & Weizmann, 2015). We will also discuss the prospects of observing the rotational analogues of the Tamm surface states in a similar experimental setup. Our results offer laser-driven molecular rotation as a new platform for studies on the localization phenomena in quantum transport. These effects are important for many processes involving highly excited rotational states, including coherent optical manipulations in molecular mixtures, and propagation of powerful laser pulses in atmosphere.
Quantum information analysis of electronic states at different molecular structures
Barcza, G; Marti, K H; Reiher, M
2010-01-01
We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We also discuss the application of the configuration interaction based dynamically extended active space procedure which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures to a great extent. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal orbital ordering and carry out efficient calculations on transition metal clusters. We propose a recipe to perform DMRG calculations in a black-box fashion and we point out the connections of our work to other tensor network state approaches.
Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism
DEFF Research Database (Denmark)
Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik;
2016-01-01
The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R......)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers...... indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site...
Grand canonical Molecular Dynamics Simulations
Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K
2011-01-01
For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.
Nonlinear dynamics and quantum chaos an introduction
Wimberger, Sandro
2014-01-01
The field of nonlinear dynamics and chaos has grown very much over the last few decades and is becoming more and more relevant in different disciplines. This book presents a clear and concise introduction to the field of nonlinear dynamics and chaos, suitable for graduate students in mathematics, physics, chemistry, engineering, and in natural sciences in general. It provides a thorough and modern introduction to the concepts of Hamiltonian dynamical systems' theory combining in a comprehensive way classical and quantum mechanical description. It covers a wide range of topics usually not found in similar books. Motivations of the respective subjects and a clear presentation eases the understanding. The book is based on lectures on classical and quantum chaos held by the author at Heidelberg University. It contains exercises and worked examples, which makes it ideal for an introductory course for students as well as for researchers starting to work in the field.
Smooth Quantum Dynamics of Mixmaster Universe
Bergeron, Hervé; Gazeau, Jean Pierre; Małkiewicz, Przemysław; Piechocki, Włodzimierz
2015-01-01
We present a quantum version of the vacuum Bianchi IX model by implementing affine coherent state quantization combined with a Born-Oppenheimer-like adiabatic approximation. The analytical treatment is carried out on both quantum and semiclassical levels. The resolution of the classical singularity occurs by means of a repulsive potential generated by our quantization procedure. The quantization of the oscillatory degrees of freedom produces a radiation energy density term in the semiclassical constraint equation. The Friedmann-like lowest energy eigenstates of the system are found to be dynamically stable.
Dynamic conductance of a ballistic quantum wire
Energy Technology Data Exchange (ETDEWEB)
Quan Jun [School of Physics Science and Technology, Zhanjiang Normal University, Zhanjiang 524048 (China); Tian Ying [Center of Liberal Education, Zhanjiang Normal University, Zhanjiang 524048 (China); Zhang, Jun, E-mail: ntu_submit@yahoo.c [School of Physics Science and Technology, Zhanjiang Normal University, Zhanjiang 524048 (China); Shenzhen Institute of Advanced Integration Technology, Shenzhen 518055 (China); Shao Lexi [School of Physics Science and Technology, Zhanjiang Normal University, Zhanjiang 524048 (China)
2011-04-01
Within the framework of exact linear response theory, we derive a general formula, with which the dynamic conductance of mesoscopic system can be determined in the absence of Coulomb interaction. In addition, we present a solution to the problem of current partition in the system. These allow the derivation of dynamic conductance in time-dependent case. As a natural consequence, the current (charge) conservation and gauge invariance conditions are fulfilled. To give an example, we discuss the dynamic conductance of a ballistic quantum wire, and the effect of contacts on the conductance is also discussed.
Quantum dynamical maps and Markovianity
Devi, A R Usha; Sudha,
2011-01-01
It is known that the time evolution of a subsystem from an initial state to two later times, t1, t2 (t2 > t1), are both completely positive (CP) but it is shown here that in the intermediate times between t1 and t2, in general, it need not be CP. This reveals the key to the Markov (if CP) and nonMarkov (if NCP) avataras of the intermediate dynamics. This is brought out based on A and B dynamical maps - without resorting to Master equation approach. The choice of tensor product form for the global initial state points towards the system-environment interaction dynamics as the sole cause for Markovianity/non-Markovianity. A succinct summary of the results is given in the form of a table.
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
Available Instruments for Analyzing Molecular Dynamics Trajectories.
Likhachev, I V; Balabaev, N K; Galzitskaya, O V
2016-01-01
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed.
Dynamical Non-Equilibrium Molecular Dynamics
Directory of Open Access Journals (Sweden)
Giovanni Ciccotti
2013-12-01
Full Text Available In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD, which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from the problem of sampling the initial condition. D-NEMD provides the theoretical framework to compute time-dependent macroscopic dynamical behaviors by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions generated from a suitable (equilibrium or non-equilibrium distribution at time zero. We also discuss how to generate a large class of initial distributions. The same approach applies also to the calculation of the rate constants of activated processes. The range of problems treatable by this method is illustrated by discussing applications to a few key hydrodynamic processes (the “classical” flow under shear, the formation of convective cells and the relaxation of an interface between two immiscible liquids.
Composition of quantum states and dynamical subadditivity
Energy Technology Data Exchange (ETDEWEB)
Roga, Wojciech [Instytut Fizyki im. Smoluchowskiego, Uniwersytet Jagiellonski, PL-30-059 Cracow (Poland); Fannes, Mark [Instituut voor Theoretische Fysica, Universiteit Leuven, B-3001 Leuven (Belgium); Zyczkowski, Karol [Instytut Fizyki im. Smoluchowskiego, Uniwersytet Jagiellonski, PL-30-059 Cracow (Poland)
2008-01-25
We introduce a composition of quantum states of a bipartite system which is based on the reshuffling of density matrices. This non-Abelian product is associative and stems from the composition of quantum maps acting on a simple quantum system. It induces a semi-group in the subset of states with maximally mixed partial traces. Subadditivity of the von Neumann entropy with respect to this product is proved. It is equivalent to subadditivity of the entropy of bistochastic maps with respect to their composition, where the entropy of a map is the entropy of the corresponding state under the Jamiolkowski isomorphism. Strong dynamical subadditivity of a concatenation of three bistochastic maps is established. Analogous bounds for the entropy of a composition are derived for general stochastic maps. In the classical case they lead to new bounds for the entropy of a product of two stochastic matrices.
Classical and quantum dynamics of the sphere
Lasukov, Vladimir; Moldovanova, Evgeniia; Abdrashitova, Maria; Malik, Hitendra; Gorbacheva, Ekaterina
2016-07-01
In Minkowski space, there has been developed the mathematic quantum model of the real particle located on the sphere evolving owing to the negative pressure inside the sphere. The developed model is analogous to the geometrodynamic model of the Lemaitre-Friedmann primordial atom in superspace-time, whose spatial coordinate is the scale factor functioning as a radial coordinate. There is a formulation of quantum geometrodynamics in which the spatial coordinate is an offset of the scale factor and wave function at the same time. With the help of the Dirac procedure for extracting the root from the Hamiltonian operator we have constructed a Dirac quantum dynamics of the sphere with fractional spin.
Dynamical Response near Quantum Critical Points
Lucas, Andrew; Gazit, Snir; Podolsky, Daniel; Witczak-Krempa, William
2017-02-01
We study high-frequency response functions, notably the optical conductivity, in the vicinity of quantum critical points (QCPs) by allowing for both detuning from the critical coupling and finite temperature. We consider general dimensions and dynamical exponents. This leads to a unified understanding of sum rules. In systems with emergent Lorentz invariance, powerful methods from quantum field theory allow us to fix the high-frequency response in terms of universal coefficients. We test our predictions analytically in the large-N O (N ) model and using the gauge-gravity duality and numerically via quantum Monte Carlo simulations on a lattice model hosting the interacting superfluid-insulator QCP. In superfluid phases, interacting Goldstone bosons qualitatively change the high-frequency optical conductivity and the corresponding sum rule.
Zaboli, Maryam; Raissi, Heidar
2018-01-05
In the current study, the probability of complex formation between mercaptopurine drug with cucurbit[6]urils and cucurbit[7]urils has been investigated. The calculations for geometry optimization of complexes have been carried out by means of DFT (B3LYP), DFT-D (B3LYP-D) and M06-2X methods. The Atoms In Molecules (AIM), Natural Bond Orbital (NBO), NMR, the density of states (DOSs) and frontier molecular orbital (MO) analyses have been done on the inclusion complexes. In addition, the UV-Vis spectra of the first eight states have been obtained by CAM-B3LYP/TD-DFT calculation. The obtained results of the complexation process reveal that CB[7]-DRG complexes are more favorable than that of CB[6]-DRG interactions. Furthermore, our theoretical results show that configurations III and I are the most stable configurations related to the CB[6]/DRG and CB[7]/DRG interactions, respectively. The positive ∇(2)ρ(r) and HC values at the bond critical points indicate that exist the weak H-bonds between CB[6] and CB[7] with H atoms of the drug molecule. The obtained negative binding energy values of CB[7]-DRG interaction in solution phase show the stability of these complexes in the aqueous medium. Also, all of the observed parameters of molecular dynamics simulation such as the number of contacts, hydrogen bonding, center-of-mass distance and van der Waals energy values confirm the encapsulation of mercaptopurine molecule inside the cucurbit[7]urils cavity at about 3.2ns. Copyright © 2017 Elsevier B.V. All rights reserved.
Effective evolution equations from quantum dynamics
Benedikter, Niels; Schlein, Benjamin
2016-01-01
These notes investigate the time evolution of quantum systems, and in particular the rigorous derivation of effective equations approximating the many-body Schrödinger dynamics in certain physically interesting regimes. The focus is primarily on the derivation of time-dependent effective theories (non-equilibrium question) approximating many-body quantum dynamics. The book is divided into seven sections, the first of which briefly reviews the main properties of many-body quantum systems and their time evolution. Section 2 introduces the mean-field regime for bosonic systems and explains how the many-body dynamics can be approximated in this limit using the Hartree equation. Section 3 presents a method, based on the use of coherent states, for rigorously proving the convergence towards the Hartree dynamics, while the fluctuations around the Hartree equation are considered in Section 4. Section 5 focuses on a discussion of a more subtle regime, in which the many-body evolution can be approximated by means of t...
Dynamical Equations for Quantum Information and Application in Information Channel
Institute of Scientific and Technical Information of China (English)
BI Qiao; XING Xiu-San; H. E. Ruda
2005-01-01
@@ We establish several dynamical equations for quantum information density. It is demonstrated that quantum information density shares the same formalism of the Liouville equation, subdynamics kinetic equation and Fokker-Planck equation as the density operator and also possesses the superposition property. These allow one to use quantum information density directly to model quantum information. The kinetic equations for quantum information density reveal that the dynamical process of quantum information may be related to dissipative,Markovian, or diffusional information flows, together causing irreversibility. Finally, we discuss superposition of quantum information density, which allows us to construct a quantum information channel in the coherent state representation using harmonic oscillator based encoded quantum information, and obtain a formula for quantum dynamical mutual information.
Dynamics of quantum wave packets
Energy Technology Data Exchange (ETDEWEB)
Gosnell, T.R.; Taylor, A.J.; Rodriguez, G.; Clement, T.S.
1998-11-01
This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The objective of this project was to develop ultrafast laser techniques for the creation and measurement of quantum vibrational wave packets in gas phase diatomic molecules. Moreover, the authors sought to manipulate the constitution of these wave packets in terms of harmonic-oscillator basis wavefunctions by manipulating the time-dependent amplitude and phase of the incident ultrashort laser pulse. They specifically investigated gaseous diatomic potassium (K{sub 2}), and discovered variations in the shape of the wave packets as a result of changing the linear chirp in the ultrashort preparation pulse. In particular, they found evidence for wave-packet compression for a specific degree of chirp. Important ancillary results include development of new techniques for denoising and deconvolution of femtosecond time traces and techniques for diagnosing the phase and amplitude of the electric field of femtosecond laser pulses.
A Dynamics for Discrete Quantum Gravity
Gudder, Stan
2013-01-01
This paper is based on the causal set approach to discrete quantum gravity. We first describe a classical sequential growth process (CSGP) in which the universe grows one element at a time in discrete steps. At each step the process has the form of a causal set (causet) and the "completed" universe is given by a path through a discretely growing chain of causets. We then quantize the CSGP by forming a Hilbert space $H$ on the set of paths. The quantum dynamics is governed by a sequence of positive operators $\\rho_n$ on $H$ that satisfy normalization and consistency conditions. The pair $(H,\\brac{\\rho_n})$ is called a quantum sequential growth process (QSGP). We next discuss a concrete realization of a QSGP in terms of a natural quantum action. This gives an amplitude process related to the sum over histories" approach to quantum mechanics. Finally, we briefly discuss a discrete form of Einstein's field equation and speculate how this may be employed to compare the present framework with classical general rela...
