From localization to anomalous diffusion in the dynamics of coupled kicked rotors

NASA Astrophysics Data System (ADS)

Notarnicola, Simone; Iemini, Fernando; Rossini, Davide; Fazio, Rosario; Silva, Alessandro; Russomanno, Angelo

2018-02-01

We study the effect of many-body quantum interference on the dynamics of coupled periodically kicked systems whose classical dynamics is chaotic and shows an unbounded energy increase. We specifically focus on an N -coupled kicked rotors model: We find that the interplay of quantumness and interactions dramatically modifies the system dynamics, inducing a transition between energy saturation and unbounded energy increase. We discuss this phenomenon both numerically and analytically through a mapping onto an N -dimensional Anderson model. The thermodynamic limit N →∞ , in particular, always shows unbounded energy growth. This dynamical delocalization is genuinely quantum and very different from the classical one: Using a mean-field approximation, we see that the system self-organizes so that the energy per site increases in time as a power law with exponent smaller than 1. This wealth of phenomena is a genuine effect of quantum interference: The classical system for N ≥2 always behaves ergodically with an energy per site linearly increasing in time. Our results show that quantum mechanics can deeply alter the regularity or ergodicity properties of a many-body-driven system.

Classical theory of atom-surface scattering: The rainbow effect

NASA Astrophysics Data System (ADS)

Miret-Artés, Salvador; Pollak, Eli

2012-07-01

The scattering of heavy atoms and molecules from surfaces is oftentimes dominated by classical mechanics. A large body of experiments have gathered data on the angular distributions of the scattered species, their energy loss distribution, sticking probability, dependence on surface temperature and more. For many years these phenomena have been considered theoretically in the framework of the “washboard model” in which the interaction of the incident particle with the surface is described in terms of hard wall potentials. Although this class of models has helped in elucidating some of the features it left open many questions such as: true potentials are clearly not hard wall potentials, it does not provide a realistic framework for phonon scattering, and it cannot explain the incident angle and incident energy dependence of rainbow scattering, nor can it provide a consistent theory for sticking. In recent years we have been developing a classical perturbation theory approach which has provided new insight into the dynamics of atom-surface scattering. The theory includes both surface corrugation as well as interaction with surface phonons in terms of harmonic baths which are linearly coupled to the system coordinates. This model has been successful in elucidating many new features of rainbow scattering in terms of frictions and bath fluctuations or noise. It has also given new insight into the origins of asymmetry in atomic scattering from surfaces. New phenomena deduced from the theory include friction induced rainbows, energy loss rainbows, a theory of super-rainbows, and more. In this review we present the classical theory of atom-surface scattering as well as extensions and implications for semiclassical scattering and the further development of a quantum theory of surface scattering. Special emphasis is given to the inversion of scattering data into information on the particle-surface interactions.

Classical theory of atom-surface scattering: The rainbow effect

NASA Astrophysics Data System (ADS)

Miret-Artés, Salvador; Pollak, Eli

The scattering of heavy atoms and molecules from surfaces is oftentimes dominated by classical mechanics. A large body of experiments have gathered data on the angular distributions of the scattered species, their energy loss distribution, sticking probability, dependence on surface temperature and more. For many years these phenomena have been considered theoretically in the framework of the "washboard model" in which the interaction of the incident particle with the surface is described in terms of hard wall potentials. Although this class of models has helped in elucidating some of the features it left open many questions such as: true potentials are clearly not hard wall potentials, it does not provide a realistic framework for phonon scattering, and it cannot explain the incident angle and incident energy dependence of rainbow scattering, nor can it provide a consistent theory for sticking. In recent years we have been developing a classical perturbation theory approach which has provided new insight into the dynamics of atom-surface scattering. The theory includes both surface corrugation as well as interaction with surface phonons in terms of harmonic baths which are linearly coupled to the system coordinates. This model has been successful in elucidating many new features of rainbow scattering in terms of frictions and bath fluctuations or noise. It has also given new insight into the origins of asymmetry in atomic scattering from surfaces. New phenomena deduced from the theory include friction induced rainbows, energy loss rainbows, a theory of super-rainbows, and more. In this review we present the classical theory of atom-surface scattering as well as extensions and implications for semiclassical scattering and the further development of a quantum theory of surface scattering. Special emphasis is given to the inversion of scattering data into information on the particle-surface interactions.

Derivation of the cut-off length from the quantum quadratic enhancement of a mass in vacuum energy constant Lambda

NASA Astrophysics Data System (ADS)

Fukushima, Kimichika; Sato, Hikaru

2018-04-01

Ultraviolet self-interaction energies in field theory sometimes contain meaningful physical quantities. The self-energies in such as classical electrodynamics are usually subtracted from the rest mass. For the consistent treatment of energies as sources of curvature in the Einstein field equations, this study includes these subtracted self-energies into vacuum energy expressed by the constant Lambda (used in such as Lambda-CDM). In this study, the self-energies in electrodynamics and macroscopic classical Einstein field equations are examined, using the formalisms with the ultraviolet cut-off scheme. One of the cut-off formalisms is the field theory in terms of the step-function-type basis functions, developed by the present authors. The other is a continuum theory of a fundamental particle with the same cut-off length. Based on the effectiveness of the continuum theory with the cut-off length shown in the examination, the dominant self-energy is the quadratic term of the Higgs field at a quantum level (classical self-energies are reduced to logarithmic forms by quantum corrections). The cut-off length is then determined to reproduce today's tiny value of Lambda for vacuum energy. Additionally, a field with nonperiodic vanishing boundary conditions is treated, showing that the field has no zero-point energy.

Mass stability in classical Stueckelberg-Horwitz-Piron electrodynamics

NASA Astrophysics Data System (ADS)

Land, Martin

2017-05-01

It is well-known that the 5D gauge structure of Stueckelberg-Horwitz-Piron (SHP) electrodynamics permits the exchange of mass between particles and the electromagnetic fields induced by their motion, even at the classical level. This phenomenon presents two closely related problems: (1) Under what circumstances can real particles evolve sufficiently off-shell to account for mass changing phenomena such as flavor-changing neutrino interactions and low energy nuclear reactions? (2) What accounts for the stability of the measured masses of the known particles? To approach these questions, we first propose a toy model in which a particle evolving through a complex charged environment can acquire a significant mass shift for a short time. We then consider a classical self-interaction that tends to restore on-shell propagation.

Integrated information storage and transfer with a coherent magnetic device

PubMed Central

Jia, Ning; Banchi, Leonardo; Bayat, Abolfazl; Dong, Guangjiong; Bose, Sougato

2015-01-01

Quantum systems are inherently dissipation-less, making them excellent candidates even for classical information processing. We propose to use an array of large-spin quantum magnets for realizing a device which has two modes of operation: memory and data-bus. While the weakly interacting low-energy levels are used as memory to store classical information (bits), the high-energy levels strongly interact with neighboring magnets and mediate the spatial movement of information through quantum dynamics. Despite the fact that memory and data-bus require different features, which are usually prerogative of different physical systems – well isolation for the memory cells, and strong interactions for the transmission – our proposal avoids the notorious complexity of hybrid structures. The proposed mechanism can be realized with different setups. We specifically show that molecular magnets, as the most promising technology, can implement hundreds of operations within their coherence time, while adatoms on surfaces probed by a scanning tunneling microscope is a future possibility. PMID:26347152

Statistical mechanical foundation of the peridynamic nonlocal continuum theory: energy and momentum conservation laws.

PubMed

Lehoucq, R B; Sears, Mark P

2011-09-01

The purpose of this paper is to derive the energy and momentum conservation laws of the peridynamic nonlocal continuum theory using the principles of classical statistical mechanics. The peridynamic laws allow the consideration of discontinuous motion, or deformation, by relying on integral operators. These operators sum forces and power expenditures separated by a finite distance and so represent nonlocal interaction. The integral operators replace the differential divergence operators conventionally used, thereby obviating special treatment at points of discontinuity. The derivation presented employs a general multibody interatomic potential, avoiding the standard assumption of a pairwise decomposition. The integral operators are also expressed in terms of a stress tensor and heat flux vector under the assumption that these fields are differentiable, demonstrating that the classical continuum energy and momentum conservation laws are consequences of the more general peridynamic laws. An important conclusion is that nonlocal interaction is intrinsic to continuum conservation laws when derived using the principles of statistical mechanics.

Mutual capture of dipolar molecules at low and very low energies. I. Approximate analytical treatment.

PubMed

Nikitin, E E; Troe, J

2010-09-16

Approximate analytical expressions are derived for the low-energy rate coefficients of capture of two identical dipolar polarizable rigid rotors in their lowest nonresonant (j(1) = 0 and j(2) = 0) and resonant (j(1) = 0,1 and j(2) = 1,0) states. The considered range extends from the quantum, ultralow energy regime, characterized by s-wave capture, to the classical regime described within fly wheel and adiabatic channel approaches, respectively. This is illustrated by the table of contents graphic (available on the Web) that shows the scaled rate coefficients for the mutual capture of rotors in the resonant state versus the reduced wave vector between the Bethe zero-energy (left arrows) and classical high-energy (right arrow) limits for different ratios δ of the dipole-dipole to dispersion interaction.

Quantum correction to classical gravitational interaction between two polarizable objects

NASA Astrophysics Data System (ADS)

Wu, Puxun; Hu, Jiawei; Yu, Hongwei

2016-12-01

When gravity is quantized, there inevitably exist quantum gravitational vacuum fluctuations which induce quadrupole moments in gravitationally polarizable objects and produce a quantum correction to the classical Newtonian interaction between them. Here, based upon linearized quantum gravity and the leading-order perturbation theory, we study, from a quantum field-theoretic prospect, this quantum correction between a pair of gravitationally polarizable objects treated as two-level harmonic oscillators. We find that the interaction potential behaves like r-11 in the retarded regime and r-10 in the near regime. Our result agrees with what were recently obtained in different approaches. Our study seems to indicate that linearized quantum gravity is robust in dealing with quantum gravitational effects at low energies.

Classical field configurations and infrared slavery

NASA Astrophysics Data System (ADS)

Swanson, Mark S.

1987-09-01

The problem of determining the energy of two spinor particles interacting through massless-particle exchange is analyzed using the path-integral method. A form for the long-range interaction energy is obtained by analyzing an abridged vertex derived from the parent theory. This abridged vertex describes the radiation of zero-momentum particles by pointlike sources. A path-integral formalism for calculating the energy of the radiation field associated with this abridged vertex is developed and applications are made to determine the energy necessary for adiabatic separation of two sources in quantum electrodynamics and for an SU(2) Yang-Mills theory. The latter theory is shown to be consistent with confinement via infrared slavery.

Cross-Over Between Different Symmetries

NASA Astrophysics Data System (ADS)

Frauendorf, S.