Stochastic description of quantum Brownian dynamics
Yan, Yun-An; Shao, Jiushu
2016-08-01
Classical Brownian motion has well been investigated since the pioneering work of Einstein, which inspired mathematicians to lay the theoretical foundation of stochastic processes. A stochastic formulation for quantum dynamics of dissipative systems described by the system-plus-bath model has been developed and found many applications in chemical dynamics, spectroscopy, quantum transport, and other fields. This article provides a tutorial review of the stochastic formulation for quantum dissipative dynamics. The key idea is to decouple the interaction between the system and the bath by virtue of the Hubbard-Stratonovich transformation or Itô calculus so that the system and the bath are not directly entangled during evolution, rather they are correlated due to the complex white noises introduced. The influence of the bath on the system is thereby defined by an induced stochastic field, which leads to the stochastic Liouville equation for the system. The exact reduced density matrix can be calculated as the stochastic average in the presence of bath-induced fields. In general, the plain implementation of the stochastic formulation is only useful for short-time dynamics, but not efficient for long-time dynamics as the statistical errors go very fast. For linear and other specific systems, the stochastic Liouville equation is a good starting point to derive the master equation. For general systems with decomposable bath-induced processes, the hierarchical approach in the form of a set of deterministic equations of motion is derived based on the stochastic formulation and provides an effective means for simulating the dissipative dynamics. A combination of the stochastic simulation and the hierarchical approach is suggested to solve the zero-temperature dynamics of the spin-boson model. This scheme correctly describes the coherent-incoherent transition (Toulouse limit) at moderate dissipation and predicts a rate dynamics in the overdamped regime. Challenging problems
Quantum phase transitions with dynamical flavors
Bea, Yago; Ramallo, Alfonso V
2016-01-01
We study the properties of a D6-brane probe in the ABJM background with smeared massless dynamical quarks in the Veneziano limit. Working at zero temperature and non-vanishing charge density, we show that the system undergoes a quantum phase transition in which the topology of the brane embedding changes from a black hole to a Minkowski embedding. In the unflavored background the phase transition is of second order and takes place when the charge density vanishes. We determine the corresponding critical exponents and show that the scaling behavior near the quantum critical point has multiplicative logarithmic corrections. In the background with dynamical quarks the phase transition is of first order and occurs at non-zero charge density. In this case we compute the discontinuity of several physical quantities as functions of the number $N_f$ of unquenched quarks of the background.
Quantum phase transitions with dynamical flavors
Bea, Yago; Jokela, Niko; Ramallo, Alfonso V.
2016-07-01
We study the properties of a D6-brane probe in the Aharony-Bergman-Jafferis-Maldacena (ABJM) background with smeared massless dynamical quarks in the Veneziano limit. Working at zero temperature and nonvanishing charge density, we show that the system undergoes a quantum phase transition in which the topology of the brane embedding changes from a black hole to a Minkowski embedding. In the unflavored background the phase transition is of second order and takes place when the charge density vanishes. We determine the corresponding critical exponents and show that the scaling behavior near the quantum critical point has multiplicative logarithmic corrections. In the background with dynamical quarks the phase transition is of first order and occurs at nonzero charge density. In this case we compute the discontinuity of several physical quantities as functions of the number Nf of unquenched quarks of the background.
Effective Dynamics of Disordered Quantum Systems
Kropf, Chahan M.; Gneiting, Clemens; Buchleitner, Andreas
2016-07-01
We derive general evolution equations describing the ensemble-average quantum dynamics generated by disordered Hamiltonians. The disorder average affects the coherence of the evolution and can be accounted for by suitably tailored effective coupling agents and associated rates that encode the specific statistical properties of the Hamiltonian's eigenvectors and eigenvalues, respectively. Spectral disorder and isotropically disordered eigenvector distributions are considered as paradigmatic test cases.
Momentum Dynamics of One Dimensional Quantum Walks
Fuss, I; Sherman, P J; Naguleswaran, S; Fuss, Ian; White, langord B.; Sherman, Peter J.; Naguleswaran, Sanjeev
2006-01-01
We derive the momentum space dynamic equations and state functions for one dimensional quantum walks by using linear systems and Lie group theory. The momentum space provides an analytic capability similar to that contributed by the z transform in discrete systems theory. The state functions at each time step are expressed as a simple sum of three Chebyshev polynomials. The functions provide an analytic expression for the development of the walks with time.
Discrepancies in quantum electro-dynamics
Chantler, C. T.
2004-10-01
Experimental tests of quantum electro-dynamics (QED) have developed dramatically for simple atomic systems such as hydrogen. However, a range of anomalies has been discovered recently. There has also been significant progress for medium- Z hydrogenic and helium-like atoms. In this area tests are often based on X-ray spectroscopic measurements. Future prospects for critical insight into the nature and convergence of QED in multi-electron systems will be discussed.
Discrepancies in quantum electro-dynamics
Energy Technology Data Exchange (ETDEWEB)
Chantler, C.T. E-mail: chantler@ph.unimelb.edu.au
2004-11-01
Experimental tests of quantum electro-dynamics (QED) have developed dramatically for simple atomic systems such as hydrogen. However, a range of anomalies has been discovered recently. There has also been significant progress for medium-Z hydrogenic and helium-like atoms. In this area tests are often based on X-ray spectroscopic measurements. Future prospects for critical insight into the nature and convergence of QED in multi-electron systems will be discussed.
Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-01-01
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and
Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-01-01
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and
Scalable molecular dynamics with NAMD.
Phillips, James C; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D; Kalé, Laxmikant; Schulten, Klaus
2005-12-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. (c) 2005 Wiley Periodicals, Inc.
Rheology via nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.
Quantum Dynamics of the HMF Model
Plestid, Ryan; Mahon, Perry; O'Dell, Duncan
2016-01-01
We study the dynamics of the quantized Hamiltonian Mean Field (HMF) model assuming a gas of bosons in the large N limit. We characterize the full set of stationary states, and study the dynamics of the model numerically focussing on competition between classical and quantum effects. We make contact with the existing literature on the HMF model as a classical system, and stress universal features which can be inferred in the semi-classical limit.In particular we show that the characteristic ch...
Energy Technology Data Exchange (ETDEWEB)
Matsuoka, Leo, E-mail: leo-matsuoka@hiroshima-u.ac.jp [Graduate School of Engineering, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8527 (Japan); Segawa, Etsuo [Graduate School of Information Sciences, Tohoku University, Aoba, Sendai 980-8579 (Japan); Yuki, Kenta [Graduate School of Engineering, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8527 (Japan); Konno, Norio [Department of Applied Mathematics, Faculty of Engineering, Yokohama National University, Hodogaya, Yokohama 240-8501 (Japan); Obata, Nobuaki [Graduate School of Information Sciences, Tohoku University, Aoba, Sendai 980-8579 (Japan)
2017-06-09
We performed a mathematical analysis of the time-dependent dynamics of a quantum-kicked rotor implemented in a diatomic molecule under the condition of ideal quantum resonance. We examined a model system featuring a diatomic molecule in a periodic train of terahertz pulses, regarding the molecule as a rigid rotor with the state-dependent transition moment and including the effect of the magnetic quantum number M. We derived the explicit expression for the asymptotic distribution of a rotational population by making the transition matrix correspondent with a sequence of ultraspherical polynomials. The mathematical results obtained were validated by numerical simulations. - Highlights: • The behavior of the molecular quantum-kicked rotor was mathematically investigated. • The matrix elements were made correspondent with the ultraspherical polynomials. • The explicit formula for asymptotic distribution was obtained. • Complete agreement with the numerical simulation was verified.
Charge and Energy Transfer Dynamics in Molecular Systems
May, Volkhard
2004-01-01
This second edition is based on the successful concept of the first edition in presenting a unified perspective on molecular charge and energy transfer processes. The authors bridge the regimes of coherent and dissipative dynamics, thus establishing the connection between classic rate theories and modern treatments of ultrafast phenomena. The book serves as an introduction for graduate students and researchers. Among the new topics of this second edition are. - semiclassical and quantum-classical hybrid formulations of molecular dynamics. - the basics of femtosecond nonlinear spectroscopy. - e
Casalino, Lorenzo; Palermo, Giulia; Abdurakhmonova, Nodira; Rothlisberger, Ursula; Magistrato, Alessandra
2017-01-10
The vital contribution of Mg(2+) ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg(2+) exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg(2+) force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg(2+) ions in different coordination motifs. As a result, a total of ∼2.5 μs MD simulations (100/200 ns for each run) for two prototypical Mg(2+)-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg(2+)-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg(2+) ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg(2+) ion parameters is not in line with the physical origin of the Mg(2+)-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg(2+) models and provides novel insights for the rational development of next-generation Mg(2+) FFs to be employed for atomistic simulations of RNA.
Molecular structures and intramolecular dynamics of pentahalides
Ischenko, A. A.
2017-03-01
This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.
Better, Cheaper, Faster Molecular Dynamics
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
Applications of Quantum Probability Theory to Dynamic Decision Making
2015-08-13
quantum learning algorithm for the dynamic environments; and most importantly, (c) To experimentally test whether the quantum reinforcement learning...seeking tasks, which are relevant to Air Force applications. In particular, we developed a new quantum reinforcement learning algorithm for MDP’s. The... quantum reinforcement-learning algorithm does not require a quantum computer, and can be directly used to learn to perform practical sequential
Control of Exciton Dynamics in Nanodots for Quantum Operations
Chen, Pochung; Piermarocchi, C.; Sham, L. J.
2001-08-01
We present a theory to further a new perspective of proactive control of exciton dynamics in the quantum limit. Circularly polarized optical pulses in a semiconductor nanodot are used to control the dynamics of two interacting excitons of opposite polarizations. Shaping of femtosecond laser pulses keeps the quantum operation within the decoherence time. Computation of the fidelity of the operations and application to the complete solution of a minimal quantum computing algorithm demonstrate in theory the feasibility of quantum control.
Magnetic polyoxometalates: from molecular magnetism to molecular spintronics and quantum computing.
Clemente-Juan, Juan M; Coronado, Eugenio; Gaita-Ariño, Alejandro
2012-11-21
In this review we discuss the relevance of polyoxometalate (POM) chemistry to provide model objects in molecular magnetism. We present several potential applications in nanomagnetism, in particular, in molecular spintronics and quantum computing.
Conditional and unconditional Gaussian quantum dynamics
Genoni, Marco G.; Lami, Ludovico; Serafini, Alessio
2016-07-01
This article focuses on the general theory of open quantum systems in the Gaussian regime and explores a number of diverse ramifications and consequences of the theory. We shall first introduce the Gaussian framework in its full generality, including a classification of Gaussian (also known as 'general-dyne') quantum measurements. In doing so, we will give a compact proof for the parametrisation of the most general Gaussian completely positive map, which we believe to be missing in the existing literature. We will then move on to consider the linear coupling with a white noise bath, and derive the diffusion equations that describe the evolution of Gaussian states under such circumstances. Starting from these equations, we outline a constructive method to derive general master equations that apply outside the Gaussian regime. Next, we include the general-dyne monitoring of the environmental degrees of freedom and recover the Riccati equation for the conditional evolution of Gaussian states. Our derivation relies exclusively on the standard quantum mechanical update of the system state, through the evaluation of Gaussian overlaps. The parametrisation of the conditional dynamics we obtain is novel and, at variance with existing alternatives, directly ties in to physical detection schemes. We conclude our study with two examples of conditional dynamics that can be dealt with conveniently through our formalism, demonstrating how monitoring can suppress the noise in optical parametric processes as well as stabilise systems subject to diffusive scattering.
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Energy Technology Data Exchange (ETDEWEB)
Kapil, V.; Ceriotti, M., E-mail: michele.ceriotti@epfl.ch [Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland); VandeVondele, J., E-mail: joost.vandevondele@mat.ethz.ch [Department of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich (Switzerland)
2016-02-07
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.
Dynamical response near quantum critical points
Lucas, Andrew; Podolsky, Daniel; Witczak-Krempa, William
2016-01-01
We study high frequency response functions, notably the optical conductivity, in the vicinity of quantum critical points (QCPs) by allowing for both detuning from the critical coupling and finite temperature. We consider general dimensions and dynamical exponents. This leads to a unified understanding of sum rules. In systems with emergent Lorentz invariance, powerful methods from conformal field theory allow us to fix the high frequency response in terms of universal coefficients. We test our predictions analytically in the large-N O(N) model and using the gauge-gravity duality, and numerically via Quantum Monte Carlo simulations on a lattice model hosting the interacting superfluid-insulator QCP. In superfluid phases, interacting Goldstone bosons qualitatively change the high frequency optical conductivity, and the corresponding sum rule.
Coherent spin dynamics in semiconductor quantum dots
Energy Technology Data Exchange (ETDEWEB)
Amand, T.; Senes, M.; Marie, X.; Renucci, P. [Laboratoire de Nanophysique, Magnetisme et Optoelectronique-LPMC, INSA, 135 avenue de Rangueil, 31077 Toulouse cedex 4 (France); Urbaszek, B. [Laboratoire de Nanophysique, Magnetisme et Optoelectronique-LPMC, INSA, 135 avenue de Rangueil, 31077 Toulouse cedex 4 (France); Department of Physics, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Krebs, O.; Laurent, S.; Voisin, P. [Laboratoire de Photonique et Nanostructures, route de Nozay, 91460 Marcoussis (France); Warburton, R.J. [Department of Physics, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom)
2005-05-01
The anisotropic exchange interaction (AEI) between electrons and holes is shown to play a central role in quantum dots (QDs) spin dynamics. In neutral QDs, AEI is at the origin of spin quantum beats observed under resonant excitation between the lowest energy doublet of linearly dipole-active eigenstates. In negatively charged QDs, AEI is at the origin of QD emission with opposite helicity to the optic al excitation, under non-resonant excitation conditions. Finally, the possibility of leaving a spin information in the system after recombination of the photo-injected electron-hole pair is discussed with respect to the type and the level of the doping. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Quantum dynamical entropy and decoherence rate
Energy Technology Data Exchange (ETDEWEB)
Alicki, Robert [Institute of Theoretical Physics and Astrophysics, University of Gdansk, ul. Wita Stwosza 57, PL 80-952 Gdansk (Poland); Lozinski, Artur [Institute of Physics, Jagiellonian University, ul. Reymonta 4, 30-059 Cracow (Poland); Pakonski, Prot [Institute of Physics, Jagiellonian University, ul. Reymonta 4, 30-059 Cracow (Poland); Zyczkowski, Karol [Institute of Physics, Jagiellonian University, ul. Reymonta 4, 30-059 Krakow (Poland)
2004-05-14
We investigate quantum dynamical systems defined on a finite-dimensional Hilbert space and subjected to an interaction with an environment. The rate of decoherence of initially pure states, measured by the increase of their von Neumann entropy, averaged over an ensemble of random pure states, is proved to be bounded from above by the partial entropy used to define the ALF-dynamical entropy. The rate of decoherence induced by the sequence of the von Neumann projectors measurements is shown to be maximal, if the measurements are performed in a randomly chosen basis. The numerically observed linear increase of entropies is attributed to free independence of the measured observable and the unitary dynamical map.
Quantum dynamical entropy and decoherence rate
Alicki, R; Pakonski, P; Zyczkowski, K; Alicki, Robert; Lozinski, Artur; Pakonski, Prot; Zyczkowski, Karol
2004-01-01
We investigate quantum dynamical systems defined on a finite dimensional Hilbert space and subjected to an interaction with an environment. The rate of decoherence of initially pure states, measured by the increase of their von Neumann entropy, averaged over an ensemble of random pure states, is proved to be bounded from above by the partial entropy used to define the ALF dynamical entropy. The rate of decoherence induced by the sequence of the von Neumann projectors measurements is shown to be maximal, if the measurements are performed in a randomly chosen basis. The numerically observed linear increase of entropies is attributed to free-independence of the measured observable and the unitary dynamical map.
Quantum dynamics of two-photon quantum Rabi model
Lü, Zhiguo; Zhao, Chunjian; Zheng, Hang
2017-02-01
We apply a simple analytical method based on a unitary transformation to calculate the ground state, its excitation spectrum and quantum dynamic evolution of physical quantities for the double-photon quantum Rabi Hamiltonian over the wide coupling-strength range. The concise analytical method possesses the same mathematical simplicity as the approach of the rotating wave approximation (RWA). By quantitative comparison with the numerically exact result obtained by matrix diagonalization, we confirm that our calculated results obtained by transformed rotating-wave method are not only accurate in the weak coupling regime but also correct in intermediate strong-coupling case. In the intermediate ultrastrong-coupling regime, the calculated values of the ground state and lower lying excited states are nearly the same as the exact ones. It turns out that our calculation for the energy spectrum is beyond the ordinary-RWA. Meanwhile, we demonstrate the signatures resulting from the counter-rotating wave terms by monitoring the population, the coherence, the squeezing of the photon under the ultra-strong conditions. In particular, we find that when the frequency of the photon is much larger than the transition frequency of the system, the lineshape of the time evolution becomes complicated with the increase of the coupling strength, which may be verified experimentally.
Quantum walk coherences on a dynamical percolation graph
Elster, Fabian; Barkhofen, Sonja; Nitsche, Thomas; Novotný, Jaroslav; Gábris, Aurél; Jex, Igor; Silberhorn, Christine
2015-08-01
Coherent evolution governs the behaviour of all quantum systems, but in nature it is often subjected to influence of a classical environment. For analysing quantum transport phenomena quantum walks emerge as suitable model systems. In particular, quantum walks on percolation structures constitute an attractive platform for studying open system dynamics of random media. Here, we present an implementation of quantum walks differing from the previous experiments by achieving dynamical control of the underlying graph structure. We demonstrate the evolution of an optical time-multiplexed quantum walk over six double steps, revealing the intricate interplay between the internal and external degrees of freedom. The observation of clear non-Markovian signatures in the coin space testifies the high coherence of the implementation and the extraordinary degree of control of all system parameters. Our work is the proof-of-principle experiment of a quantum walk on a dynamical percolation graph, paving the way towards complex simulation of quantum transport in random media.
Quantum walk coherences on a dynamical percolation graph.
Elster, Fabian; Barkhofen, Sonja; Nitsche, Thomas; Novotný, Jaroslav; Gábris, Aurél; Jex, Igor; Silberhorn, Christine
2015-08-27
Coherent evolution governs the behaviour of all quantum systems, but in nature it is often subjected to influence of a classical environment. For analysing quantum transport phenomena quantum walks emerge as suitable model systems. In particular, quantum walks on percolation structures constitute an attractive platform for studying open system dynamics of random media. Here, we present an implementation of quantum walks differing from the previous experiments by achieving dynamical control of the underlying graph structure. We demonstrate the evolution of an optical time-multiplexed quantum walk over six double steps, revealing the intricate interplay between the internal and external degrees of freedom. The observation of clear non-Markovian signatures in the coin space testifies the high coherence of the implementation and the extraordinary degree of control of all system parameters. Our work is the proof-of-principle experiment of a quantum walk on a dynamical percolation graph, paving the way towards complex simulation of quantum transport in random media.
Pseudospectral Gaussian quantum dynamics: Efficient sampling of potential energy surfaces
Heaps, Charles W.; Mazziotti, David A.
2016-04-01
Trajectory-based Gaussian basis sets have been tremendously successful in describing high-dimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussian-based method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O ( N ) potential energy calculations, in contrast to O ( N 2 ) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O ( N ) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant.
Chaos and Nonlinear Dynamics in a Quantum Artificial Economy
Gonçalves, Carlos Pedro
2012-01-01
Chaos and nonlinear economic dynamics are addressed for a quantum coupled map lattice model of an artificial economy, with quantized supply and demand equilibrium conditions. The measure theoretic properties and the patterns that emerge in both the economic business volume dynamics' diagrams as well as in the quantum mean field averages are addressed and conclusions are drawn in regards to the application of quantum chaos theory to address signatures of chaotic dynamics in relevant discrete economic state variables.
Surface hopping in laser-driven molecular dynamics
Fiedlschuster, T.; Handt, J.; Gross, E. K. U.; Schmidt, R.
2017-06-01
A theoretical justification of the empirical surface hopping method for the laser-driven molecular dynamics is given by utilizing the formalism of the exact factorization of the molecular wave function [Abedi et al., Phys. Rev. Lett. 105, 123002 (2010), 10.1103/PhysRevLett.105.123002] in its quantum-classical limit. Employing an exactly solvable H2+-like model system, it is shown that the deterministic classical nuclear motion on a single time-dependent surface in this approach describes the same physics as stochastic (hopping-induced) motion on several surfaces, provided Floquet surfaces are applied. Both quantum-classical methods do describe reasonably well the exact nuclear wave-packet dynamics for extremely different dissociation scenarios. Hopping schemes using Born-Oppenheimer surfaces or instantaneous Born-Oppenheimer surfaces fail completely.
Surface hopping methodology in laser-driven molecular dynamics
Fiedlschuster, T; Gross, E K U; Schmidt, R
2016-01-01
A theoretical justification of the empirical surface hopping method for the laser-driven molecular dynamics is given utilizing the formalism of the exact factorization of the molecular wavefunction [Abedi et al., PRL $\\textbf{105}$, 123002 (2010)] in its quantum-classical limit. Employing an exactly solvable $\\textrm H_2^{\\;+}$-like model system, it is shown that the deterministic classical nuclear motion on a single time-dependent surface in this approach describes the same physics as stochastic (hopping-induced) motion on several surfaces, provided Floquet surfaces are applied. Both quantum-classical methods do describe reasonably well the exact nuclear wavepacket dynamics for extremely different dissociation scenarios. Hopping schemes using Born-Oppenheimer surfaces or instantaneous Born-Oppenheimer surfaces fail completely.
Heaps, Charles W
2016-01-01
Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schr\\"{o}dinger equation with $N$ Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from $\\mathcal{O}(N^2)$ to $\\mathcal{O}(N)$. By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems; the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-d...
Dynamics of Super Quantum Correlations and Quantum Correlations for a System of Three Qubits
Siyouri, F.; El Baz, M.; Rfifi, S.; Hassouni, Y.
2016-04-01
The dynamics of quantum discord for two qubits independently interacting with dephasing reservoirs have been studied recently. The authors [Phys. Rev. A 88 (2013) 034304] found that for some Bell-diagonal states (BDS) which interact with their environments the calculation of quantum discord could experience a sudden transition in its dynamics, this phenomenon is known as the sudden change. Here in the present paper, we analyze the dynamics of normal quantum discord and super quantum discord for tripartite Bell-diagonal states independently interacting with dephasing reservoirs. Then, we find that basis change does not necessary mean sudden change of quantum correlations.
Topological blocking in quantum quench dynamics
Kells, G.; Sen, D.; Slingerland, J. K.; Vishveshwara, S.
2014-06-01
We study the nonequilibrium dynamics of quenching through a quantum critical point in topological systems, focusing on one of their defining features: ground-state degeneracies and associated topological sectors. We present the notion of "topological blocking," experienced by the dynamics due to a mismatch in degeneracies between two phases, and we argue that the dynamic evolution of the quench depends strongly on the topological sector being probed. We demonstrate this interplay between quench and topology in models stemming from two extensively studied systems, the transverse Ising chain and the Kitaev honeycomb model. Through nonlocal maps of each of these systems, we effectively study spinless fermionic p-wave paired topological superconductors. Confining the systems to ring and toroidal geometries, respectively, enables us to cleanly address degeneracies, subtle issues of fermion occupation and parity, and mismatches between topological sectors. We show that various features of the quench, which are related to Kibble-Zurek physics, are sensitive to the topological sector being probed, in particular, the overlap between the time-evolved initial ground state and an appropriate low-energy state of the final Hamiltonian. While most of our study is confined to translationally invariant systems, where momentum is a convenient quantum number, we briefly consider the effect of disorder and illustrate how this can influence the quench in a qualitatively different way depending on the topological sector considered.
Colloquium: Non-Markovian dynamics in open quantum systems
Breuer, Heinz-Peter; Laine, Elsi-Mari; Piilo, Jyrki; Vacchini, Bassano
2016-04-01
The dynamical behavior of open quantum systems plays a key role in many applications of quantum mechanics, examples ranging from fundamental problems, such as the environment-induced decay of quantum coherence and relaxation in many-body systems, to applications in condensed matter theory, quantum transport, quantum chemistry, and quantum information. In close analogy to a classical Markovian stochastic process, the interaction of an open quantum system with a noisy environment is often modeled phenomenologically by means of a dynamical semigroup with a corresponding time-independent generator in Lindblad form, which describes a memoryless dynamics of the open system typically leading to an irreversible loss of characteristic quantum features. However, in many applications open systems exhibit pronounced memory effects and a revival of genuine quantum properties such as quantum coherence, correlations, and entanglement. Here recent theoretical results on the rich non-Markovian quantum dynamics of open systems are discussed, paying particular attention to the rigorous mathematical definition, to the physical interpretation and classification, as well as to the quantification of quantum memory effects. The general theory is illustrated by a series of physical examples. The analysis reveals that memory effects of the open system dynamics reflect characteristic features of the environment which opens a new perspective for applications, namely, to exploit a small open system as a quantum probe signifying nontrivial features of the environment it is interacting with. This Colloquium further explores the various physical sources of non-Markovian quantum dynamics, such as structured environmental spectral densities, nonlocal correlations between environmental degrees of freedom, and correlations in the initial system-environment state, in addition to developing schemes for their local detection. Recent experiments addressing the detection, quantification, and control of
Variational path integral molecular dynamics study of a water molecule
Miura, Shinichi
2013-08-01
In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.
Thermal vibration of a single-walled carbon nanotube predicted by semiquantum molecular dynamics.
Liu, Rumeng; Wang, Lifeng
2015-02-21
Quantum effects should be considered in the thermal vibrations of carbon nanotubes (CNTs). To this end, molecular dynamics based on modified Langevin dynamics, which accounts for quantum statistics by introducing a quantum heat bath, is used to simulate the thermal vibration of a cantilevered single-walled CNT (SWCNT). A nonlocal elastic Timoshenko beam model with quantum effects (TBQN), which can take the effect of microstructure into consideration, has been established to explain the resulting power spectral density of the SWCNT. The root of mean squared (RMS) amplitude of the thermal vibration of the SWCNT obtained from semiquantum molecular dynamics (SQMD) is lower than that obtained from classical molecular dynamics, especially at very low temperature and high-order modes. The natural frequencies of the SWCNT obtained from the Timoshenko beam model are closer to those obtained from molecular dynamics if the nonlocal effect is taken into consideration. However, the nonlocal Timoshenko beam model with the law of energy equipartition (TBCN) can only predict the RMS amplitude of the SWCNT obtained from classical molecular dynamics without considering quantum effects. The RMS amplitude of the SWCNT obtained from SQMD and that obtained from TBQN coincide very well. These results indicate that quantum effects are important for the thermal vibration of the SWCNT in the case of high-order modes, short length and low temperature.