2014-09-01

The yrast states of even even vibrational and transitional nuclei are interpreted as a rotating condensate of interacting d-bosons. The corresponding semi-classical tidal wave concept is used for microscopic calculations of energies and E2 transition probabilities. The strong octupole correlations in the light rare earth and actinide nuclides are interpreted as rotation-induced condensation of interacting f-bosons.

Accurate description of charged excitations in molecular solids from embedded many-body perturbation theory

NASA Astrophysics Data System (ADS)

Li, Jing; D'Avino, Gabriele; Duchemin, Ivan; Beljonne, David; Blase, Xavier

2018-01-01

We present a novel hybrid quantum/classical approach to the calculation of charged excitations in molecular solids based on the many-body Green's function G W formalism. Molecules described at the G W level are embedded into the crystalline environment modeled with an accurate classical polarizable scheme. This allows the calculation of electron addition and removal energies in the bulk and at crystal surfaces where charged excitations are probed in photoelectron experiments. By considering the paradigmatic case of pentacene and perfluoropentacene crystals, we discuss the different contributions from intermolecular interactions to electronic energy levels, distinguishing between polarization, which is accounted for combining quantum and classical polarizabilities, and crystal field effects, that can impact energy levels by up to ±0.6 eV. After introducing band dispersion, we achieve quantitative agreement (within 0.2 eV) on the ionization potential and electron affinity measured at pentacene and perfluoropentacene crystal surfaces characterized by standing molecules.

Estimating and testing interactions when explanatory variables are subject to non-classical measurement error.

PubMed

Murad, Havi; Kipnis, Victor; Freedman, Laurence S

2016-10-01

Assessing interactions in linear regression models when covariates have measurement error (ME) is complex.We previously described regression calibration (RC) methods that yield consistent estimators and standard errors for interaction coefficients of normally distributed covariates having classical ME. Here we extend normal based RC (NBRC) and linear RC (LRC) methods to a non-classical ME model, and describe more efficient versions that combine estimates from the main study and internal sub-study. We apply these methods to data from the Observing Protein and Energy Nutrition (OPEN) study. Using simulations we show that (i) for normally distributed covariates efficient NBRC and LRC were nearly unbiased and performed well with sub-study size ≥200; (ii) efficient NBRC had lower MSE than efficient LRC; (iii) the naïve test for a single interaction had type I error probability close to the nominal significance level, whereas efficient NBRC and LRC were slightly anti-conservative but more powerful; (iv) for markedly non-normal covariates, efficient LRC yielded less biased estimators with smaller variance than efficient NBRC. Our simulations suggest that it is preferable to use: (i) efficient NBRC for estimating and testing interaction effects of normally distributed covariates and (ii) efficient LRC for estimating and testing interactions for markedly non-normal covariates. © The Author(s) 2013.

Understanding quantum work in a quantum many-body system.

PubMed

Wang, Qian; Quan, H T

2017-03-01

Based on previous studies in a single-particle system in both the integrable [Jarzynski, Quan, and Rahav, Phys. Rev. X 5, 031038 (2015)2160-330810.1103/PhysRevX.5.031038] and the chaotic systems [Zhu, Gong, Wu, and Quan, Phys. Rev. E 93, 062108 (2016)1539-375510.1103/PhysRevE.93.062108], we study the the correspondence principle between quantum and classical work distributions in a quantum many-body system. Even though the interaction and the indistinguishability of identical particles increase the complexity of the system, we find that for a quantum many-body system the quantum work distribution still converges to its classical counterpart in the semiclassical limit. Our results imply that there exists a correspondence principle between quantum and classical work distributions in an interacting quantum many-body system, especially in the large particle number limit, and further justify the definition of quantum work via two-point energy measurements in quantum many-body systems.

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

PubMed

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

2018-04-05

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

Quantum dynamics of hydrogen atoms on graphene. II. Sticking.

PubMed

Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

2015-09-28

Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

Quantum dynamics of hydrogen atoms on graphene. II. Sticking

NASA Astrophysics Data System (ADS)

Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene; Martinazzo, Rocco

2015-09-01

Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (˜0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

Electron Capture in Slow Collisions of Si4+ With Atomic Hydrogen

NASA Astrophysics Data System (ADS)

Joseph, D. C.; Gu, J. P.; Saha, B. C.

2009-10-01

In recent years the charge transfer involving Si4+ and H at low energies has drawn considerable attention both theoretically and experimentally due to its importance not only in astronomical environments but also in modern semiconductor industries. Accurate information regarding its molecular structures and interactions are essential to understand the low energy collision dynamics. Ab initio calculations are performed using the multireference single- and double-excitation configuration-interaction (MRD-CI) method to evaluate potential energies. State selective cross sections are calculate using fully quantum and semi-classical molecular-orbital close coupling (MOCC) methods in the adiabatic representation. Detail results will be presented in the conference.

Proton energy loss in multilayer graphene and carbon nanotubes

NASA Astrophysics Data System (ADS)

Uribe, Juan D.; Mery, Mario; Fierro, Bernardo; Cardoso-Gil, Raul; Abril, Isabel; Garcia-Molina, Rafael; Valdés, Jorge E.; Esaulov, Vladimir A.

2018-02-01

Results of a study of electronic energy loss of low keV protons interacting with multilayer graphene targets are presented. Proton energy loss shows an unexpectedly high value as compared with measurements in amorphous carbon and carbon nanotubes. Furthermore, we observe a classical linear behavior of the energy loss with the ion velocity but with an apparent velocity threshold around 0.1 a.u., which is not observed in other carbon allotropes. This suggests low dimensionality effects which can be due to the extraordinary graphene properties.

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

DOE PAGES

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

2016-07-05

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

Manipulating molecular quantum states with classical metal atom inputs: demonstration of a single molecule NOR logic gate.

PubMed

Soe, We-Hyo; Manzano, Carlos; Renaud, Nicolas; de Mendoza, Paula; De Sarkar, Abir; Ample, Francisco; Hliwa, Mohamed; Echavarren, Antonio M; Chandrasekhar, Natarajan; Joachim, Christian

2011-02-22

Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.

Toward an Experimental Quantum Chemistry: Exploring a New Energy Partitioning.

PubMed

Rahm, Martin; Hoffmann, Roald

2015-08-19

Following the work of L. C. Allen, this work begins by relating the central chemical concept of electronegativity with the average binding energy of electrons in a system. The average electron binding energy, χ̅, is in principle accessible from experiment, through photoelectron and X-ray spectroscopy. It can also be estimated theoretically. χ̅ has a rigorous and understandable connection to the total energy. That connection defines a new kind of energy decomposition scheme. The changing total energy in a reaction has three primary contributions to it: the average electron binding energy, the nuclear-nuclear repulsion, and multielectron interactions. This partitioning allows one to gain insight into the predominant factors behind a particular energetic preference. We can conclude whether an energy change in a transformation is favored or resisted by collective changes to the binding energy of electrons, the movement of nuclei, or multielectron interactions. For example, in the classical formation of H2 from atoms, orbital interactions dominate nearly canceling nuclear-nuclear repulsion and two-electron interactions. While in electron attachment to an H atom, the multielectron interactions drive the reaction. Looking at the balance of average electron binding energy, multielectron, and nuclear-nuclear contributions one can judge when more traditional electronegativity arguments can be justifiably invoked in the rationalization of a particular chemical event.

Symmetry-Based Techniques for Qualitative Understanding of Rovibrational Effects in Spherical-Top Molecular Spectra and Dynamics

NASA Astrophysics Data System (ADS)

Mitchell, Justin Chadwick

2011-12-01

Using light to probe the structure of matter is as natural as opening our eyes. Modern physics and chemistry have turned this art into a rich science, measuring the delicate interactions possible at the molecular level. Perhaps the most commonly used tool in computational spectroscopy is that of matrix diagonalization. While this is invaluable for calculating everything from molecular structure and energy levels to dipole moments and dynamics, the process of numerical diagonalization is an opaque one. This work applies symmetry and semi-classical techniques to elucidate numerical spectral analysis for high-symmetry molecules. Semi-classical techniques, such as the Potential Energy Surfaces, have long been used to help understand molecular vibronic and rovibronic spectra and dynamics. This investigation focuses on newer semi-classical techniques that apply Rotational Energy Surfaces (RES) to rotational energy level clustering effects in high-symmetry molecules. Such clusters exist in rigid rotor molecules as well as deformable spherical tops. This study begins by using the simplicity of rigid symmetric top molecules to clarify the classical-quantum correspondence of RES semi-classical analysis and then extends it to a more precise and complete theory of modern high-resolution spectra. RES analysis is extended to molecules having more complex and higher rank tensorial rotational and rovibrational Hamiltonians than were possible to understand before. Such molecules are shown to produce an extraordinary range of rotational level clusters, corresponding to a panoply of symmetries ranging from C4v to C2 and C1 (no symmetry) with a corresponding range of new angular momentum localization and J-tunneling effects. Using RES topography analysis and the commutation duality relations between symmetry group operators in the lab-frame to those in the body-frame, it is shown how to better describe and catalog complex splittings found in rotational level clusters. Symmetry character analysis is generalized to give analytic eigensolutions. An appendix provides vibrational analogies. For the first time, interactions between molecular vibrations (polyads) are described semi-classically by multiple RES. This is done for the nu 3/2nu4 dyad of CF4. The nine-surface RES topology of the U(9)-dyad agrees with both computational and experimental work. A connection between this and a simpler U(2) example is detailed in an Appendix.

Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies.

PubMed

Gnanasekaran, Ramachandran

2017-11-08

We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein. This approach locates energy transport channels from the dTTP to remote regions of the protein via residues and water molecules. We examine the water dynamics near the catalytic site of HIV-1 RT by molecular dynamics (MD) simulations. We find that, within the catalytic site, the relaxation of water molecules is similar to that of the hydration water molecules present in other proteins and the relaxation time scale is fast enough to transport energy and helps in communication between dTTP and other residues in the system. To quantify energy transfer, we also calculate the interaction energies of dTTP, 2Mg 2+ , doxy-guanosine nucleotide (DG22) with their surrounding residues by using the B3LYP-D3 method. The results, from classical vibrational energy diffusivity and QM interaction energy, are complementary to identify the important residues involved in the process of polymerization. The positive and negative interactions by dTTP with different types of residues in the catalytic region make the residues transfer energy through vibrational communication.

Electromagnetic cascade in high-energy electron, positron, and photon interactions with intense laser pulses

NASA Astrophysics Data System (ADS)

Bulanov, S. S.; Schroeder, C. B.; Esarey, E.; Leemans, W. P.