Non-Markovian Dynamics of Quantum Systems
Chruściński, Dariusz; Kossakowski, Andrzej
2011-01-01
We analyze a local approach to the non-Markovian evolution of open quantum systems. It turns out that any dynamical map representing evolution of such a system may be described either by non-local master equation with memory kernel or equivalently by equation which is local in time. The price one pays for the local approach is that the corresponding generator might be highly singular and it keeps the memory about the starting point 't0'. Remarkably, singularities of generator may lead to interesting physical phenomena like revival of coherence or sudden death and revival of entanglement.
Quantum Dynamics of Mesoscopic Driven Duffing Oscillators
Guo, Lingzhen; Li, Xin-Qi
2009-01-01
We investigate the nonlinear dynamics of a mesoscopic driven Duffing oscillator in a quantum regime. In terms of Wigner function, we identify the nature of state near the bifurcation point, and analyze the transient process which reveals two distinct stages of quenching and escape. The rate process in the escape stage allows us to extract the transition rate, which displays perfect scaling behavior with the driving distance to the bifurcation point. We numerically determine the scaling exponent, compare it with existing analytic result, and suggest its possible observation.
Quantum Dynamics as a Stochastic Process
Figueiredo, J M A
2002-01-01
We study the classical motion of a particle subject to a stochastic force. We then present a perturbative schema for the associated Fokker-Planck equation where, in the limit of a vanishingly small noise source, a consistent dynamical model is obtained. The resulting theory is similar to Quantum Mechanics, having the same field equations for probability measures, the same operator structure and symmetric ordering of operators. The model is valid for general electromagnetic interaction as well as many body systems with mutual interactions of general nature.
Quantum Computing Resource Estimate of Molecular Energy Simulation
Whitfield, James D; Aspuru-Guzik, Alán
2010-01-01
Over the last century, ingenious physical and mathematical insights paired with rapidly advancing technology have allowed the field of quantum chemistry to advance dramatically. However, efficient methods for the exact simulation of quantum systems on classical computers do not exist. The present paper reports an extension of one of the authors' previous work [Aspuru-Guzik et al., Science {309} p. 1704, (2005)] where it was shown that the chemical Hamiltonian can be efficiently simulated using a quantum computer. In particular, we report in detail how a set of molecular integrals can be used to create a quantum circuit that allows the energy of a molecular system with fixed nuclear geometry to be extracted using the phase estimation algorithm proposed by Abrams and Lloyd [Phys. Rev. Lett. {83} p. 5165, (1999)]. We extend several known results related to this idea and present numerical examples of the state preparation procedure required in the algorithm. With future quantum devices in mind, we provide a compl...
Molecular Dynamics and Picosecond Vibrational Spectra.
1980-07-01
and Identify by block number) molecular dynamics picosecond infra-red spectra crmputer simulation vibrational spectra array processor linear rcsponse...that for molecular dynamics theoretical computation is now long enough, to significantly overlap. This overlap of theory and experiment can, at least...to discover these microscopic atomic trajectories, i.e. the molecular dynamics of solution processes, we must be able to both theoretically compute
Molecular Dynamics in the Vacuum Ultraviolet
1989-01-30
CLASSIFICATION OF THIS PAGE COMPLETED PROJECT SUMMARY TITLE: Molecular dynamics in the Vacuum Ultraviolet PRINCIPAL INVESTIGATOR: Paul L. Houston...DTIC TAB 0 Unannounced 0 By Distr ibution I Availability Codes Avail and I or Dist Special I Molecular Dynamics In the Vacuum Ultraviolet Final Technical...Further development of tunable vacuum ultraviolet sources has opened wide areas of molecular dynamics for study. Completed Research Photodissociation of
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Brownian motion from molecular dynamics
Shin, Hyun Kyung; Talkner, Peter; Lee, Eok Kyun
2010-01-01
Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force which enter the generalized Langevin equation of the Brownian particle are determined and their dependence on mass and diameter are investigated for two different fluid densities. Deviations of the fluctuating force distribution from a Gaussian form are observed for small particle diameters. For heavy particles the deviations of the fluctuating force from the total force acting on the Brownian particle decrease linearly with the mass ratio m/M where m denotes the mass of a fluid particle.
Quantum Entanglement Growth Under Random Unitary Dynamics
Nahum, Adam; Vijay, Sagar; Haah, Jeongwan
2016-01-01
Characterizing how entanglement grows with time in a many-body system, for example after a quantum quench, is a key problem in non-equilibrium quantum physics. We study this problem for the case of random unitary dynamics, representing either Hamiltonian evolution with time--dependent noise or evolution by a random quantum circuit. Our results reveal a universal structure behind noisy entanglement growth, and also provide simple new heuristics for the `entanglement tsunami' in Hamiltonian systems without noise. In 1D, we show that noise causes the entanglement entropy across a cut to grow according to the celebrated Kardar--Parisi--Zhang (KPZ) equation. The mean entanglement grows linearly in time, while fluctuations grow like $(\\text{time})^{1/3}$ and are spatially correlated over a distance $\\propto (\\text{time})^{2/3}$. We derive KPZ universal behaviour in three complementary ways, by mapping random entanglement growth to: (i) a stochastic model of a growing surface; (ii) a `minimal cut' picture, reminisce...
Quantum dynamics of fast chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Light, J.C. [Univ. of Chicago, IL (United States)
1993-12-01
The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.
Classical vs Quantum Games: Continuous-time Evolutionary Strategy Dynamics
Leung, Ming Lam
2011-01-01
This paper unifies the concepts of evolutionary games and quantum strategies. First, we state the formulation and properties of classical evolutionary strategies, with focus on the destinations of evolution in 2-player 2-strategy games. We then introduce a new formalism of quantum evolutionary dynamics, and give an example where an evolving quantum strategy gives reward if played against its classical counterpart.
Geometric reduction of dynamical nonlocality in nanoscale quantum circuits
Strambini, E.; Makarenko, K.S.; Abulizi, G.; Jong, de M.P.; Wiel, van der W.G.
2016-01-01
Nonlocality is a key feature discriminating quantum and classical physics. Quantum-interference phenomena, such as Young’s double slit experiment, are one of the clearest manifestations of nonlocality, recently addressed as dynamical to specify its origin in the quantum equations of motion. It is we
Quantum dynamics of the damped harmonic oscillator
Philbin, T G
2012-01-01
The quantum theory of the damped harmonic oscillator has been a subject of continual investigation since the 1930s. The obstacle to quantization created by the dissipation of energy is usually dealt with by including a discrete set of additional harmonic oscillators as a reservoir. But a discrete reservoir cannot directly yield dynamics such as Ohmic damping (proportional to velocity) of the oscillator of interest. By using a continuum of oscillators as a reservoir, we canonically quantize the harmonic oscillator with Ohmic damping and also with general damping behaviour. The dynamics of a damped oscillator is determined by an arbitrary effective susceptibility that obeys Kramers-Kronig relations. This approach offers an alternative description of nano-mechanical oscillators and opto-mechanical systems.
Polymer Quantum Dynamics of the Taub Universe
Battisti, Marco Valerio; Montani, Giovanni
2008-01-01
Within the framework of non-standard (Weyl) representations of the canonical commutation relations, we investigate the polymer quantization of the Taub cosmological model. The Taub model is analyzed within the Arnowitt-Deser-Misner reduction of its dynamics, by which a time variable arises. While the energy variable and its conjugate momentum are treated as ordinary Heisenberg operators, the anisotropy variable and its conjugate momentum are represented by the polymer technique. The model is analyzed at both classical and quantum level. As a result, classical trajectories flatten with respect to the potential wall, and the cosmological singularity is not probabilistically removed. In fact, the dynamics of the wave packets is characterized by an interference phenomenon, which, however, is not able to stop the evolution towards the classical singularity.
Molecular dynamics of membrane proteins.
Energy Technology Data Exchange (ETDEWEB)
Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); Crozier, Paul Stewart; Stevens, Mark Jackson
2004-10-01
Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.
Quantum mechanics emerging from stochastic dynamics of virtual particles
Tsekov, R
2015-01-01
It is demonstrated how quantum mechanics emerges from the stochastic dynamics of force-carriers. It is shown that the quantum Moyal equation corresponds to some dynamic correlations between the momentum of a real particle and the position of a virtual particle, which are not present in classical mechanics. The new concept throws light on the physical meaning of quantum theory, showing that the Planck constant square is a second-second cross-cumulant. The novel approach to quantum systems is extended to the relativistic case and an expression is derived for the relativistic mass in the Wigner quantum phase-space.
Dynamics of Quantum Entanglement in Reservoir with Memory Effects
Institute of Scientific and Technical Information of China (English)
郝翔; 沙金巧; 孙坚; 朱士群
2012-01-01
The non-Markovian dynamics of quantum entanglement is studied by the Shabani-Lidar master equation when one of entangled quantum systems is coupled to a local reservoir with memory effects. The completely positive reduced dynamical map can be constructed in the Kraus representation. Quantum entanglement decays more slowly in the non-Markovian environment. The decoherence time for quantum entanglement can be markedly increased with the change of the memory kernel. It is found out that the entanglement sudden death between quantum systems and entanglement sudden birth between the system and reservoir occur at different instants.
Quantum Computing, $NP$-complete Problems and Chaotic Dynamics
Ohya, M; Ohya, Masanori; Volovich, Igor V.
1999-01-01
An approach to the solution of NP-complete problems based on quantumcomputing and chaotic dynamics is proposed. We consider the satisfiabilityproblem and argue that the problem, in principle, can be solved in polynomialtime if we combine the quantum computer with the chaotic dynamics amplifierbased on the logistic map. We discuss a possible implementation of such achaotic quantum computation by using the atomic quantum computer with quantumgates described by the Hartree-Fock equations. In this case, in principle, onecan build not only standard linear quantum gates but also nonlinear gates andmoreover they obey to Fermi statistics. This new type of entaglement relatedwith Fermi statistics can be interesting also for quantum communication theory.
Programming an Interpreter Using Molecular Dynamics
Directory of Open Access Journals (Sweden)
C.A. Middelburg
2007-01-01
Full Text Available PGA (ProGram Algebra is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.
Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.
Shen, Lin; Wu, Jingheng; Yang, Weitao
2016-10-11
Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.
Quantum Entanglement Growth under Random Unitary Dynamics
Nahum, Adam; Ruhman, Jonathan; Vijay, Sagar; Haah, Jeongwan
2017-07-01
Characterizing how entanglement grows with time in a many-body system, for example, after a quantum quench, is a key problem in nonequilibrium quantum physics. We study this problem for the case of random unitary dynamics, representing either Hamiltonian evolution with time-dependent noise or evolution by a random quantum circuit. Our results reveal a universal structure behind noisy entanglement growth, and also provide simple new heuristics for the "entanglement tsunami" in Hamiltonian systems without noise. In 1D, we show that noise causes the entanglement entropy across a cut to grow according to the celebrated Kardar-Parisi-Zhang (KPZ) equation. The mean entanglement grows linearly in time, while fluctuations grow like (time )1/3 and are spatially correlated over a distance ∝(time )2/3. We derive KPZ universal behavior in three complementary ways, by mapping random entanglement growth to (i) a stochastic model of a growing surface, (ii) a "minimal cut" picture, reminiscent of the Ryu-Takayanagi formula in holography, and (iii) a hydrodynamic problem involving the dynamical spreading of operators. We demonstrate KPZ universality in 1D numerically using simulations of random unitary circuits. Importantly, the leading-order time dependence of the entropy is deterministic even in the presence of noise, allowing us to propose a simple coarse grained minimal cut picture for the entanglement growth of generic Hamiltonians, even without noise, in arbitrary dimensionality. We clarify the meaning of the "velocity" of entanglement growth in the 1D entanglement tsunami. We show that in higher dimensions, noisy entanglement evolution maps to the well-studied problem of pinning of a membrane or domain wall by disorder.