2013-06-01

The interaction of high-energy electrons, positrons, and photons with intense laser pulses is studied in head-on collision geometry. It is shown that electrons and/or positrons undergo a cascade-type process involving multiple emissions of photons. These photons can consequently convert into electron-positron pairs. As a result charged particles quickly lose their energy developing an exponentially decaying energy distribution, which suppresses the emission of high-energy photons, thus reducing the number of electron-positron pairs being generated. Therefore, this type of interaction suppresses the development of the electromagnetic avalanche-type discharge, i.e., the exponential growth of the number of electrons, positrons, and photons does not occur in the course of interaction. The suppression will occur when three-dimensional effects can be neglected in the transverse particle orbits, i.e., for sufficiently broad laser pulses with intensities that are not too extreme. The final distributions of electrons, positrons, and photons are calculated for the case of a high-energy e-beam interacting with a counterstreaming, short intense laser pulse. The energy loss of the e-beam, which requires a self-consistent quantum description, plays an important role in this process, as well as provides a clear experimental observable for the transition from the classical to quantum regime of interaction.

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

DOE PAGES

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

2017-04-10

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

Energetics and solvation structure of a dihalogen dopant (I2) in (4)He clusters.

PubMed

Pérez de Tudela, Ricardo; Barragán, Patricia; Valdés, Álvaro; Prosmiti, Rita

2014-08-21

The energetics and structure of small HeNI2 clusters are analyzed as the size of the system changes, with N up to 38. The full interaction between the I2 molecule and the He atoms is based on analytical ab initio He-I2 potentials plus the He-He interaction, obtained from first-principle calculations. The most stable structures, as a function of the number of solvent He atoms, are obtained by employing an evolutionary algorithm and compared with CCSD(T) and MP2 ab initio computations. Further, the classical description is completed by explicitly including thermal corrections and quantum features, such as zero-point-energy values and spatial delocalization. From quantum PIMC calculations, the binding energies and radial/angular probability density distributions of the thermal equilibrium state for selected-size clusters are computed at a low temperature. The sequential formation of regular shell structures is analyzed and discussed for both classical and quantum treatments.

Interaction of two walkers: wave-mediated energy and force.

PubMed

Borghesi, Christian; Moukhtar, Julien; Labousse, Matthieu; Eddi, Antonin; Fort, Emmanuel; Couder, Yves

2014-12-01

A bouncing droplet, self-propelled by its interaction with the waves it generates, forms a classical wave-particle association called a "walker." Previous works have demonstrated that the dynamics of a single walker is driven by its global surface wave field that retains information on its past trajectory. Here we investigate the energy stored in this wave field for two coupled walkers and how it conveys an interaction between them. For this purpose, we characterize experimentally the "promenade modes" where two walkers are bound and propagate together. Their possible binding distances take discrete values, and the velocity of the pair depends on their mutual binding. The mean parallel motion can be either rectilinear or oscillating. The experimental results are recovered analytically with a simple theoretical framework. A relation between the kinetic energy of the droplets and the total energy of the standing waves is established.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum-classical approximation. II. Proton transfer reaction in non-polar solvent

NASA Astrophysics Data System (ADS)

Kojima, H.; Yamada, A.; Okazaki, S.

2015-05-01

The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum-classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute-solvent interactions.

Simple universal models capture all classical spin physics.

PubMed

De las Cuevas, Gemma; Cubitt, Toby S

2016-03-11

Spin models are used in many studies of complex systems because they exhibit rich macroscopic behavior despite their microscopic simplicity. Here, we prove that all the physics of every classical spin model is reproduced in the low-energy sector of certain "universal models," with at most polynomial overhead. This holds for classical models with discrete or continuous degrees of freedom. We prove necessary and sufficient conditions for a spin model to be universal and show that one of the simplest and most widely studied spin models, the two-dimensional Ising model with fields, is universal. Our results may facilitate physical simulations of Hamiltonians with complex interactions. Copyright © 2016, American Association for the Advancement of Science.

Correlations in quantum thermodynamics: Heat, work, and entropy production

PubMed Central

Alipour, S.; Benatti, F.; Bakhshinezhad, F.; Afsary, M.; Marcantoni, S.; Rezakhani, A. T.

2016-01-01

We provide a characterization of energy in the form of exchanged heat and work between two interacting constituents of a closed, bipartite, correlated quantum system. By defining a binding energy we derive a consistent quantum formulation of the first law of thermodynamics, in which the role of correlations becomes evident, and this formulation reduces to the standard classical picture in relevant systems. We next discuss the emergence of the second law of thermodynamics under certain—but fairly general—conditions such as the Markovian assumption. We illustrate the role of correlations and interactions in thermodynamics through two examples. PMID:27767124

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

Horn, Paul R., E-mail: prhorn@berkeley.edu; Mao, Yuezhi; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu

In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms formore » test cases that include the neon dimer, ammonia borane, water-Na{sup +}, water-Cl{sup −}, and the naphthalene dimer.« less

Effects of an electric field on interaction of aromatic systems.

PubMed

Youn, Il Seung; Cho, Woo Jong; Kim, Kwang S

2016-04-30

The effect of uniform external electric field on the interactions between small aromatic compounds and an argon atom is investigated using post-HF (MP2, SCS-MP2, and CCSD(T)) and density functional (PBE0-D3, PBE0-TS, and vdW-DF2) methods. The electric field effect is quantified by the difference of interaction energy calculated in the presence and absence of the electric field. All the post-HF methods describe electric field effects accurately although the interaction energy itself is overestimated by MP2. The electric field effect is explained by classical electrostatic models, where the permanent dipole moment from mutual polarization mainly determines its sign. The size of π-conjugated system does not have significant effect on the electric field dependence. We found out that PBE0-based methods give reasonable interaction energies and electric field response in every case, while vdW-DF2 sometimes shows spurious artifact owing to its sensitivity toward the real space electron density. © 2015 Wiley Periodicals, Inc.

Quantum chaos: an introduction via chains of interacting spins-1/2

NASA Astrophysics Data System (ADS)

Gubin, Aviva; Santos, Lea

2012-02-01

We discuss aspects of quantum chaos by focusing on spectral statistical properties and structures of eigenstates of quantum many-body systems. Quantum systems whose classical counterparts are chaotic have properties that differ from those of quantum systems whose classical counterparts are regular. One of the main signatures of what became known as quantum chaos is a spectrum showing repulsion of the energy levels. We show how level repulsion may develop in one-dimensional systems of interacting spins-1/2 which are devoid of random elements and involve only two-body interactions. We present a simple recipe to unfold the spectrum and emphasize the importance of taking into account the symmetries of the system. In addition to the statistics of eigenvalues, we analyze also how the structure of the eigenstates may indicate chaos. This is done by computing quantities that measure the level of delocalization of the eigenstates.

Kuang's Semi-Classical Formalism for Calculating Electron Capture Cross Sections: A Space- Physics Application

NASA Technical Reports Server (NTRS)

Barghouty, A. F.

2014-01-01

Accurate estimates of electroncapture cross sections at energies relevant to the modeling of the transport, acceleration, and interaction of energetic neutral atoms (ENA) in space (approximately few MeV per nucleon) and especially for multi-electron ions must rely on detailed, but computationally expensive, quantum-mechanical description of the collision process. Kuang's semi-classical approach is an elegant and efficient way to arrive at these estimates. Motivated by ENA modeling efforts for apace applications, we shall briefly present this approach along with sample applications and report on current progress.

PITCH-ANGLE SCATTERING: RESONANCE VERSUS NONRESONANCE, A BASIC TEST OF THE QUASILINEAR DIFFUSIVE RESULT

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

Ragot, B. R.

2012-01-01

Due to the very broad range of the scales available for the development of turbulence in space and astrophysical plasmas, the energy at the resonant scales of wave-particle interaction often constitutes only a tiny fraction of the total magnetic turbulent energy. Despite the high efficiency of resonant wave-particle interaction, one may therefore question whether resonant interaction really is the determining interaction process between particles and turbulent fields. By evaluating and comparing resonant and nonresonant effects in the frame of a quasilinear calculation, the dominance of resonance is here put to the test. By doing so, a basic test of themore » classical resonant quasilinear diffusive result for the pitch-angle scattering of charged energetic particles is also performed.« less

Vibrational properties of the amide group in acetanilide: A molecular-dynamics study

NASA Astrophysics Data System (ADS)

Campa, Alessandro; Giansanti, Andrea; Tenenbaum, Alexander

1987-09-01

A simplified classical model of acetanilide crystal is built in order to study the mechanisms of vibrational energy transduction in a hydrogen-bonded solid. The intermolecular hydrogen bond is modeled by an electrostatic interaction between neighboring excess charges on hydrogen and oxygen atoms. The intramolecular interaction in the peptide group is provided by a dipole-charge interaction. Forces are calculated up to second-order terms in the atomic displacements from equilibrium positions; the model is thus a chain of nonlinear coupled oscillators. Numerical molecular-dynamics experiments are performed on chain segments of five molecules. The dynamics is ordered, at all temperatures. Energy is widely exchanged between the stretching and the bending of the N-H bond, with characteristic times of the order of 0.2 ps. Energy transduction through the H bond is somewhat slower and of smaller amplitude, and is strongly reduced when the energies of the two bound molecules are very different: This could reduce the dissipation of localized energy fluctuations.

Density-functional theory simulation of large quantum dots

NASA Astrophysics Data System (ADS)

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

2003-10-01

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

Selective preparation of hard dental tissue: classical and laser treatments comparison

NASA Astrophysics Data System (ADS)

Dostálova, Tat'jana; Jelínkova, Helena; Němec, Michal; Koranda, Petr; Miyagi, Mitsunobu; Iwai, Katsumasa; Shi, Yi-Wei; Matsuura, Yuji

2006-02-01

For the purpose of micro-selective preparation which is part of the modern dentistry four various methods were examined: ablation by Er:YAG laser radiation (free-running or Q-switching regime), preparation of tissues by ultrasonic round ball tip, and by the classical dental drilling machine using diamond round bur. In the case of Er:YAG laser application the interaction energy 40 mJ in pulse of 200 us yielding to the interaction intensity 62 kW/cm2, and 20 mJ in pulse of 100 ns yielding to the interaction intensity 62 MW/cm2 was used for the case of free running, and Q-switch regime, respectively. For comparisson with the classical methods the ultrasound preparation tip (Sonixflex cariex TC, D - Sonicsys micro) and dental driller together with usual preparation burrs and standard handpiece were used. For the interaction experiment the samples of extracted human teeth and ebony cut into longitudinal sections and polished were used. The thickness of the prepared samples ranged from 5 to 7 mm. The methods were compared from the point of prepared cavity shape (SEM), inner surface, and possibility of selective removal of carries. The composite filling material was used to reconstruct the cavities. The dye penetrating analysis was performed.

Collision-energy-resolved angular distribution of Penning electrons for N 2-He ∗(2 3S)

NASA Astrophysics Data System (ADS)

Hanzawa, Yoshinori; Kishimoto, Naoki; Yamazaki, Masakazu; Ohno, Koichi

2006-07-01

The collision-energy-resolved angular distributions of Penning electrons for individual ionic state of N 2-He ∗(2 3S) were measured. The angular distributions showed increasing intensity in the backward (rebounding) directions with respect to initial He ∗(2 3S) beam vector because Penning ionization occurs with a collision against repulsive interaction wall followed by the electron emission from 2s orbital of He ∗. We also analyzed internal angular distribution by means of fitting parameters using classical trajectory calculations for N 2-He ∗(2 3S) on the modified interaction potential. These internal angular distributions suggested the electron emission from 2s orbital of He ∗ and they depended on collision energy and electron kinetic energy.

Nonequilibrium dynamics of the O( N ) model on dS3 and AdS crunches

NASA Astrophysics Data System (ADS)

Kumar, S. Prem; Vaganov, Vladislav

2018-03-01

We study the nonperturbative quantum evolution of the interacting O( N ) vector model at large- N , formulated on a spatial two-sphere, with time dependent couplings which diverge at finite time. This model - the so-called "E-frame" theory, is related via a conformal transformation to the interacting O( N ) model in three dimensional global de Sitter spacetime with time independent couplings. We show that with a purely quartic, relevant deformation the quantum evolution of the E-frame model is regular even when the classical theory is rendered singular at the end of time by the diverging coupling. Time evolution drives the E-frame theory to the large- N Wilson-Fisher fixed point when the classical coupling diverges. We study the quantum evolution numerically for a variety of initial conditions and demonstrate the finiteness of the energy at the classical "end of time". With an additional (time dependent) mass deformation, quantum backreaction lowers the mass, with a putative smooth time evolution only possible in the limit of infinite quartic coupling. We discuss the relevance of these results for the resolution of crunch singularities in AdS geometries dual to E-frame theories with a classical gravity dual.

Explicit polarization: a quantum mechanical framework for developing next generation force fields.

PubMed

Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel

2014-09-16

Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis.

High-energy gravitational scattering and the general relativistic two-body problem

NASA Astrophysics Data System (ADS)

Damour, Thibault

2018-02-01

A technique for translating the classical scattering function of two gravitationally interacting bodies into a corresponding (effective one-body) Hamiltonian description has been recently introduced [Phys. Rev. D 94, 104015 (2016), 10.1103/PhysRevD.94.104015]. Using this technique, we derive, for the first time, to second-order in Newton's constant (i.e. one classical loop) the Hamiltonian of two point masses having an arbitrary (possibly relativistic) relative velocity. The resulting (second post-Minkowskian) Hamiltonian is found to have a tame high-energy structure which we relate both to gravitational self-force studies of large mass-ratio binary systems, and to the ultra high-energy quantum scattering results of Amati, Ciafaloni and Veneziano. We derive several consequences of our second post-Minkowskian Hamiltonian: (i) the need to use special phase-space gauges to get a tame high-energy limit; and (ii) predictions about a (rest-mass independent) linear Regge trajectory behavior of high-angular-momenta, high-energy circular orbits. Ways of testing these predictions by dedicated numerical simulations are indicated. We finally indicate a way to connect our classical results to the quantum gravitational scattering amplitude of two particles, and we urge amplitude experts to use their novel techniques to compute the two-loop scattering amplitude of scalar masses, from which one could deduce the third post-Minkowskian effective one-body Hamiltonian.

Conformational and stereoelectronic investigation in 1,2-difluoropropane: The gauche effect

NASA Astrophysics Data System (ADS)

Bitencourt, Michelle; Freitas, Matheus P.; Rittner, Roberto

2007-09-01

The effect of attaching an additional fluorine atom at C-2 in 1-fluoropropane (FP), giving 1,2-difluoropropane (DFP), on its conformational equilibrium, is theoretically evaluated. This substitution causes critical implications on the conformer stabilities of DFP (TG, GT and GG conformations) and the steric and electrostatic interactions should favor the conformer with fluorine atoms trans. However, the gauche effect plays a major role in describing the energies balance in DFP, shifting the equilibrium towards the conformation in which the two fluorine atoms are gauche. The origin of this effect is discussed through an NBO analysis, which allows the evaluation of both classical and non-classical (hyperconjugation and bent bonds) interactions as the prevailing factors governing the conformational equilibrium of molecules containing the 1,2-difluoroethane fragment.

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

PubMed

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

2012-07-19

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

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum–classical approximation. II. Proton transfer reaction in non-polar solvent

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

Kojima, H.; Yamada, A.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp

2015-05-07

The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum–classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates ismore » reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute–solvent interactions.« less

Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface.

PubMed

Buryak, Ilya; Vigasin, Andrey A

2015-12-21

The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

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

Buryak, Ilya; Vigasin, Andrey A., E-mail: vigasin@ifaran.ru

The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data basedmore » on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.« less

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Classical electromagnetic fields from quantum sources in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Holliday, Robert; McCarty, Ryan; Peroutka, Balthazar; Tuchin, Kirill

2017-01-01

Electromagnetic fields are generated in high energy nuclear collisions by spectator valence protons. These fields are traditionally computed by integrating the Maxwell equations with point sources. One might expect that such an approach is valid at distances much larger than the proton size and thus such a classical approach should work well for almost the entire interaction region in the case of heavy nuclei. We argue that, in fact, the contrary is true: due to the quantum diffusion of the proton wave function, the classical approximation breaks down at distances of the order of the system size. We compute the electromagnetic field created by a charged particle described initially as a Gaussian wave packet of width 1 fm and evolving in vacuum according to the Klein-Gordon equation. We completely neglect the medium effects. We show that the dynamics, magnitude and even sign of the electromagnetic field created by classical and quantum sources are different.

Effective description of general extensions of the Standard Model: the complete tree-level dictionary

NASA Astrophysics Data System (ADS)

de Blas, J.; Criado, J. C.; Pérez-Victoria, M.; Santiago, J.

2018-03-01

We compute all the tree-level contributions to the Wilson coefficients of the dimension-six Standard-Model effective theory in ultraviolet completions with general scalar, spinor and vector field content and arbitrary interactions. No assumption about the renormalizability of the high-energy theory is made. This provides a complete ultraviolet/infrared dictionary at the classical level, which can be used to study the low-energy implications of any model of interest, and also to look for explicit completions consistent with low-energy data.

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field

NASA Astrophysics Data System (ADS)

Dziedzic, Jacek; Mao, Yuezhi; Shao, Yihan; Ponder, Jay; Head-Gordon, Teresa; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-09-01

We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression for the Hamiltonian of the coupled QM/MM system, which we minimize using gradient methods. The QM subsystem is described by the onetep linear-scaling DFT approach, which makes use of strictly localized orbitals expressed in a set of periodic sinc basis functions equivalent to plane waves. The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in tinker. Distributed multipole analysis is used to obtain, on the fly, a classical representation of the QM subsystem in terms of atom-centered multipoles. This auxiliary representation is used for all polarization interactions between QM and MM, allowing us to treat them on the same footing as in AMOEBA. We validate our method in tests of solute-solvent interaction energies, for neutral and charged molecules, demonstrating the simultaneous optimization of the quantum and classical degrees of freedom. Encouragingly, we find that the inclusion of explicit polarization in the MM part of QM/MM improves the agreement with fully QM calculations.

Observation of anisotropic interactions between metastable atoms and target molecules by two-dimensional collisional ionization electron spectroscopy

NASA Astrophysics Data System (ADS)

Kishimoto, Naoki; Ohno, Koichi

Excited metastable atoms colliding with target molecules can sensitively probe outer properties of molecules by chemi-ionization (Penning ionization) from molecular orbitals in the outer region, since metastable atoms cannot penetrate into the repulsive interaction wall around the molecules. By means of two-dimensional measurements using kinetic energy analysis of electrons combined with a velocity-resolved metastable beam, one can obtain information on the anisotropic interaction between the colliding particles without any control of orientation or alignment of target molecules. We have developed a classical trajectory method to calculate the collision energy dependence of partial ionization cross-sections (CEDPICS) on the anisotropic interaction potential energy surface, which has enabled us to study stereodynamics between metastable atoms and target molecules as well as the spatial distribution of molecular orbitals and electron ejection functions which have a relation with entrance and exit channels of the reaction. Based on the individual CEDPICS, the electronic structure of molecules can also be elucidated.

Fano Interference in Classical Oscillators

ERIC Educational Resources Information Center

Satpathy, S.; Roy, A.; Mohapatra, A.

2012-01-01

We seek to illustrate Fano interference in a classical coupled oscillator by using classical analogues of the atom-laser interaction. We present an analogy between the dressed state picture of coherent atom-laser interaction and a classical coupled oscillator. The Autler-Townes splitting due to the atom-laser interaction is analogous to the…

Energy density and energy flow of plasmonic waves in bilayer graphene

NASA Astrophysics Data System (ADS)

Moradi, Afshin

2017-07-01

The propagation of plasmonic waves in bilayer graphene is studied based on the classical electrodynamics. The interactions between conduction electrons confined to move on the surface of each layer are taken into account via the two-dimensional linearized hydrodynamic model. The energy theorem of electrodynamics is cast in a form which yields expressions for energy density and energy flow of p-polarized surface plasmon polariton waves in bilayer graphene. Numerical results show that the presence of two layers causes the appearance of two branches in the dispersion relation that introduce alterations in the physical behavior of the energy, power flow and the energy transport velocity, in comparison with the results of monolayer graphene.

Molecular dynamics simulations of bubble nucleation in dark matter detectors.

PubMed

Denzel, Philipp; Diemand, Jürg; Angélil, Raymond

2016-01-01

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

Exotic states of matter with polariton chains

NASA Astrophysics Data System (ADS)

Kalinin, Kirill P.; Lagoudakis, Pavlos G.; Berloff, Natalia G.

2018-04-01

We consider linear periodic chains of exciton-polariton condensates formed by pumping polaritons nonresonantly into a linear network. To the leading order such a sequence of condensates establishes relative phases as to minimize a classical one-dimensional X Y Hamiltonian with nearest and next-to-nearest neighbors. We show that the low-energy states of polaritonic linear chains demonstrate various classical regimes: ferromagnetic, antiferromagnetic, and frustrated spiral phases where quantum or thermal fluctuations are expected to give rise to a spin-liquid state. At the same time nonlinear interactions at higher pumping intensities bring about phase chaos and novel exotic phases.

Electrokinetic mechanism of wettability alternation at oil-water-rock interface

NASA Astrophysics Data System (ADS)

Tian, Huanhuan; Wang, Moran

2017-12-01

Design of ions for injection water may change the wettability of oil-brine-rock (OBR) system, which has very important applications in enhanced oil recovery. Though ion-tuned wettability has been verified by various experiments, the mechanism is still not clear. In this review paper, we first present a comprehensive summarization of possible wettability alteration mechanisms, including fines migration or dissolution, multicomponent ion-exchange (MIE), electrical double layer (EDL) interaction between rock and oil, and repulsive hydration force. To clarify the key mechanism, we introduce a complete frame of theories to calculate attribution of EDL repulsion to wettability alteration by assuming constant binding forces (no MIE) and rigid smooth surface (no fines migration or dissolution). The frame consists of three parts: the classical Gouy-Chapman model coupled with interface charging mechanisms to describe EDL in oil-brine-rock systems, three methods with different boundary assumptions to evaluate EDL interaction energy, and the modified Young-Dupré equation to link EDL interaction energy with contact angle. The quantitative analysis for two typical oil-brine-rock systems provides two physical maps that show how the EDL interaction influences contact angle at different ionic composition. The result indicates that the contribution of EDL interaction to ion-tuned wettability for the studied system is not quite significant. The classical and advanced experimental work using microfabrication is reviewed briefly on the contribution of EDL repulsion to wettability alteration and compared with the theoretical results. It is indicated that the roughness of real rock surface may enhance EDL interaction. Finally we discuss some pending questions, perspectives and promising applications based on the mechanism.