Quantum Entanglement Growth under Random Unitary Dynamics
Directory of Open Access Journals (Sweden)
Adam Nahum
2017-07-01
Full Text Available Characterizing how entanglement grows with time in a many-body system, for example, after a quantum quench, is a key problem in nonequilibrium quantum physics. We study this problem for the case of random unitary dynamics, representing either Hamiltonian evolution with time-dependent noise or evolution by a random quantum circuit. Our results reveal a universal structure behind noisy entanglement growth, and also provide simple new heuristics for the “entanglement tsunami” in Hamiltonian systems without noise. In 1D, we show that noise causes the entanglement entropy across a cut to grow according to the celebrated Kardar-Parisi-Zhang (KPZ equation. The mean entanglement grows linearly in time, while fluctuations grow like (time^{1/3} and are spatially correlated over a distance ∝(time^{2/3}. We derive KPZ universal behavior in three complementary ways, by mapping random entanglement growth to (i a stochastic model of a growing surface, (ii a “minimal cut” picture, reminiscent of the Ryu-Takayanagi formula in holography, and (iii a hydrodynamic problem involving the dynamical spreading of operators. We demonstrate KPZ universality in 1D numerically using simulations of random unitary circuits. Importantly, the leading-order time dependence of the entropy is deterministic even in the presence of noise, allowing us to propose a simple coarse grained minimal cut picture for the entanglement growth of generic Hamiltonians, even without noise, in arbitrary dimensionality. We clarify the meaning of the “velocity” of entanglement growth in the 1D entanglement tsunami. We show that in higher dimensions, noisy entanglement evolution maps to the well-studied problem of pinning of a membrane or domain wall by disorder.
Morphogenesis and dynamics of quantum state
Leifer, Peter
2008-01-01
New construction of 4D dynamical space-time (DST) has been proposed in the framework of unification of relativity and quantum theory. Such unification is based solely on the fundamental notion of generalized coherent state (GCS) of N-level system and the geometry of unitary group SU(N) acting in state space $C^N$. Neither contradictable notion of quantum particle, nor space-time coordinates (that cannot be a priori attached to nothing) are used in this construction. Morphogenesis of the "field shell"-lump of GCS and its dynamics have been studied for N=2 in DST. The main technical problem is to find non-Abelian gauge field arising from conservation law of the local Hailtonian vector field. The last one may be expressed as parallel transport of local Hamiltonian in projective Hilbert space $CP(N-1)$. Co-movable local "Lorentz frame" being attached to GCS is used for qubit encoding result of comparison of the parallel transported local Hamiltonian in infinitesimally close points. This leads to quasi-linear rela...
Modeling quantum fluid dynamics at nonzero temperatures
Berloff, Natalia G.; Brachet, Marc; Proukakis, Nick P.
2014-03-01
The detailed understanding of the intricate dynamics of quantum fluids, in particular in the rapidly growing subfield of quantum turbulence which elucidates the evolution of a vortex tangle in a superfluid, requires an in-depth understanding of the role of finite temperature in such systems. The Landau two-fluid model is the most successful hydrodynamical theory of superfluid helium, but by the nature of the scale separations it cannot give an adequate description of the processes involving vortex dynamics and interactions. In our contribution we introduce a framework based on a nonlinear classical-field equation that is mathematically identical to the Landau model and provides a mechanism for severing and coalescence of vortex lines, so that the questions related to the behavior of quantized vortices can be addressed self-consistently. The correct equation of state as well as nonlocality of interactions that leads to the existence of the roton minimum can also be introduced in such description. We review and apply the ideas developed for finite-temperature description of weakly interacting Bose gases as possible extensions and numerical refinements of the proposed method. We apply this method to elucidate the behavior of the vortices during expansion and contraction following the change in applied pressure. We show that at low temperatures, during the contraction of the vortex core as the negative pressure grows back to positive values, the vortex line density grows through a mechanism of vortex multiplication. This mechanism is suppressed at high temperatures.
Dynamics of a Quantum Reference Frame
Poulin, D; Poulin, David; Yard, Jon
2006-01-01
We analyze a quantum mechanical gyroscope, which is modeled as a large spin and used as a reference against which to measure the angular momenta of spin-1/2 particles. These measurements induce a back-action on the reference which is the central focus of our study. We begin by deriving explicit expressions for the quantum channel representing the back-action. Then, we analyze the dynamics incurred by the reference when it is used to sequentially measure particles drawn from a fixed ensemble. We prove that the reference thermalizes with the measured particles and find that generically, the thermal state is reached in time which scales linearly with the size of the reference. This contrasts a recent conclusion of Bartlett et al. that this takes a quadratic amount of time when the particles are completely unpolarized. We now understand their result in terms of a simple physical principle based on symmetries and conservation laws. Finally, we initiate the study of the non-equilibrium dynamics of the reference. He...
Dynamical phase transitions in quantum mechanics
Directory of Open Access Journals (Sweden)
Rotter Ingrid
2012-02-01
Full Text Available The nucleus is described as an open many-body quantum system with a non-Hermitian Hamilton operator the eigenvalues of which are complex, in general. The eigenvalues may cross in the complex plane (exceptional points, the phases of the eigenfunctions are not rigid in approaching the crossing points and the widths bifurcate. By varying only one parameter, the eigenvalue trajectories usually avoid crossing and width bifurcation occurs at the critical value of avoided crossing. An analog spectroscopic redistribution takes place for discrete states below the particle decay threshold. By this means, a dynamical phase transition occurs in the many-level system starting at a critical value of the level density. Hence the properties of the low-lying nuclear states (described well by the shell model and those of highly excited nuclear states (described by random ensembles differ fundamentally from one another. The statement of Niels Bohr on the collective features of compound nucleus states at high level density is therefore not in contradiction to the shell-model description of nuclear (and atomic states at low level density. Dynamical phase transitions are observed experimentally in different quantum mechanical systems by varying one or two parameters.
Universal Quantum Gates Based on Both Geometric and Dynamic Phases in Quantum Dots
Institute of Scientific and Technical Information of China (English)
杨开宇; 朱诗亮; 汪子丹
2003-01-01
A large-scalable quantum computer model, whose qubits are represented by the subspace subtended by the ground state and the single exciton state on semiconductor quantum dots, is proposed. A universal set of quantum gates in this system may be achieved by a mixed approach, composed of dynamic evolution and nonadiabatic geometric phase.
Quantum Sensing of Noisy and Complex Systems under Dynamical Control
Directory of Open Access Journals (Sweden)
Gershon Kurizki
2016-12-01
Full Text Available We review our unified optimized approach to the dynamical control of quantum-probe interactions with noisy and complex systems viewed as thermal baths. We show that this control, in conjunction with tools of quantum estimation theory, may be used for inferring the spectral and spatial characteristics of such baths with high precision. This approach constitutes a new avenue in quantum sensing, dubbed quantum noise spectroscopy.
Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation.
Polyak, Iakov; Benighaus, Tobias; Boulanger, Eliot; Thiel, Walter
2013-08-14
The dual Hamiltonian free energy perturbation (DH-FEP) method is designed for accurate and efficient evaluation of the free energy profile of chemical reactions in quantum mechanical/molecular mechanical (QM/MM) calculations. In contrast to existing QM/MM FEP variants, the QM region is not kept frozen during sampling, but all degrees of freedom except for the reaction coordinate are sampled. In the DH-FEP scheme, the sampling is done by semiempirical QM/MM molecular dynamics (MD), while the perturbation energy differences are evaluated from high-level QM/MM single-point calculations at regular intervals, skipping a pre-defined number of MD sampling steps. After validating our method using an analytic model potential with an exactly known solution, we report a QM/MM DH-FEP study of the enzymatic reaction catalyzed by chorismate mutase. We suggest guidelines for QM/MM DH-FEP calculations and default values for the required computational parameters. In the case of chorismate mutase, we apply the DH-FEP approach in combination with a single one-dimensional reaction coordinate and with a two-dimensional collective coordinate (two individual distances), with superior results for the latter choice.
Nonlinear Dynamics and Quantum Transport in Small Systems
2012-02-22
Dynamics and Quantum Transport in Small Systems.” The PI is Ying-Cheng Lai from Arizona State University. The duration of the project was 12/1/2008...military systems may contain some graphene components. To understand various fundamental aspects of quantum transport dynamics is key to developing...conductance fluctuations, not seen previously in any quantum transport systems. This phenomenon has profound implications to the development of graphene
High Fidelity Adiabatic Quantum Computation via Dynamical Decoupling
Quiroz, Gregory
2012-01-01
We introduce high-order dynamical decoupling strategies for open system adiabatic quantum computation. Our numerical results demonstrate that a judicious choice of high-order dynamical decoupling method, in conjunction with an encoding which allows computation to proceed alongside decoupling, can dramatically enhance the fidelity of adiabatic quantum computation in spite of decoherence.
Geometric reduction of dynamical nonlocality in nanoscale quantum circuits
Strambini, E.; Makarenko, K. S.; Abulizi, G.; de Jong, M. P.; van der Wiel, W. G.
2016-01-01
Nonlocality is a key feature discriminating quantum and classical physics. Quantum-interference phenomena, such as Young’s double slit experiment, are one of the clearest manifestations of nonlocality, recently addressed as dynamical to specify its origin in the quantum equations of motion. It is well known that loss of dynamical nonlocality can occur due to (partial) collapse of the wavefunction due to a measurement, such as which-path detection. However, alternative mechanisms affecting dynamical nonlocality have hardly been considered, although of crucial importance in many schemes for quantum information processing. Here, we present a fundamentally different pathway of losing dynamical nonlocality, demonstrating that the detailed geometry of the detection scheme is crucial to preserve nonlocality. By means of a solid-state quantum-interference experiment we quantify this effect in a diffusive system. We show that interference is not only affected by decoherence, but also by a loss of dynamical nonlocality based on a local reduction of the number of quantum conduction channels of the interferometer. With our measurements and theoretical model we demonstrate that this mechanism is an intrinsic property of quantum dynamics. Understanding the geometrical constraints protecting nonlocality is crucial when designing quantum networks for quantum information processing.
Geometric reduction of dynamical nonlocality in nanoscale quantum circuits
Strambini, E.; Makarenko, K. S.; Abulizi, G.; de Jong, M. P.; van der Wiel, W. G.
2016-01-01
Nonlocality is a key feature discriminating quantum and classical physics. Quantum-interference phenomena, such as Young’s double slit experiment, are one of the clearest manifestations of nonlocality, recently addressed as dynamical to specify its origin in the quantum equations of motion. It is well known that loss of dynamical nonlocality can occur due to (partial) collapse of the wavefunction due to a measurement, such as which-path detection. However, alternative mechanisms affecting dynamical nonlocality have hardly been considered, although of crucial importance in many schemes for quantum information processing. Here, we present a fundamentally different pathway of losing dynamical nonlocality, demonstrating that the detailed geometry of the detection scheme is crucial to preserve nonlocality. By means of a solid-state quantum-interference experiment we quantify this effect in a diffusive system. We show that interference is not only affected by decoherence, but also by a loss of dynamical nonlocality based on a local reduction of the number of quantum conduction channels of the interferometer. With our measurements and theoretical model we demonstrate that this mechanism is an intrinsic property of quantum dynamics. Understanding the geometrical constraints protecting nonlocality is crucial when designing quantum networks for quantum information processing. PMID:26732751
Tunneling Dynamics Between Atomic and Molecular Bose-Einstein Condensates
Institute of Scientific and Technical Information of China (English)
CHEN Chang-Yong
2004-01-01
Tunneling dynamics of multi-atomic molecules between atomic and multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated.It is indicated that the tunneling in the two Bose-Einstein condensates depends on not only the inter-atomic-molecular nonlinear interactions and the initial number of atoms in these condensates,but also the tunneling coupling between the atomic condensate and the multi-atomic molecular condensate.It is discovered that besides oscillating tunneling current between the atomic condensate and the multi-atomic molecular condensate,the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance:a macroscopic quantum self-trapping effect.The influence of de-coherence caused by non-condensate atoms on the tunneling dynamics is studied.It is shown that de-coherence suppresses the multi-atomic molecular tunneling.Moreover,the conception of the molecular Bose-Einstein condensate,which is different from the conventional single-atomic Bose-Einstein condensate,is specially emphasized in this paper.
Exponential rise of dynamical complexity in quantum computing through projections.
Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya
2014-10-10
The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.
Orbital free molecular dynamics; Approche sans orbitale des plasmas denses
Energy Technology Data Exchange (ETDEWEB)
Lambert, F
2007-08-15
The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)
Energy Technology Data Exchange (ETDEWEB)
Kinugawa, Kenichi [Nara Women`s Univ., Nara (Japan). Dept. of Chemistry
1998-10-01
It has been unsuccessful to solve a set of time-dependent Schroedinger equations numerically for many-body quantum systems which involve, e.g., a number of hydrogen molecules, protons, and excess electrons at a low temperature, where quantum effect evidently appears. This undesirable situation is fatal for the investigation of real low-temperature chemical systems because they are essentially composed of many quantum degrees of freedom. However, if we use a new technique called `path integral centroid molecular dynamics (CMD) simulation` proposed by Cao and Voth in 1994, the real-time semi-classical dynamics of many degrees of freedom can be computed by utilizing the techniques already developed in the traditional classical molecular dynamics (MD) simulations. Therefore, the CMD simulation is expected to be very powerful tool for the quantum dynamics studies or real substances. (J.P.N.)
Tunneling Dynamics of Two-Species Molecular Bose-Einstein Condensates
Institute of Scientific and Technical Information of China (English)
CHEN Chang-Yong; GAO Ke-Lin
2004-01-01
We study tunneling dynamics of atomic group in two-species molecular Bose-Einstein condensates. It is shown that the tunneling of the atom group depends on not only the tunneling coupling constant between the atomic pair molecular condensate and the three-atomic group molecular condensate, but also the inter-molecular nonlinear interactions and the initial number of atoms in these condensates. It is discovered that besides oscillating tunneling current between the atomic pair molecular condensate and the three-atomic group molecular condensate, the nonlinear atomic group tunneling dynamics sustains a self-maintained population imbalance: a macroscopic quantum self-trapping effect.