Gyroscopic effect in low-energy classical capture of a rotating quadrupolar diatom by an ion.

PubMed

Dashevskaya, Elena; Litvin, Iliya; Nikitin, Evgueni

2006-03-09

The low-energy capture of homonuclear diatoms by ions is due mainly to the long-range part of the interpartner potential with leading terms that correspond to charge-quadrupole interaction and charge-induced dipole interaction. The capture dynamics is described by the perturbed-rotor adiabatic potentials and the Coriolis interaction between manifold of states that belong to a given value of the intrinsic angular momentum. When the latter is large enough, it can noticeably affect the capture cross section calculated in the adiabatic channel approximation due to the gyroscopic property of a rotating diatom. This paper presents the low-energy (low-temperature) state-selected partial and mean capture cross sections (rate coefficients) for the charge-quadrupole interaction that include the gyroscopic effect (decoupling of intrinsic angular momentum from the collision axis), quantum correction for the diatom rotation, and the correction for the charge-induced dipole interaction. These results complement recent studies on the gyroscopic effect in the quantum regime of diatom-ion capture (Dashevskaya, E. I.; Litvin, I.; Nikitin, E. E.; Troe, J. J. Chem. Phys. 2004, 120, 9989-9997).

Interpreting Vibrational Sum-frequency Spectra of Sulfur Dioxide at the Air/Water Interface: A Comprehensive Molecular Dynamics Study

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

Baer, Marcel; Mundy, Christopher J.; Chang, Tsun-Mei

We investigated the solvation and spectroscopic properties of SO2 at the air/water interface using molecular simulation techniques. Molecular interactions from both Kohn-Sham (KS) density functional theory (DFT) and classical polarizable models were utilized to understand the properties of SO2:(H2O)x complexes in the vicinity of the air/water interface. The KS-DFT was included to allow comparisons with sum-frequency generation spectroscopy through the identification of surface SO2:(H2O)x complexes. Using our simulation results, we were able to develop a much more detailed picture for the surface structure of SO2 that is consistent with the spectroscopic data obtained Richmond and coworkers (J. Am. Chem. Soc.more » 127, 16806 (2005)). We also found many similarities and differences between to the two interaction potentials, including a noticeable weakness of the classical potential model in reproducing the asymmetric hydrogen bonding of water with SO2 due to its inability to account for SO2 resonance structures. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Glueball spectrum and hadronic processes in low-energy QCD

NASA Astrophysics Data System (ADS)

Frasca, Marco

2010-10-01

Low-energy limit of quantum chromodynamics (QCD) is obtained using a mapping theorem recently proved. This theorem states that, classically, solutions of a massless quartic scalar field theory are approximate solutions of Yang-Mills equations in the limit of the gauge coupling going to infinity. Low-energy QCD is described by a Yukawa theory further reducible to a Nambu-Jona-Lasinio model. At the leading order one can compute glue-quark interactions and one is able to calculate the properties of the σ and η-η mesons. Finally, it is seen that all the physics of strong interactions, both in the infrared and ultraviolet limit, is described by a single constant Λ arising in the ultraviolet by dimensional transmutation and in the infrared as an integration constant.

Fully stable cosmological solutions with a non-singular classical bounce

DOE PAGES

Ijjas, Anna; Steinhardt, Paul J.

2016-11-28

Recently, we showed how it is possible to use a cubic Galileon action to construct classical cosmological solutions that enter a contracting null energy condition (NEC) violating phase, bounce at finite values of the scale factor and exit into an expanding NEC-satisfying phase without encountering any singularities or pathologies. One drawback of these examples is that singular behavior is encountered at some time either just before or just after the NEC-violating phase. In this Letter, we show that it is possible to circumvent this problem by extending our method to actions that include the next order L 4 Galileon interaction.more » In using this approach, we construct non-singular classical bouncing cosmological solutions that are non-pathological for all times.« less

Testing violation of the Leggett-Garg-type inequality in neutrino oscillations of the Daya Bay experiment

NASA Astrophysics Data System (ADS)

Fu, Qiang; Chen, Xurong

2017-11-01

The Leggett-Garg inequality (LGI), derived under the assumption of realism, acts as the temporal Bell inequality. It is studied in electromagnetic and strong interaction like photonics, superconducting qubits and nuclear spin. The weak interaction two-state oscillations of neutrinos affirmed the violation of Leggett-Garg-type inequalities (LGtI). We make an empirical test for the deviation of experimental results with the classical limits by analyzing the survival probability data of reactor neutrinos at a distinct range of baseline dividing energies, as an analog to a single neutrino detected at different times. A study of the updated data of the Daya Bay experiment unambiguously depicts an obvious cluster of data over the classical bound of LGtI and shows a 6.1σ significance of the violation of them.

The ‘non-Coulombic’ character of classical electrostatic interaction between charges near interfaces

NASA Astrophysics Data System (ADS)

Gabovich, A. M.; Voitenko, A. I.

2018-07-01

The textbook problem of classical electrostatics concerning the charge–charge interaction energy W in a two-layer system is revisited. In particular, the actual dependence of W on the horizontal distance L between the charges located at the same distance x from the interface is shown to substantially differ from the original Coulomb law due to image charges. The deviations are governed by the ratio L/x and the ratio between the dielectric constants of adjacent media. Thus, the dependence W(L) is never conventionally Coulombic (∼L ‑1) and may even be close to a dipole–dipole one (∼L ‑3). Although these results are implicitly contained in the well-known formulas, they are often overlooked while teaching electrostatics. The results are of interest not only from a purely academic viewpoint but are important for modern surface science, where the electrostatic contribution to the ion–ion interaction is often treated as Coulombic without any reservations.

Soft beams: When capillarity induces axial compression

NASA Astrophysics Data System (ADS)

Neukirch, S.; Antkowiak, A.; Marigo, J.-J.

2014-01-01

We study the interaction of an elastic beam with a liquid drop in the case where bending and extensional effects are both present. We use a variational approach to derive equilibrium equations and constitutive relation for the beam. This relation is shown to include a term due to surface energy in addition to the classical Young's modulus term, leading to a modification of Hooke's law. At the triple point where solid, liquid, and vapor phases meet, we find that the external force applied on the beam is parallel to the liquid-vapor interface. Moreover, in the case where solid-vapor and solid-liquid interface energies do not depend on the extension state of the beam, we show that the extension in the beam is continuous at the triple point and that the wetting angle satisfies the classical Young-Dupré relation.

Soft beams: when capillarity induces axial compression.

PubMed

Neukirch, S; Antkowiak, A; Marigo, J-J

2014-01-01

We study the interaction of an elastic beam with a liquid drop in the case where bending and extensional effects are both present. We use a variational approach to derive equilibrium equations and constitutive relation for the beam. This relation is shown to include a term due to surface energy in addition to the classical Young's modulus term, leading to a modification of Hooke's law. At the triple point where solid, liquid, and vapor phases meet, we find that the external force applied on the beam is parallel to the liquid-vapor interface. Moreover, in the case where solid-vapor and solid-liquid interface energies do not depend on the extension state of the beam, we show that the extension in the beam is continuous at the triple point and that the wetting angle satisfies the classical Young-Dupré relation.

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

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

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

Influence of collective nonideal shielding on fusion reaction in partially ionized classical nonideal plasmas

NASA Astrophysics Data System (ADS)

Lee, Myoung-Jae; Jung, Young-Dae

2017-04-01

The collective nonideal effects on the nuclear fusion reaction process are investigated in partially ionized classical nonideal hydrogen plasmas. The effective pseudopotential model taking into account the collective and plasma shielding effects is applied to describe the interaction potential in nonideal plasmas. The analytic expressions of the Sommerfeld parameter, the fusion penetration factor, and the cross section for the nuclear fusion reaction in nonideal plasmas are obtained as functions of the nonideality parameter, Debye length, and relative kinetic energy. It is found that the Sommerfeld parameter is suppressed due to the influence of collective nonideal shielding. However, the collective nonideal shielding is found to enhance the fusion penetration factor in partially ionized classical nonideal plasmas. It is also found that the fusion penetration factors in nonideal plasmas represented by the pseudopotential model are always greater than those in ideal plasmas represented by the Debye-Hückel model. In addition, it is shown that the collective nonideal shielding effect on the fusion penetration factor decreases with an increase of the kinetic energy.

Initial-state-independent equilibration at the breakdown of the eigenstate thermalization hypothesis

NASA Astrophysics Data System (ADS)

Khodja, Abdellah; Schmidtke, Daniel; Gemmer, Jochen

2016-04-01

This work aims at understanding the interplay between the eigenstate thermalization hypothesis (ETH), initial state independent equilibration, and quantum chaos in systems that do not have a direct classical counterpart. It is based on numerical investigations of asymmetric Heisenberg spin ladders with varied interaction strengths between the legs, i.e., along the rungs. The relaxation of the energy difference between the legs is investigated. Two different parameters, both intended to quantify the degree of accordance with the ETH, are computed. Both indicate violation of the ETH at large interaction strengths but at different thresholds. Indeed, the energy difference is found not to relax independently of its initial value above some critical interaction strength, which coincides with one of the thresholds. At the same point the level statistics shift from Poisson-type to Wigner-type. Hence, the system may be considered to become integrable again in the strong interaction limit.

A recipe for free-energy functionals of polarizable molecular fluids

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.

2014-04-01

Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We present a general recipe for constructing functionals for small-molecular liquids based only on bulk experimental properties and ab initio calculations of a single solvent molecule. This recipe combines the exact free energy of the non-interacting system with fundamental measure theory for the repulsive contribution and a weighted density functional for the short-ranged attractive interactions. We add to these ingredients a weighted polarization functional for the long-range correlations in both the rotational and molecular-polarizability contributions to the dielectric response. We also perform molecular dynamics calculations for the free energy of cavity formation and the high-field dielectric response, and show that our free-energy functional adequately describes these properties (which are key for accurate solvation calculations) for all three solvents in our study: water, chloroform, and carbon tetrachloride.

Measurement of the adsorption energy difference between ortho- and para-D2 on an amorphous ice surface.

PubMed

Amiaud, L; Momeni, A; Dulieu, F; Fillion, J H; Matar, E; Lemaire, J-L

2008-02-08

Molecular hydrogen interaction on water ice surfaces is a major process taking place in interstellar dense clouds. By coupling laser detection and classical thermal desorption spectroscopy, it is possible to study the effect of rotation of D(2) on adsorption on amorphous solid water ice surfaces. The desorption profiles of ortho- and para-D(2) are different. This difference is due to a shift in the adsorption energy distribution of the two lowest rotational states. Molecules in J''=1 rotational state are on average more strongly bound to the ice surface than those in J''=0 rotational state. This energy difference is estimated to be 1.4+/-0.3 meV. This value is in agreement with previous calculation and interpretation. The nonspherical wave function J'' =1 has an interaction with the asymmetric part of the adsorption potential and contributes positively in the binding energy.

Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes.

PubMed

Lee, Mi Kyung; Coker, David F

2016-08-18

An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation.

Proton-impact ionization cross sections of adenine measured at 0.5 and 2.0 MeV by electron spectroscopy

NASA Astrophysics Data System (ADS)

Iriki, Y.; Kikuchi, Y.; Imai, M.; Itoh, A.

2011-11-01

Double-differential ionization cross sections (DDCSs) of vapor-phase adenine molecules (C5H5N5) by 0.5- and 2.0-MeV proton impact have been measured by the electron spectroscopy method. Electrons ejected from adenine were analyzed by a 45∘ parallel-plate electrostatic spectrometer over an energy range of 1.0-1000 eV at emission angles from 15∘ to 165∘. Single-differential cross sections (SDCSs) and total ionization cross sections (TICSs) were also deduced. It was found from the Platzman plot, defined as SDCSs divided by the classical Rutherford knock-on cross sections per target electron, that the SDCSs at higher electron energies are proportional to the total number of valence electrons (50) of adenine, while those at low-energy electrons are highly enhanced due to dipole and higher-order interactions. The present results of TICS are in fairly good agreement with recent classical trajectory Monte Carlo calculations, and moreover, a simple analytical formula gives nearly equivalent cross sections in magnitude at the incident proton energies investigated.

AMOEBA 2.0: A physics-first approach to biomolecular simulations

NASA Astrophysics Data System (ADS)

Rackers, Joshua; Ponder, Jay

The goal of the AMOEBA force field project is to use classical physics to understand and predict the nature of interactions between biological molecules. While making significant advances over the past decade, the ultimate goal of predicting binding energies with ``chemical accuracy'' remains elusive. The primary source of this inaccuracy comes from the physics of how molecules interact at short range. For example, despite AMOEBA's advanced treatment of electrostatics, the force field dramatically overpredicts the electrostatic energy of DNA stacking interactions. AMOEBA 2.0 works to correct these errors by including simple, first principles physics-based terms to account for the quantum mechanical nature of these short-range molecular interactions. We have added a charge penetration term that considerably improves the description of electrostatic interactions at short range. We are reformulating the polarization term of AMOEBA in terms of basic physics assertions. And we are reevaluating the van der Waals term to match ab initio energy decompositions. These additions and changes promise to make AMOEBA more predictive. By including more physical detail of the important short-range interactions of biological molecules, we hope to move closer to the ultimate goal of true predictive power.

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

PubMed

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

2012-09-07

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

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

Experimental Demonstration of Coherent Control in Quantum Chaotic Systems

NASA Astrophysics Data System (ADS)

Bitter, M.; Milner, V.

2017-01-01

We experimentally demonstrate coherent control of a quantum system, whose dynamics is chaotic in the classical limit. Interaction of diatomic molecules with a periodic sequence of ultrashort laser pulses leads to the dynamical localization of the molecular angular momentum, a characteristic feature of the chaotic quantum kicked rotor. By changing the phases of the rotational states in the initially prepared coherent wave packet, we control the rotational distribution of the final localized state and its total energy. We demonstrate the anticipated sensitivity of control to the exact parameters of the kicking field, as well as its disappearance in the classical regime of excitation.

Particle and surfactant interactions effected polar and dispersive components of interfacial energy in nanocolloids

NASA Astrophysics Data System (ADS)

Harikrishnan, A. R.; Das, Sarit K.; Agnihotri, Prabhat K.; Dhar, Purbarun

2017-08-01

We segregate and report experimentally for the first time the polar and dispersive interfacial energy components of complex nanocolloidal dispersions. In the present study, we introduce a novel inverse protocol for the classical Owens Wendt method to determine the constitutive polar and dispersive elements of surface tension in such multicomponent fluidic systems. The effect of nanoparticles alone and aqueous surfactants alone are studied independently to understand the role of the concentration of the dispersed phase in modulating the constitutive elements of surface energy in fluids. Surfactants are capable of altering the polar component, and the combined particle and surfactant nanodispersions are shown to be effective in modulating the polar and dispersive components of surface tension depending on the relative particle and surfactant concentrations as well as the morphological and electrostatic nature of the dispersed phases. We observe that the combined surfactant and particle colloid exhibits a similar behavior to that of the particle only case; however, the amount of modulation of the polar and dispersive constituents is found to be different from the particle alone case which brings to the forefront the mechanisms through which surfactants modulate interfacial energies in complex fluids. Accordingly, we are able to show that the observations can be merged into a form of quasi-universal trend in the trends of polar and dispersive components in spite of the non-universal character in the wetting behavior of the fluids. We analyze the different factors affecting the polar and dispersive interactions in such complex colloids, and the physics behind such complex interactions has been explained by appealing to the classical dispersion theories by London, Debye, and Keesom as well as by Derjaguin-Landau-Verwey-Overbeek theory. The findings shed light on the nature of wetting behavior of such complex fluids and help in predicting the wettability and the degree of interfacial interaction with a substrate in such multicomponent nanocolloidal systems.

Experimental and theoretical study of rotationally inelastic diffraction of H2(D2) from methyl-terminated Si(111)

NASA Astrophysics Data System (ADS)

Nihill, Kevin J.; Hund, Zachary M.; Muzas, Alberto; Díaz, Cristina; del Cueto, Marcos; Frankcombe, Terry; Plymale, Noah T.; Lewis, Nathan S.; Martín, Fernando; Sibener, S. J.

2016-08-01

Fundamental details concerning the interaction between H2 and CH3-Si(111) have been elucidated by the combination of diffractive scattering experiments and electronic structure and scattering calculations. Rotationally inelastic diffraction (RID) of H2 and D2 from this model hydrocarbon-decorated semiconductor interface has been confirmed for the first time via both time-of-flight and diffraction measurements, with modest j = 0 → 2 RID intensities for H2 compared to the strong RID features observed for D2 over a large range of kinematic scattering conditions along two high-symmetry azimuthal directions. The Debye-Waller model was applied to the thermal attenuation of diffraction peaks, allowing for precise determination of the RID probabilities by accounting for incoherent motion of the CH3-Si(111) surface atoms. The probabilities of rotationally inelastic diffraction of H2 and D2 have been quantitatively evaluated as a function of beam energy and scattering angle, and have been compared with complementary electronic structure and scattering calculations to provide insight into the interaction potential between H2 (D2) and hence the surface charge density distribution. Specifically, a six-dimensional potential energy surface (PES), describing the electronic structure of the H2(D2)/CH3-Si(111) system, has been computed based on interpolation of density functional theory energies. Quantum and classical dynamics simulations have allowed for an assessment of the accuracy of the PES, and subsequently for identification of the features of the PES that serve as classical turning points. A close scrutiny of the PES reveals the highly anisotropic character of the interaction potential at these turning points. This combination of experiment and theory provides new and important details about the interaction of H2 with a hybrid organic-semiconductor interface, which can be used to further investigate energy flow in technologically relevant systems.

Crystallization tendencies of modelled Lennard-Jones liquids with different attractions

NASA Astrophysics Data System (ADS)

Valdès, L.-C.; Gerges, J.; Mizuguchi, T.; Affouard, F.

2018-01-01

Molecular dynamics simulations are performed on simple models composed of monoatomic Lennard-Jones atoms for which the repulsive interaction is the same but the attractive part is tuned. We investigate the precise role of the attractive part of the interaction potential on different structural, dynamical, and thermodynamical properties of these systems in the liquid and crystalline states. It includes crystallization trends for which the main physical ingredients involved have been computed: the diffusion coefficient, the Gibbs energy difference between the liquid and the crystalline state, and the crystal-liquid interfacial free energy. Results are compared with predictions from the classical nucleation theory including transient and steady-state regimes at moderate and deeper undercooling. The question of the energetic and entropic impact of the repulsive and attractive part of the interaction potential towards crystallization is also addressed.

Quantum weak turbulence with applications to semiconductor lasers

NASA Astrophysics Data System (ADS)

Lvov, Y. V.; Binder, R.; Newell, A. C.

1998-10-01

Based on a model Hamiltonian appropriate for the description of fermionic systems such as semiconductor lasers, we describe a natural asymptotic closure of the BBGKY hierarchy in complete analogy with that derived for classical weak turbulence. The main features of the interaction Hamiltonian are the inclusion of full Fermi statistics containing Pauli blocking and a simple, phenomenological, uniformly weak two-particle interaction potential equivalent to the static screening approximation. We find a new class of solutions to the quantum kinetic equation which are analogous to the Kolmogorov spectra of hydrodynamics and classical weak turbulence. They involve finite fluxes of particles and energy in momentum space and are particularly relevant for describing the behavior of systems containing sources and sinks. We make a prima facie case that these finite flux solutions can be important in the context of semiconductor lasers and show how they might be used to enhance laser performance.

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

Experimental demonstration of information to energy conversion in a quantum system at the Landauer limit.

PubMed

Peterson, J P S; Sarthour, R S; Souza, A M; Oliveira, I S; Goold, J; Modi, K; Soares-Pinto, D O; Céleri, L C

2016-04-01

Landauer's principle sets fundamental thermodynamical constraints for classical and quantum information processing, thus affecting not only various branches of physics, but also of computer science and engineering. Despite its importance, this principle was only recently experimentally considered for classical systems. Here we employ a nuclear magnetic resonance set-up to experimentally address the information to energy conversion in a quantum system. Specifically, we consider a three nuclear spins [Formula: see text] (qubits) molecule-the system, the reservoir and the ancilla-to measure the heat dissipated during the implementation of a global system-reservoir unitary interaction that changes the information content of the system. By employing an interferometric technique, we were able to reconstruct the heat distribution associated with the unitary interaction. Then, through quantum state tomography, we measured the relative change in the entropy of the system. In this way, we were able to verify that an operation that changes the information content of the system must necessarily generate heat in the reservoir, exactly as predicted by Landauer's principle. The scheme presented here allows for the detailed study of irreversible entropy production in quantum information processors.

The phonon theory of liquid thermodynamics

PubMed Central

Bolmatov, D.; Brazhkin, V. V.; Trachenko, K.