Linear and cubic dynamic susceptibilities in quantum spin glass
Busiello, G; Sushkova, V G
2001-01-01
The low temperature behaviour of the dynamic nonlinear (cubic) susceptibility chi sub 3 sup ' (omega, T) in quantum d-dimensional Ising spin glass with short-range interactions between spins is investigated in terms of the quantum droplet model and the quantum-mechanical nonlinear response theory is employed. We have revealed a glassy like behaviour of droplet dynamics. The frequency dependence of chi sub 3 sup ' (omega, T) is very remarkable, the temperature dependence is found at very low temperatures (quantum regime). The nonlinear response depends on the tunneling rate for a droplet which regulates the strength of quantum fluctuations. This response has a strong dependence on the distribution of droplet free energies and on the droplet length scale average. Implications for experiments in quantum spin glasses like disordered dipolar quantum Ising magnet LiHo sub x Y sub 1 sub - sub x F sub 4 and pseudospin are noted.
Strong Analog Classical Simulation of Coherent Quantum Dynamics
Wang, Dong-Sheng
2017-02-01
A strong analog classical simulation of general quantum evolution is proposed, which serves as a novel scheme in quantum computation and simulation. The scheme employs the approach of geometric quantum mechanics and quantum informational technique of quantum tomography, which applies broadly to cases of mixed states, nonunitary evolution, and infinite dimensional systems. The simulation provides an intriguing classical picture to probe quantum phenomena, namely, a coherent quantum dynamics can be viewed as a globally constrained classical Hamiltonian dynamics of a collection of coupled particles or strings. Efficiency analysis reveals a fundamental difference between the locality in real space and locality in Hilbert space, the latter enables efficient strong analog classical simulations. Examples are also studied to highlight the differences and gaps among various simulation methods. Funding support from NSERC of Canada and a research fellowship at Department of Physics and Astronomy, University of British Columbia are acknowledged
Harnessing Disordered-Ensemble Quantum Dynamics for Machine Learning
Fujii, Keisuke; Nakajima, Kohei
2017-08-01
The quantum computer has an amazing potential of fast information processing. However, the realization of a digital quantum computer is still a challenging problem requiring highly accurate controls and key application strategies. Here we propose a platform, quantum reservoir computing, to solve these issues successfully by exploiting the natural quantum dynamics of ensemble systems, which are ubiquitous in laboratories nowadays, for machine learning. This framework enables ensemble quantum systems to universally emulate nonlinear dynamical systems including classical chaos. A number of numerical experiments show that quantum systems consisting of 5-7 qubits possess computational capabilities comparable to conventional recurrent neural networks of 100-500 nodes. This discovery opens up a paradigm for information processing with artificial intelligence powered by quantum physics.
Kondo effect in quantum dots and molecular devices
Institute of Scientific and Technical Information of China (English)
JIANG Lang; LI Hongxiang; HU Wenping; ZHU Daoben
2005-01-01
Kondo effect is a very important many-body phenomenon in condensed matter physics,which explains why the resistance increases as the temperature is lowered (usually <10 K) in dilute magnetic alloy, and why the conductance increases as temperature is decreased in quantum dots. This paper simply introduces equilibrium and non- equilibrium Kondo effects in quantum dots together with the Kondo effect in quantum dots with even number of electrons (when the singlet and triplet states are degenerate). Furthermore, Kondo effect in single atom/molecular transistors is introduced, which indicates a new way to study Kondo effect.
Programming an interpreter using molecular dynamics
2008-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primari...
Programming an Interpreter Using Molecular Dynamics
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily...
Randomized Dynamical Decoupling Techniques for Coherent Quantum Control
Viola, L; Viola, Lorenza; Santos, Lea F.
2006-01-01
The need for strategies able to accurately manipulate quantum dynamics is ubiquitous in quantum control and quantum information processing. We investigate two scenarios where randomized dynamical decoupling techniques become more advantageous with respect to standard deterministic methods in switching off unwanted dynamical evolution in a closed quantum system: when dealing with decoupling cycles which involve a large number of control actions and/or when seeking long-time quantum information storage. Highly effective hybrid decoupling schemes, which combine deterministic and stochastic features are discussed, as well as the benefits of sequentially implementing a concatenated method, applied at short times, followed by a hybrid protocol, employed at longer times. A quantum register consisting of a chain of spin-1/2 particles interacting via the Heisenberg interaction is used as a model for the analysis throughout.
Garashchuk, Sophya; Jakowski, Jacek; Wang, Lei; Sumpter, Bobby G
2013-12-10
A massively parallel, direct quantum molecular dynamics method is described. The method combines a quantum trajectory (QT) representation of the nuclear wave function discretized into an ensemble of trajectories with an electronic structure (ES) description of electrons, namely using the density functional tight binding (DFTB) theory. Quantum nuclear effects are included into the dynamics of the nuclei via quantum corrections to the classical forces. To reduce computational cost and increase numerical accuracy, the quantum corrections to dynamics resulting from localization of the nuclear wave function are computed approximately and included into selected degrees of freedom representing light particles where the quantum effects are expected to be the most pronounced. A massively parallel implementation, based on the message passing interface allows for efficient simulations of ensembles of thousands of trajectories at once. The QTES-DFTB dynamics approach is employed to study the role of quantum nuclear effects on the interaction of hydrogen with a model graphene sheet, revealing that neglect of nuclear effects can lead to an overestimation of adsorption.
Quantum chaotic dynamics and random polynomials
Energy Technology Data Exchange (ETDEWEB)
Bogomolny, E.; Bohigas, O.; Leboeuf, P.
1995-11-01
The distribution of roots of polynomials of high degree with random coefficients is investigated which, among others, appear naturally in the context of `quantum chaotic dynamics`. It is shown that under quite general conditions their roots tend to concentrate near the unit circle in the complex plane. In order to further increase this tendency, the particular case of self-inverse random polynomials is studied, and it is shown that for them a finite portion of all roots lies exactly on the unit circle. Correlation functions of these roots are also computed analytically, and compared to the correlations of eigenvalues of random matrices. The problem of ergodicity of chaotic wavefunctions is also considered. Special attention is devoted to the role of symmetries in the distribution of roots of random polynomials. (author). 32 refs.
Wave operator theory of quantum dynamics
Durand, Philippe; Paidarová, Ivana
1998-09-01
An energy-dependent wave operator theory of quantum dynamics is derived for time-independent and time-dependent Hamiltonians. Relationships between Green's functions, wave operators, and effective Hamiltonians are investigated. Analytical properties of these quantities are especially relevant for studying resonances. A derivation of the relationship between the Green's functions and the (t,t') method of Peskin and Moiseyev [J. Chem. Phys. 99, 4590 (1993)] is presented. The observable quantities can be derived from the wave operators determined with the use of efficient iterative procedures. As in the theory of Bloch operators for bound states, the theory is based on a partition of the full Hilbert space into three subspaces: the model space, an intermediate space, and the outer space. On the basis of this partition an alternative definition of active spaces currently considered in large scale calculations is suggested. A numerical illustration is presented for several model systems and for the Stark effect in the hydrogen atom.
New methods for quantum mechanical reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Thompson, Ward Hugh [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
1996-12-01
Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L^{2}) representation of the outgoing wave scattering Green`s function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green`s function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC^{-} can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC^{-} geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H_{3}O^{-} system, providing information about the potential energy surface for the OH + H_{2} reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the
Nikiforov, Alexander; Gamez, Jose A; Thiel, Walter; Filatov, Michael
2016-01-07
Two new light-driven molecular rotary motors based on the N-alkylated indanylidene benzopyrrole frameworks are proposed and studied using quantum chemical calculations and nonadiabatic molecular dynamics simulations. These new motors perform pure axial rotation, and the photochemical steps of the rotary cycle are dominated by the fast bond-length-alternation motion that enables ultrafast access to the S1/S0 intersection. The new motors are predicted to display a quantum efficiency higher than that of the currently available synthetic all-hydrocarbon motors. Remarkably, the quantum efficiency is not governed by the topography (peaked versus sloped) of the minimum-energy conical intersection, whereas the S1 decay time depends on the topography as well as on the energy of the intersection relative to the S1 minimum. It is the axial chirality (helicity), rather than the point chirality, that controls the sense of rotation of the motor.
The 2011 Dynamics of Molecular Collisions Conference
Energy Technology Data Exchange (ETDEWEB)
Nesbitt, David J. [JILA, NIST
2011-07-11
Yuan T. Lee & Professor George Schatz. Professor Lee’s research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lee’s work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatz’s research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed
Quantum Dynamical Entropies and Gács Algorithmic Entropy
Directory of Open Access Journals (Sweden)
Fabio Benatti
2012-07-01
Full Text Available Several quantum dynamical entropies have been proposed that extend the classical Kolmogorov–Sinai (dynamical entropy. The same scenario appears in relation to the extension of algorithmic complexity theory to the quantum realm. A theorem of Brudno establishes that the complexity per unit time step along typical trajectories of a classical ergodic system equals the KS-entropy. In the following, we establish a similar relation between the Connes–Narnhofer–Thirring quantum dynamical entropy for the shift on quantum spin chains and the Gács algorithmic entropy. We further provide, for the same system, a weaker linkage between the latter algorithmic complexity and a different quantum dynamical entropy proposed by Alicki and Fannes.
Protected quantum computing: interleaving gate operations with dynamical decoupling sequences.
Zhang, Jingfu; Souza, Alexandre M; Brandao, Frederico Dias; Suter, Dieter
2014-02-07
Implementing precise operations on quantum systems is one of the biggest challenges for building quantum devices in a noisy environment. Dynamical decoupling attenuates the destructive effect of the environmental noise, but so far, it has been used primarily in the context of quantum memories. Here, we experimentally demonstrate a general scheme for combining dynamical decoupling with quantum logical gate operations using the example of an electron-spin qubit of a single nitrogen-vacancy center in diamond. We achieve process fidelities >98% for gate times that are 2 orders of magnitude longer than the unprotected dephasing time T2.
Quantum Dynamics of Magnetic and Electric Dipoles and Berry's Phase
Furtado, C; Furtado, Claudio
2003-01-01
We study the quantum dynamics of neutral particle that posseses a permanent magnetic and electric dipole moments in the presence of an electromagnetic field. The analysis of this dynamics demonstrates the appearance of a quantum phase that combines the Aharonov-Casher effect and the He-Mckellar-Wilkens effect. We demonstrate that this phase is a special case of the Berry's quantum phase. A series of field configurations where this phase would be found are presented. A generalized Casella-type effect is found in one these configurations. A physical scenario for the quantum phase in an interferometric experiment is proposed.
Acevedo, Óscar L.; Quiroga, Luis; Rodríguez, Ferney J.; Johnson, Neil F.
2014-03-01
Dynamical quantum phase crossings of spin networks have recently received increased attention thanks to their relation to adiabatic quantum computing, and their feasible realizations using ultra-cold atomic and molecular systems with a highly tunable degree of connectivity. Dynamical scaling of spatially distributed systems like Ising models have been widely studied, and successfully related to well-known theories like the Kibble-Zurek mechanism. The case of totally connected networks such as the Dicke Model and Lipkin-Meshkov-Glick Model, however, is known to exhibit a breakdown of these frameworks. Our analysis overcomes the lack of spatial correlation structure by developing a general approach which (i) is valid regardless the connectivity of the system, (ii) goes beyond critical exponents, and (iii) provides a time-resolved picture of dynamical scaling. By treating these models as a method for macroscopic quantum control of their subsystems, we have found microscopic signatures of the dynamical scaling as well as instances of dynamical enhancement of distinctive quantum properties such as entanglement and coherence. Our results yield novel prescriptions for the fields of quantum simulations and quantum control, and deepen our fundamental understanding of phase transitions.
Efficient Quantum Private Communication Based on Dynamic Control Code Sequence
Cao, Zheng-Wen; Feng, Xiao-Yi; Peng, Jin-Ye; Zeng, Gui-Hua; Qi, Jin
2016-12-01
Based on chaos and quantum properties, we propose a quantum private communication scheme with dynamic control code sequence. The initial sequence is obtained via chaotic systems, and the control code sequence is derived by grouping, XOR and extracting. A shift cycle algorithm is designed to enable the dynamic change of control code sequence. Analysis shows that transmission efficiency could reach 100 % with high dynamics and security.
Efficient Quantum Private Communication Based on Dynamic Control Code Sequence
Cao, Zheng-Wen; Feng, Xiao-Yi; Peng, Jin-Ye; Zeng, Gui-Hua; Qi, Jin
2017-04-01
Based on chaos and quantum properties, we propose a quantum private communication scheme with dynamic control code sequence. The initial sequence is obtained via chaotic systems, and the control code sequence is derived by grouping, XOR and extracting. A shift cycle algorithm is designed to enable the dynamic change of control code sequence. Analysis shows that transmission efficiency could reach 100 % with high dynamics and security.