2012-01-01

Heat capacity of matter is considered to be its most important property because it holds information about system's degrees of freedom as well as the regime in which the system operates, classical or quantum. Heat capacity is well understood in gases and solids but not in the third main state of matter, liquids, and is not discussed in physics textbooks as a result. The perceived difficulty is that interactions in a liquid are both strong and system-specific, implying that the energy strongly depends on the liquid type and that, therefore, liquid energy can not be calculated in general form. Here, we develop a phonon theory of liquids where this problem is avoided. The theory covers both classical and quantum regimes. We demonstrate good agreement of calculated and experimental heat capacity of 21 liquids, including noble, metallic, molecular and hydrogen-bonded network liquids in a wide range of temperature and pressure. PMID:22639729

The role of broken symmetry in solvation of a spherical cavity in classical and quantum water models

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

Remsing, Richard C.; Baer, Marcel D.; Schenter, Gregory K.

2014-08-21

Insertion of a hard sphere cavity in liquid water breaks translational symmetry and generates an electrostatic potential difference between the region near the cavity and the bulk. Here, we clarify the physical interpretation of this potential and its calculation. We also show that the electrostatic potential in the center of small, medium, and large cavities depends very sensitively on the form of the assumed molecular interactions for dfferent classical simple point-charge models and quantum mechanical DFT-based interaction potentials, as reected in their description of donor and acceptor hydrogen bonds near the cavity. These dfferences can signifcantly affect the magnitude ofmore » the scalar electrostatic potential. We argue that the result of these studies will have direct consequences toward our understanding of the thermodynamics of ion solvation through the cavity charging process. JDW and RCR are supported by the National Science Foundation (Grants CHE0848574 and CHE1300993). CJM and GKS are supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL. We acknowledge illuminating discussions and sharing of ideas and preprints with Dr. Shawn M. Kathmann and Prof. Tom Beck. The DFT simulations used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program.« less

Energy repartition in the nonequilibrium steady state

NASA Astrophysics Data System (ADS)

Yan, Peng; Bauer, Gerrit E. W.; Zhang, Huaiwu

2017-01-01

The concept of temperature in nonequilibrium thermodynamics is an outstanding theoretical issue. We propose an energy repartition principle that leads to a spectral (mode-dependent) temperature in steady-state nonequilibrium systems. The general concepts are illustrated by analytic solutions of the classical Heisenberg spin chain connected to Langevin heat reservoirs with arbitrary temperature profiles. Gradients of external magnetic fields are shown to localize spin waves in a Wannier-Zeemann fashion, while magnon interactions renormalize the spectral temperature. Our generic results are applicable to other thermodynamic systems such as Newtonian liquids, elastic solids, and Josephson junctions.

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

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

Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ionmore » hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.« less

Quantum Metropolis sampling.

PubMed

Temme, K; Osborne, T J; Vollbrecht, K G; Poulin, D; Verstraete, F

2011-03-03

The original motivation to build a quantum computer came from Feynman, who imagined a machine capable of simulating generic quantum mechanical systems--a task that is believed to be intractable for classical computers. Such a machine could have far-reaching applications in the simulation of many-body quantum physics in condensed-matter, chemical and high-energy systems. Part of Feynman's challenge was met by Lloyd, who showed how to approximately decompose the time evolution operator of interacting quantum particles into a short sequence of elementary gates, suitable for operation on a quantum computer. However, this left open the problem of how to simulate the equilibrium and static properties of quantum systems. This requires the preparation of ground and Gibbs states on a quantum computer. For classical systems, this problem is solved by the ubiquitous Metropolis algorithm, a method that has basically acquired a monopoly on the simulation of interacting particles. Here we demonstrate how to implement a quantum version of the Metropolis algorithm. This algorithm permits sampling directly from the eigenstates of the Hamiltonian, and thus evades the sign problem present in classical simulations. A small-scale implementation of this algorithm should be achievable with today's technology.

Microbial syntrophy: interaction for the common good.

PubMed

Morris, Brandon E L; Henneberger, Ruth; Huber, Harald; Moissl-Eichinger, Christine

2013-05-01

Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Quantum-mechanical analysis of low-gain free-electron laser oscillators

NASA Astrophysics Data System (ADS)

Fares, H.; Yamada, M.; Chiadroni, E.; Ferrario, M.

2018-05-01

In the previous classical theory of the low-gain free-electron laser (FEL) oscillators, the electron is described as a point-like particle, a delta function in the spatial space. On the other hand, in the previous quantum treatments, the electron is described as a plane wave with a single momentum state, a delta function in the momentum space. In reality, an electron must have statistical uncertainties in the position and momentum domains. Then, the electron is neither a point-like charge nor a plane wave of a single momentum. In this paper, we rephrase the theory of the low-gain FEL where the interacting electron is represented quantum mechanically by a plane wave with a finite spreading length (i.e., a wave packet). Using the concepts of the transformation of reference frames and the statistical quantum mechanics, an expression for the single-pass radiation gain is derived. The spectral broadening of the radiation is expressed in terms of the spreading length of an electron, the relaxation time characterizing the energy spread of electrons, and the interaction time. We introduce a comparison between our results and those obtained in the already known classical analyses where a good agreement between both results is shown. While the correspondence between our results and the classical results are shown, novel insights into the electron dynamics and the interaction mechanism are presented.

A Classical Based Derivation of Time Dilation Providing First Order Accuracy to Schwarzschild's Solution of Einstein's Field Equations

NASA Astrophysics Data System (ADS)

Austin, Rickey W.

In Einstein's theory of Special Relativity (SR), one method to derive relativistic kinetic energy is via applying the classical work-energy theorem to relativistic momentum. This approach starts with a classical based work-energy theorem and applies SR's momentum to the derivation. One outcome of this derivation is relativistic kinetic energy. From this derivation, it is rather straight forward to form a kinetic energy based time dilation function. In the derivation of General Relativity a common approach is to bypass classical laws as a starting point. Instead a rigorous development of differential geometry and Riemannian space is constructed, from which classical based laws are derived. This is in contrast to SR's approach of starting with classical laws and applying the consequences of the universal speed of light by all observers. A possible method to derive time dilation due to Newtonian gravitational potential energy (NGPE) is to apply SR's approach to deriving relativistic kinetic energy. It will be shown this method gives a first order accuracy compared to Schwarzschild's metric. The SR's kinetic energy and the newly derived NGPE derivation are combined to form a Riemannian metric based on these two energies. A geodesic is derived and calculations compared to Schwarzschild's geodesic for an orbiting test mass about a central, non-rotating, non-charged massive body. The new metric results in high accuracy calculations when compared to Einsteins General Relativity's prediction. The new method provides a candidate approach for starting with classical laws and deriving General Relativity effects. This approach mimics SR's method of starting with classical mechanics when deriving relativistic equations. As a compliment to introducing General Relativity, it provides a plausible scaffolding method from classical physics when teaching introductory General Relativity. A straight forward path from classical laws to General Relativity will be derived. This derivation provides a minimum first order accuracy to Schwarzschild's solution to Einstein's field equations.

Cosmic censorship in quantum Einstein gravity

NASA Astrophysics Data System (ADS)

Bonanno, A.; Koch, B.; Platania, A.

2017-05-01

We study the quantum gravity modification of the Kuroda-Papapetrou model induced by the running of the Newton’s constant at high energy in quantum Einstein gravity. We argue that although the antiscreening character of the gravitational interaction favours the formation of a naked singularity, quantum gravity effects turn the classical singularity into a ‘whimper’ singularity which remains naked for a finite amount of advanced time.

Electrostatic Interactions in Aminoglycoside-RNA Complexes

PubMed Central

Kulik, Marta; Goral, Anna M.; Jasiński, Maciej; Dominiak, Paulina M.; Trylska, Joanna

2015-01-01

Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity. PMID:25650932

Testing of the DPMJET and VENUS hadronic interaction models with help of the atmospheric muons

NASA Astrophysics Data System (ADS)

Dedenko, L. G.; Lukyashin, A. V.; Roganova, T. M.; Fedorova, G. F.

2017-01-01

The more accurate original calculations of the atmospheric vertical muon energy spectra at energies 102 - 105 GeV have been carried out in terms of DPMJET and VENUS models. The Gaisser-Honda approximations of the measured energy spectra of primary protons, helium and nitrogen nuclei have been used. The package CORSIKA has been used to simulate cascades in the standard atmosphere induced by different primary particles with various fixed energies E. Statistics of simulated cascades for secondary particles with energies (0.01-1)·E was increased up to 106. It has been shown that predictions of the DPMJET and VENUS models for these muon fluxes are below the data of the classical experiments L3 + Cosmic, MACRO and LVD by factors of ˜ 1.6-1.95 at energies above 102 GeV. It has been concluded that these tested models underestimate the production of the most energetic secondary particles, namely, π-mesons and K-mesons, in interactions of the primary protons and other primary nuclei with nuclei in the atmosphere by the same factors.

Quantum and classical behavior in interacting bosonic systems

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

Hertzberg, Mark P.

It is understood that in free bosonic theories, the classical field theory accurately describes the full quantum theory when the occupancy numbers of systems are very large. However, the situation is less understood in interacting theories, especially on time scales longer than the dynamical relaxation time. Recently there have been claims that the quantum theory deviates spectacularly from the classical theory on this time scale, even if the occupancy numbers are extremely large. Furthermore, it is claimed that the quantum theory quickly thermalizes while the classical theory does not. The evidence for these claims comes from noticing a spectacular differencemore » in the time evolution of expectation values of quantum operators compared to the classical micro-state evolution. If true, this would have dramatic consequences for many important phenomena, including laboratory studies of interacting BECs, dark matter axions, preheating after inflation, etc. In this work we critically examine these claims. We show that in fact the classical theory can describe the quantum behavior in the high occupancy regime, even when interactions are large. The connection is that the expectation values of quantum operators in a single quantum micro-state are approximated by a corresponding classical ensemble average over many classical micro-states. Furthermore, by the ergodic theorem, a classical ensemble average of local fields with statistical translation invariance is the spatial average of a single micro-state. So the correlation functions of the quantum and classical field theories of a single micro-state approximately agree at high occupancy, even in interacting systems. Furthermore, both quantum and classical field theories can thermalize, when appropriate coarse graining is introduced, with the classical case requiring a cutoff on low occupancy UV modes. We discuss applications of our results.« less

Estimates of the Attenuation Rates of Baroclinic Tidal Energy Caused by Resonant Interactions Among Internal Waves based on the Weak Turbulence Theory

NASA Astrophysics Data System (ADS)

Onuki, Y.; Hibiya, T.