Completely positive dynamical semigroups and quantum resonance theory
Könenberg, Martin; Merkli, Marco
2017-07-01
Starting from a microscopic system-environment model, we construct a quantum dynamical semigroup for the reduced evolution of the open system. The difference between the true system dynamics and its approximation by the semigroup has the following two properties: It is (linearly) small in the system-environment coupling constant for all times, and it vanishes exponentially quickly in the large time limit. Our approach is based on the quantum dynamical resonance theory.
Thermally driven molecular linear motors - A molecular dynamics study
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence
2009-01-01
We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled...
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
2010-01-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor ...
Viola, Lorenza; Tannor, David
2011-08-01
Precisely characterizing and controlling the dynamics of realistic open quantum systems has emerged in recent years as a key challenge across contemporary quantum sciences and technologies, with implications ranging from physics, chemistry and applied mathematics to quantum information processing (QIP) and quantum engineering. Quantum control theory aims to provide both a general dynamical-system framework and a constructive toolbox to meet this challenge. The purpose of this special issue of Journal of Physics B: Atomic, Molecular and Optical Physics is to present a state-of-the-art account of recent advances and current trends in the field, as reflected in two international meetings that were held on the subject over the last summer and which motivated in part the compilation of this volume—the Topical Group: Frontiers in Open Quantum Systems and Quantum Control Theory, held at the Institute for Theoretical Atomic, Molecular and Optical Physics (ITAMP) in Cambridge, Massachusetts (USA), from 1-14 August 2010, and the Safed Workshop on Quantum Decoherence and Thermodynamics Control, held in Safed (Israel), from 22-27 August 2010. Initial developments in quantum control theory date back to (at least) the early 1980s, and have been largely inspired by the well-established mathematical framework for classical dynamical systems. As the above-mentioned meetings made clear, and as the burgeoning body of literature on the subject testifies, quantum control has grown since then well beyond its original boundaries, and has by now evolved into a highly cross-disciplinary field which, while still fast-moving, is also entering a new phase of maturity, sophistication, and integration. Two trends deserve special attention: on the one hand, a growing emphasis on control tasks and methodologies that are specifically motivated by QIP, in addition and in parallel to applications in more traditional areas where quantum coherence is nevertheless vital (such as, for instance
Conditions for strictly purity-decreasing quantum Markovian dynamics
Energy Technology Data Exchange (ETDEWEB)
Lidar, D.A. [Chemical Physics Theory Group, Chemistry Department and Center for Quantum Information and Quantum Control, University of Toronto, 80 St. George St., Toronto, Ont., M5S 3H6 (Canada)], E-mail: lidar@usc.edu; Shabani, A. [Physics Department and Center for Quantum Information and Quantum Control, University of Toronto, 60 St. George St., Toronto, Ont., M5S 1A7 (Canada); Alicki, R. [Institute of Theoretical Physics and Astrophysics, University of Gdansk (Poland)
2006-03-06
The purity, Tr({rho} {sup 2}), measures how pure or mixed a quantum state {rho} is. It is well known that quantum dynamical semigroups that preserve the identity operator (which we refer to as unital) are strictly purity-decreasing transformations. Here, we provide an almost complete characterization of the class of strictly purity-decreasing quantum dynamical semigroups. We show that in the case of finite-dimensional Hilbert spaces, a dynamical semigroup is strictly purity-decreasing if and only if it is unital, while in the infinite dimensional case, unitality is only sufficient.
Quantum-classical hybrid dynamics - a summary
Elze, Hans-Thomas
2013-01-01
A summary of a recently proposed description of quantum-classical hybrids is presented, which concerns quantum and classical degrees of freedom of a composite object that interact directly with each other. This is based on notions of classical Hamiltonian mechanics suitably extended to quantum mechanics.
Quantum dynamics of Lorentzian spacetime foam
Redmount, Ian H.; Suen, Wai-Mo
1994-05-01
A simple spacetime wormhole, which evolves classically from zero throat radius to a maximum value and recontracts, can be regarded as one possible mode of fluctuation in the microscopic ``spacetime foam'' first suggested by Wheeler. The dynamics of a particularly simple version of such a wormhole can be reduced to that of a single quantity, its throat radius; this wormhole thus provides a ``minisuperspace model'' for a mode of Lorentzian-signature foam. The classical equation of motion for the wormhole throat is obtained from the Einstein field equations and a suitable equation of state for the matter at the throat. Analysis of the quantum behavior of the hole then proceeds from an action corresponding to that equation of motion. The action obtained simply by calculating the scalar curvature of the hole spacetime yields a model with features like those of the relativistic free particle. In particular the Hamiltonian is nonlocal, and for the wormhole cannot even be given as a differential operator in closed form. Nonetheless the general solution of the Schrödinger equation for wormhole wave functions, i.e., the wave-function propagator, can be expressed as a path integral. Too complicated to perform exactly, this can yet be evaluated via a WKB approximation. The result indicates that the wormhole, classically stable, is quantum-mechanically unstable: A Feynman-Kac decomposition of the WKB propagator yields no spectrum of bound states. Although an initially localized wormhole wave function may oscillate for many classical expansion and recontraction periods, it must eventually leak to large radius values. The possibility of such a mode unstable against growth, combined with the observed absence of macroscopic wormholes, suggests that stability considerations may place constraints on the nature or even the existence of Planck-scale foamlike structure, at least of Lorentzian signature.
Dynamics of quantum cascade lasers: numerics
Van der Sande, Guy; Verschaffelt, Guy
2016-04-01
Since the original demonstration of terahertz quantum-cascade lasers (QCLs), the performance of these devices has shown rapid improvement. QCLs can now deliver milliwatts or more of continuous-wave radiation throughout the terahertz frequency range (300 GHz to 10 THz). Therefore, QCLs have become widely used in various applications such as spectroscopy, metrology or free-space telecommunications. For many of these applications there is a need for compact tuneable quantum cascade lasers. Nowadays most tuneable QCLs are based on a bulky external cavity configuration. We explore the possibility of tuning the operating wavelength through a fully integrated on-chip wavelength selective feedback applied to a dual wavelength QCL. Our numerical and analytical analyses are based on rate equation models describing the dynamics of QCLs extended to include delayed filtered optical feedback. We demonstrate the possibility to tune the operating wavelength by altering the absorption and/or amplification of the signal in the delayed feedback path. The tuning range of a laser is limited by the spectral width of its gain. For inter-band semiconductor lasers this spectral width is typically several tens of nm. Hence, the laser cavity supports the existence of multiple modes and on chip wavelength selective feedback has been demonstrated to be a promising tuning mechanism. We have selected a specific QCL gain structure with four energy levels and with two lasing transitions in the same cascade. In this scheme, the two lasing modes use a common upper level. Hence, the two modes compete in part for the same carriers to account for their optical gain. We have added delayed wavelength specific filtered optical feedback to the rate equation model describing these transitions. We have calculated the steady states and their stability in the absence of delay for the feedback field and studied numerically the case with non-zero delay. We have proven that wavelength tuning of a dual wavelength
Explicit inclusion of electronic correlation effects in molecular dynamics
Julien, Jean-Pierre; Kress, Joel D.; Zhu, Jian-Xin
2017-07-01
We design a quantum molecular dynamics method for strongly correlated electron metals. The strong electronic correlation effects are treated within a real-space version of the Gutzwiller variational approximation (GA), which is suitable for the inhomogeneity inherent in the process of quantum molecular dynamics (MD) simulations. We also propose an efficient algorithm based on the second-moment approximation to the electronic density of states for the search of the optimal variation parameters, from which the renormalized interatomic MD potentials are fully determined. By considering a minimal one-correlated-orbital Anderson model with parameterized spatial dependence of tight-binding hopping integrals, this fast GA-MD method is benchmarked with that using exact diagonalization to solve the GA variational parameters. The efficiency and accuracy are illustrated. We have demonstrated the effect of temperature coupled with electronic correlation on structural properties simulated with MD. This method will open up an unprecedented opportunity enabling large-scale quantum MD simulations of strongly correlated electronic materials.
Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.
Tavernelli, Ivano
2015-03-17
Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular
Radiative Corrections and Quantum Gates in Molecular Systems
Reina, John H.; Beausoleil, Ray G.; Spiller, Tim P.; Munro, William J.
2004-12-01
We propose a method for quantum information processing using molecules coupled to an external laser field. This utilizes molecular interactions, control of the external field, and an effective energy shift of the doubly excited state of two coupled molecules. Such a level shift has been seen in the two-photon resonance experiments recently reported by Hettich etal. Here we show that this can be explained in terms of the QED Lamb shift. We quantify the performance of the proposed quantum logic gates in the presence of dissipative mechanisms. The unitary transformations required for performing one- and two-qubit operations can be implemented with present day molecular technology. The proposed techniques can also be applied to coupled quantum dot and biomolecular systems.
Pulse Designed Coherent Dynamics of a Quantum Dot Charge Qubit
Institute of Scientific and Technical Information of China (English)
CAO Gang; WANG Li; TU Tao; LI Hai-Ou; XIAO Ming; GUO Guo-Ping
2012-01-01
We propose an effective method to design the working parameters of a pulse-driven charge qubit implemented with double quantum dot.It is shown that intrinsic qubit population leakage to undesired states in the control and measurement process can be determined by the simulation of coherent dynamics of the qubit and minimized by choosing proper working parameters such as pulse shape.The result demonstrated here bodes well for future quantum gate operations and quantum computing applications.
Post-Markovian dynamics of quantum correlations: entanglement versus discord
Mohammadi, Hamidreza
2017-02-01
Dynamics of an open two-qubit system is investigated in the post-Markovian regime, where the environments have a short-term memory. Each qubit is coupled to separate environment which is held in its own temperature. The inter-qubit interaction is modeled by XY-Heisenberg model in the presence of spin-orbit interaction and inhomogeneous magnetic field. The dynamical behavior of entanglement and discord has been considered. The results show that quantum discord is more robust than quantum entanglement, during the evolution. Also the asymmetric feature of quantum discord can be monitored by introducing the asymmetries due to inhomogeneity of magnetic field and temperature difference between the reservoirs. By employing proper parameters of the model, it is possible to maintain nonvanishing quantum correlation at high degree of temperature. The results can provide a useful recipe for studying dynamical behavior of two-qubit systems such as trapped spin electrons in coupled quantum dots.
On the Dynamical Solution of Quantum Measurement Problem
Belavkin, V P
2005-01-01
The development of quantum measurement theory, initiated by von Neumann, only indicated a possibility for resolution of the interpretational crisis of quantum mechanics. We do this by divorcing the algebra of the dynamical generators and the algebra of the actual observables, or beables. It is shown that within this approach quantum causality can be rehabilitated in the form of a superselection rule for compatibility of the past beables with the potential future. This rule, together with the self-compatibility of the measurements insuring the consistency of the histories, is called the nondemolition, or causality principle in modern quantum theory. The application of this rule in the form of the dynamical commutation relations leads in particular to the derivation of the von Neumann projection postulate. This gives a quantum stochastic solution, in the form of the dynamical filtering equations, of the notorious measurement problem which was tackled unsuccessfully by many famous physicists starting with Schroe...
Observation of quantum interference in molecular charge transport
DEFF Research Database (Denmark)
Guedon, Constant M.; Valkenier, Hennie; Markussen, Troels
2012-01-01
, phenomena such as giant magnetoresistance(5), Kondo effects(6) and conductance switching(7-11) have been observed in single molecules, and theorists have predicted that it should also be possible to observe quantum interference in molecular conductors(12-18), but until now all the evidence...
Dynamical processes in atomic and molecular physics
Ogurtsov, Gennadi
2012-01-01
Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece
Intrinsic Dynamics of Quantum-Dash Lasers
Chen, Cheng
2011-10-01
Temperature-dependent intrinsic modulation response of InAs/InAlGaAs quantum-dash lasers was investigated by using pulse optical injection modulation to minimize the effects of parasitics and self-heating. Compared to typical quantum-well lasers, the quantum-dash lasers were found to have comparable differential gain but approximately twice the gain compression factor, probably due to carrier heating by free-carrier absorption, as opposed to stimulated transition. Therefore, the narrower modulation bandwidth of the quantum-dash lasers than that of quantum-well lasers was attributed to their higher gain compression factor. In addition, as expected, quantum-dash lasers with relatively long and uniform dashes exhibit higher temperature stability than quantum-well lasers. However, the lasers with relatively short and nonuniform dashes exhibit stronger temperature dependence, probably due to their higher surface-to-volume ratio and nonuniform dash sizes. © 2011 IEEE.
Excitation Dynamics and Relaxation in a Molecular Heterodimer
Balevicius, V; Abramavicius, D; Mancal, T; Valkunas, L
2011-01-01
The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the energy gap of the molecular excitation, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
Dynamic quantum tunneling in mesoscopic driven Duffing oscillators.
Guo, Lingzhen; Zheng, Zhigang; Li, Xin-Qi; Yan, Yijing
2011-07-01
We investigate the dynamic quantum tunneling between two attractors of a mesoscopic driven Duffing oscillator. We find that, in addition to inducing a remarkable quantum shift of the bifurcation point, the mesoscopic nature also results in a perfect linear scaling behavior for the tunneling rate with the driving distance to the shifted bifurcation point.
Dynamics of a pulsed continuous-variable quantum memory
DEFF Research Database (Denmark)
Dantan, Aurelien Romain; Cviklinski, Jean; Pinard, Michel
2006-01-01
We study the transfer dynamics of nonclassical fluctuations of light to the ground-state collective spin components of an atomic ensemble during a pulsed quantum memory sequence, and evaluate the relevant physical quantities to be measured in order to characterize such a quantum memory. We show i...
Watanabe, Hiroshi C; Banno, Misa; Sakurai, Minoru
2016-03-14
Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method". In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.
Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.
Graziani, F R; Bauer, J D; Murillo, M S
2014-09-01
Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD
Calvo, F.; Parneix, P.; Van-Oanh, N.-T.
2010-03-01
The vibrational spectra of the naphthalene, pyrene, and coronene molecules have been computed in the 0-3500 cm-1 infrared range using classical and quantum molecular dynamics simulations based on a dedicated tight-binding potential energy surface. The ring-polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (CMD) methods have been employed to account for quantum nuclear effects. The contributions of quantum delocalization to the line shift and broadening are significant in the entire spectral range and of comparable magnitude as pure thermal effects. While the two methods generally produce similar results, the CMD method may converge slower at low temperature with increasing Trotter discretization number. However, and contrary to the CMD method, the RPMD approach suffers from serious resonance problems at high frequencies and low temperatures.
Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Gray, S.K. [Argonne National Laboratory, IL (United States)
1993-12-01
A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Modeling the Hydrogen Bond within Molecular Dynamics
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Quantum State Resolved Photodissociation Dynamics of the Formyl Radical.
Neyer, David William
The photodissociation dynamics of the formyl (HCO) radical have been investigated both experimentally and theoretically. HCO molecules, produced in a molecular beam by the laser photolysis of acetaldehyde, were excited to metastable levels with quantum state resolution. The rotational and vibrational states of the CO products from the dissociation of these levels were probed by laser-induced fluorescence using a tunable vacuum ultraviolet laser. Measurement of detailed state-to-state dissociation cross sections and theoretical modeling of these dynamics have provided valuable information about the potential energy surface of the ground electronic state (X) of the HCO system. HCO was excited to predissociative levels of the first electronic state (A) characterized by their vibrational and K-rotational quantum numbers, and the rotational and vibrational populations of the CO products were measured. While the K-state excited in the HCO has little effect on the CO products, the vibrational character of the parent causes specific changes in the product state distributions. Addition of bending or C-H stretching quanta to the HCO parent leads to increased rotational excitation in the CO(nu =O) products. Adding C-O stretch to the parent state produces increased vibrational excitation in the CO products, The dynamics of this dissociation process, which involves Renner-Teller coupling between the X and A states, was modeled using classical trajectories calculated on a global X-state potential energy surface. Stimulated emission pumping (SEP) was used to prepare HCO in metastable resonances on the X state of HCO with vibrational and rotational resolution. The energies and linewidths of these resonances were measured, and the rotational and vibrational distributions of the CO products were determined. The linewidths and product state distributions show highly non-statistical behavior which depends on the vibrational character of the HCO resonance. The rotational distributions
Witt, Alexander; Ivanov, Sergei D.; Shiga, Motoyuki; Forbert, Harald; Marx, Dominik
2009-05-01
Centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD) are two conceptually distinct extensions of path integral molecular dynamics that are able to generate approximate quantum dynamics of complex molecular systems. Both methods can be used to compute quasiclassical time correlation functions which have direct application in molecular spectroscopy; in particular, to infrared spectroscopy via dipole autocorrelation functions. The performance of both methods for computing vibrational spectra of several simple but representative molecular model systems is investigated systematically as a function of temperature and isotopic substitution. In this context both CMD and RPMD feature intrinsic problems which are quantified and investigated in detail. Based on the obtained results guidelines for using CMD and RPMD to compute infrared spectra of molecular systems are provided.
Generalized dynamic scaling for quantum critical relaxation in imaginary time.
Zhang, Shuyi; Yin, Shuai; Zhong, Fan
2014-10-01
We study the imaginary-time relaxation critical dynamics of a quantum system with a vanishing initial correlation length and an arbitrary initial order parameter M0. We find that in quantum critical dynamics, the behavior of M0 under scale transformations deviates from a simple power law, which was proposed for very small M0 previously. A universal characteristic function is then suggested to describe the rescaled initial magnetization, similar to classical critical dynamics. This characteristic function is shown to be able to describe the quantum critical dynamics in both short- and long-time stages of the evolution. The one-dimensional transverse-field Ising model is employed to numerically determine the specific form of the characteristic function. We demonstrate that it is applicable as long as the system is in the vicinity of the quantum critical point. The universality of the characteristic function is confirmed by numerical simulations of models belonging to the same universality class.
Analyzing Big Data with Dynamic Quantum Clustering
Weinstein, M; Hume, A; Sciau, Ph; Shaked, G; Hofstetter, R; Persi, E; Mehta, A; Horn, D
2013-01-01
How does one search for a needle in a multi-dimensional haystack without knowing what a needle is and without knowing if there is one in the haystack? This kind of problem requires a paradigm shift - away from hypothesis driven searches of the data - towards a methodology that lets the data speak for itself. Dynamic Quantum Clustering (DQC) is such a methodology. DQC is a powerful visual method that works with big, high-dimensional data. It exploits variations of the density of the data (in feature space) and unearths subsets of the data that exhibit correlations among all the measured variables. The outcome of a DQC analysis is a movie that shows how and why sets of data-points are eventually classified as members of simple clusters or as members of - what we call - extended structures. This allows DQC to be successfully used in a non-conventional exploratory mode where one searches data for unexpected information without the need to model the data. We show how this works for big, complex, real-world dataset...
Quantum Dynamics of Lorentzian Spacetime Foam
Redmount, Ian; 10.1103/PhysRevD.49.5199
2009-01-01
A simple spacetime wormhole, which evolves classically from zero throat radius to a maximum value and recontracts, can be regarded as one possible mode of fluctuation in the microscopic ``spacetime foam'' first suggested by Wheeler. The dynamics of a particularly simple version of such a wormhole can be reduced to that of a single quantity, its throat radius; this wormhole thus provides a ``minisuperspace model'' for a structure in Lorentzian-signature foam. The classical equation of motion for the wormhole throat is obtained from the Einstein field equations and a suitable equation of state for the matter at the throat. Analysis of the quantum behavior of the hole then proceeds from an action corresponding to that equation of motion. The action obtained simply by calculating the scalar curvature of the hole spacetime yields a model with features like those of the relativistic free particle. In particular the Hamiltonian is nonlocal, and for the wormhole cannot even be given as a differential operator in clos...
Molecular dynamics studies of entangled polymer chains
Bulacu, Monica Iulia
2008-01-01
The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a
A thread calculus with molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2010-01-01
We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact with services of which the states consist o
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programmi
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the
Molecular dynamical modelling of endohedral fullerenes formation in plasma
Fedorov, A. S.; Kovaleva, E. A.; Lubkova, T. A.; Popov, Z. I.; Kuzubov, A. A.; Visotin, M. A.; Irle, S.
2016-02-01
The initial stages of fullerene and endohedral metallofullerene (EMF) synthesis in carbon-helium plasma at 1500 K and 2500 K have been simulated with quantum chemical molecular dynamics (MD) based on density-functional tight-binding (DFTB). The cases of formation of large (>100 atoms) sp2-carbon clusters with scandium atoms inside were observed. These clusters are considered as precursors of fullerenes or EMFs, and thus it is shown that formation of EMFs can be explained within the framework of "shrinking hot giant" mechanism. Also, the dependence of formation rates on plasma parameters, including temperature, buffer gas and metal atoms concentrations, has been studied.
Quantum mechanics of molecular rate processes
Levine, Raphael D
1999-01-01
This survey of applications of the theory of collisions and rate processes to molecular problems explores collisions of molecules with internal structure, generalized Ehrenfest theorem, theory of reactive collisions, and role of symmetry. It also reviews partitioning technique, equivalent potentials and quasibound states, theory of direct reactions, more. 1969 edition.
Quantum transport in molecular devices and graphene
Heersche, H.B.
2006-01-01
As a result of progress in nanotechnology, smaller and smaller electronic circuits can be made. The stage of electrically contacting even a single molecule has now been reached. This stimulates both fundamental and applied research alike. Molecular electronics is hence a booming new field that draws
Quantum transport in molecular devices and graphene
Heersche, H.B.
2006-01-01
As a result of progress in nanotechnology, smaller and smaller electronic circuits can be made. The stage of electrically contacting even a single molecule has now been reached. This stimulates both fundamental and applied research alike. Molecular electronics is hence a booming new field that draws
Coherent States, Dynamics and Semiclassical Limit on Quantum Groups
Aref'eva, I Ya; Viswanathan, K S; Volovich, I V
1994-01-01
Coherent states on the quantum group $SU_q(2)$ are defined by using harmonic analysis and representation theory of the algebra of functions on the quantum group. Semiclassical limit $q\\rightarrow 1$ is discussed and the crucial role of special states on the quantum algebra in an investigation of the semiclassical limit is emphasized. An approach to $q$-deformation as a $q$-Weyl quantization and a relavence of contact geometry in this context is pointed out. Dynamics on the quantum group parametrized by a real time variable and corresponding to classical rotations is considered.
Stabilization of Quantum Information A Unified Dynamical-Algebraic Approach
Zanardi, P
2002-01-01
The notion of symmetry is shown to be at the heart of all error correction/avoidance strategies for preserving quantum coherence of an open quantum system S e.g., a quantum computer. The existence of a non-trivial group of symmetries of the dynamical algebra of S provides state-space sectors immune to decoherence. Such noiseless sectors, that can be viewed as a noncommutative version of the pointer basis, are shown to support universal quantum computation and to be robust against perturbations. When the required symmetry is not present one can generate it artificially resorting to active symmetrization procedures.
Dynamics of electron in a surface quantum well
Institute of Scientific and Technical Information of China (English)
Wang Li-Fei; Yang Guang-Can
2009-01-01
This paper studies the quantum dynamics of electrons in a surface quantum well in the time domain with autocorrelation of wave packet. The evolution of the wave packet for different manifold eigenstates with finite and infinite lifetimes is investigated analytically. It is found that the quantum coherence and evolution of the surface electronic wave packet can be controlled by the laser central energy and electric field. The results show that the finite lifetime of excited states expedites the dephasing of the coherent electronic wave packet significantly. The correspondence between classical and quantum mechanics is shown explicitly in the system.
Modeling hybrid perovskites by molecular dynamics.
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Modeling hybrid perovskites by molecular dynamics
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Quantum State Control of Trapped Atomic and Molecular Ions
Seck, Christopher M.
Full quantum control of a molecule would have a significant impact in molecular coherent control (alignment and orientation) and ultracold and quantum chemistry, quantum computing and simulation as well as hybrid quantum devices, and precision spectroscopy of importance to fundamental physics research. Precision spectroscopy of even simple diatomic molecules offers the possibility of uncovering physics beyond the standard model, specifically time variation of the proton-to-electron mass ratio, which is currently constrained by astronomical molecular observations at the 10-16 1/yr level and laboratory atomic measurements at the 10-17 1/yr level. To achieve this level of measurement and to avoid the complications of diatomic structure on traditional spectroscopy methods, molecular quantum logic spectroscopy (mQLS) will be the spectroscopy technique of choice. We discuss development of in-house external-cavity diode laser (ECDL) systems and improvements to the Libbrecht-Hall circuit, which is a well-known, low-noise current driver for narrow-linewidth diode lasers. However, as the current approaches the maximum set limit, the noise in the laser current increases dramatically. This behavior is documented and simple circuit modifications to alleviate this issue are explored. We cool trapped AlH+ molecules to their ground rotational-vibrational quantum state using an electronically-exciting broadband laser to simultaneously drive cooling resonances from many different rotational levels. We demonstrate rotational cooling on the 140(20) ms timescale from room temperature to 3.8 K, with the ground state population increasing from 3% to 95.4%. Since QLS does not require the high gate fidelities usually associated with quantum computation and quantum simulation, it is possible to make simplifying choices in ion species and quantum protocols at the expense of some fidelity. We demonstrate sideband cooling and motional state detection protocols for 138Ba+ of sufficient fidelity
Radiative corrections and quantum gates in molecular systems
Huffenberger, Kevin M
2004-01-01
We propose a method for quantum information processing using molecules coupled to an external laser field. This utilizes molecular interactions, control of the external field and an effective energy shift of the doubly-excited state of two coupled molecules. Such a level shift has been seen in the two-photon resonance experiments recently reported in Ref. [1]. Here we show that this can be explained in terms of the QED Lamb shift. We quantify the performance of the proposed quantum logic gates in the presence of dissipative mechanisms. The unitary transformations required for performing one- and two-qubit operations can be implemented with present day technology.
Molecular Dynamics Studies of Matrix Metalloproteases.
Díaz, Natalia; Suárez, Dimas
2017-01-01
Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.