2016-02-01

The baroclinic tides are thought to be the dominant energy source for turbulent mixing in the ocean interior. In contrast to the geography of the energy conversion rates from the barotropic to baroclinic tides, which has been clarified in recent numerical studies, the global distribution of the energy sink for the resulting low-mode baroclinic tides remains obscure. A key to resolve this issue is the resonant wave-wave interactions, which transfer part of the baroclinic tidal energy to the background internal wave field enhancing the local energy dissipation rates. Recent field observations and numerical studies have pointed out that parametric subharmonic instability (PSI), one of the resonant interactions, causes significant energy sink of baroclinic tidal energy at mid-latitudes. The purpose of this study is to analyze the quantitative aspect of PSI to demonstrate the global distribution of the intensity of resonant wave interactions, namely, the attenuation rate of low-mode baroclinic tidal energy. Our approach is basically following the weak turbulence theory, which is the standard theory for resonant wave-wave interactions, where techniques of singular perturbation and statistical physics are employed. This study is, however, different from the classical theory in some points; we have reformulated the weak turbulence theory to be applicable to low-mode internal waves and also developed its numerical calculation method so that the effects of stratification profile and oceanic total depth can be taken into account. We have calculated the attenuation rate of low-mode baroclinic tidal waves interacting with the background Garrett-Munk internal wave field. The calculated results clearly show the rapid attenuation of baroclinic tidal energy at mid-latitudes, in agreement with the results from field observations and also show the zonal inhomogeneity of the attenuation rate caused by the density structures associated with the subtropical gyre. This study is expected to contribute to clarify the global distribution of the dissipation rates of baroclinic tidal energy.

Driven topological systems in the classical limit

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Entangling spin-spin interactions of ions in individually controlled potential wells

NASA Astrophysics Data System (ADS)

Wilson, Andrew; Colombe, Yves; Brown, Kenton; Knill, Emanuel; Leibfried, Dietrich; Wineland, David

2014-03-01

Physical systems that cannot be modeled with classical computers appear in many different branches of science, including condensed-matter physics, statistical mechanics, high-energy physics, atomic physics and quantum chemistry. Despite impressive progress on the control and manipulation of various quantum systems, implementation of scalable devices for quantum simulation remains a formidable challenge. As one approach to scalability in simulation, here we demonstrate an elementary building-block of a configurable quantum simulator based on atomic ions. Two ions are trapped in separate potential wells that can individually be tailored to emulate a number of different spin-spin couplings mediated by the ions' Coulomb interaction together with classical laser and microwave fields. We demonstrate deterministic tuning of this interaction by independent control of the local wells and emulate a particular spin-spin interaction to entangle the internal states of the two ions with 0.81(2) fidelity. Extension of the building-block demonstrated here to a 2D-network, which ion-trap micro-fabrication processes enable, may provide a new quantum simulator architecture with broad flexibility in designing and scaling the arrangement of ions and their mutual interactions. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), ONR, and the NIST Quantum Information Program.

Nuclear quantum effects in water exchange around lithium and fluoride ions

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

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

2015-02-14

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

Simulation of wave packet tunneling of interacting identical particles

NASA Astrophysics Data System (ADS)

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

2003-02-01

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

Anisotropic interaction and stereoreactivity in a chemi-ionization process of OCS by collision with He*(2(3)S) metastable atoms.

PubMed

Horio, Takuya; Maeda, Satoshi; Kishimoto, Naoki; Ohno, Koichi

2006-09-28

Ionic-state-resolved collision energy dependence of Penning ionization cross sections for OCS with He*(2(3)S) metastable atoms was measured in a wide collision energy range from 20 to 350 meV. Anisotropic interaction potential for the OCS-He*(2(3)S) system was obtained by comparison of the experimental data with classical trajectory simulations. It has been found that attractive potential wells around the O and S atoms are clearly different in their directions. Around the O atom, the collinear approach is preferred (the well depth is ca. 90 meV), while the perpendicular approach is favored around the S atom (the well depth is ca. 40 meV). On the basis of the optimized potential energy surface and theoretical simulations, stereo reactivity around the O and S atoms was also investigated. The results were discussed in terms of anisotropy of the potential energy surface and the electron density distribution of molecular orbitals to be ionized.

Hamiltonian structure of classical N-body systems of finite-size particles subject to EM interactions

NASA Astrophysics Data System (ADS)

Cremaschini, C.; Tessarotto, M.

2012-01-01

An open issue in classical relativistic mechanics is the consistent treatment of the dynamics of classical N-body systems of mutually interacting particles. This refers, in particular, to charged particles subject to EM interactions, including both binary interactions and self-interactions ( EM-interacting N- body systems). The correct solution to the question represents an overriding prerequisite for the consistency between classical and quantum mechanics. In this paper it is shown that such a description can be consistently obtained in the context of classical electrodynamics, for the case of a N-body system of classical finite-size charged particles. A variational formulation of the problem is presented, based on the N -body hybrid synchronous Hamilton variational principle. Covariant Lagrangian and Hamiltonian equations of motion for the dynamics of the interacting N-body system are derived, which are proved to be delay-type ODEs. Then, a representation in both standard Lagrangian and Hamiltonian forms is proved to hold, the latter expressed by means of classical Poisson Brackets. The theory developed retains both the covariance with respect to the Lorentz group and the exact Hamiltonian structure of the problem, which is shown to be intrinsically non-local. Different applications of the theory are investigated. The first one concerns the development of a suitable Hamiltonian approximation of the exact equations that retains finite delay-time effects characteristic of the binary interactions and self-EM-interactions. Second, basic consequences concerning the validity of Dirac generator formalism are pointed out, with particular reference to the instant-form representation of Poincaré generators. Finally, a discussion is presented both on the validity and possible extension of the Dirac generator formalism as well as the failure of the so-called Currie "no-interaction" theorem for the non-local Hamiltonian system considered here.

The Classical Theory of Light Colors: a Paradigm for Description of Particle Interactions

NASA Astrophysics Data System (ADS)

Mazilu, Nicolae; Agop, Maricel; Gatu, Irina; Iacob, Dan Dezideriu; Butuc, Irina; Ghizdovat, Vlad

2016-06-01

The color is an interaction property: of the interaction of light with matter. Classically speaking it is therefore akin to the forces. But while forces engendered the mechanical view of the world, the colors generated the optical view. One of the modern concepts of interaction between the fundamental particles of matter - the quantum chromodynamics - aims to fill the gap between mechanics and optics, in a specific description of strong interactions. We show here that this modern description of the particle interactions has ties with both the classical and quantum theories of light, regardless of the connection between forces and colors. In a word, the light is a universal model in the description of matter. The description involves classical Yang-Mills fields related to color.

Mean-Eddy-Turbulence Interaction through Canonical Transfer Analysis: Theory and Application to the Kuroshio Extension Energetics Study

NASA Astrophysics Data System (ADS)

Liang, X. S.

2016-02-01

Central at the processes of mean-eddy-turbulence interaction, e.g., mesoscale eddy shedding, relaminarization, etc., is the transfer of energy among different scales. The existing classical transfers, however, do not take into account the issue of energy conservation and, therefore, are not faithful representations of the real interaction processes, which are fundamentally a redistribution of energy among scales. Based on a new analysis machinery, namely, multiscale window transform (Liang and Anderson, 2007), we were able to obtain a formula for this important processes, with the property of energy conservation a naturally embedded property. This formula has a form reminiscent of the Poisson bracket in Hamiltonian dynamics. It has been validated with many benchmark processes, and, particularly, has been applied with success to control the eddy shedding behind a bluff body. Presented here will be an application study of the instabilities and mean-eddy interactions in the Kuroshio Extension (KE) region. Generally, it is found that the unstable KE jet fuels the mesoscale eddies, but in the offshore eddy decaying region, the cause-effect relation reverses: it is the latter that drive the former. On the whole the eddies act to decelerate the jet in the upstream, whereas accelerating it downstream.

Nonperturbative theory of atom-surface interaction: corrections at short separations

NASA Astrophysics Data System (ADS)

Bordag, M.; Klimchitskaya, G. L.; Mostepanenko, V. M.

2018-02-01

The nonperturbative expressions for the free energy and force of interaction between a ground-state atom and a real-material surface at any temperature are presented. The transition to the Matsubara representation is performed, whereupon the comparison is made with the commonly used perturbative results based on the standard Lifshitz theory. It is shown that the Lifshitz formulas for the free energy and force of an atom-surface interaction follow from the nonperturbative ones in the lowest order of the small parameter. Numerical computations of the free energy and force for the atoms of He{\\hspace{0pt}}\\ast and Na interacting with a surface of an Au plate have been performed using the frequency-dependent dielectric permittivity of Au and highly accurate dynamic atomic polarizabilities in the framework of both the nonperturbative and perturbative theories. According to our results, the maximum deviations between the two theories are reached at the shortest atom-surface separations of about 1 nm. Simple analytic expressions for the atom-surface free energy are derived in the classical limit and for an ideal-metal plane. In the lowest order of the small parameter, they are found in agreement with the perturbative ones following from the standard Lifshitz theory. Possible applications of the obtained results in the theory of van der Waals adsorption are discussed.

Congested Aggregation via Newtonian Interaction

NASA Astrophysics Data System (ADS)

Craig, Katy; Kim, Inwon; Yao, Yao

2018-01-01

We consider a congested aggregation model that describes the evolution of a density through the competing effects of nonlocal Newtonian attraction and a hard height constraint. This provides a counterpoint to existing literature on repulsive-attractive nonlocal interaction models, where the repulsive effects instead arise from an interaction kernel or the addition of diffusion. We formulate our model as the Wasserstein gradient flow of an interaction energy, with a penalization to enforce the constraint on the height of the density. From this perspective, the problem can be seen as a singular limit of the Keller-Segel equation with degenerate diffusion. Two key properties distinguish our problem from previous work on height constrained equations: nonconvexity of the interaction kernel (which places the model outside the scope of classical gradient flow theory) and nonlocal dependence of the velocity field on the density (which causes the problem to lack a comparison principle). To overcome these obstacles, we combine recent results on gradient flows of nonconvex energies with viscosity solution theory. We characterize the dynamics of patch solutions in terms of a Hele-Shaw type free boundary problem and, using this characterization, show that in two dimensions patch solutions converge to a characteristic function of a disk in the long-time limit, with an explicit rate on the decay of the energy. We believe that a key contribution of the present work is our blended approach, combining energy methods with viscosity solution theory.

Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

PubMed

Nelson, Tammie R; Chaban, Vitaly V; Kalugin, Oleg N; Prezhdo, Oleg V

2010-04-08

The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance. Solvent molecules confined within CNTs are more strongly coupled to the tubes than the outside molecules. The energy exchange is facilitated by slow collective motions, including CNT radial breathing modes (RBM). The transfer rate between CNTs and the inside solvent shows strong dependence on the CNT diameter. In smaller tubes, the transfer is faster and the solvent coupling to RBMs is stronger. The magnitude of the CNT-outside solvent interaction scales with the CNT surface area, while that of the CNT-inside solvent exhibits scaling that is intermediate between the CNT volume and surface. The Coulomb interaction between the solvent molecules inside and outside of the CNTs is much weaker than the CNT-solvent interactions. The results indicate that the excitation energy supplied to CNTs in chemical and biological applications is rapidly deposited to the active molecular agents and should remain localized sufficiently long in order to perform the desired function.

Extraction of highly charged ions from the Berlin Electron Beam Ion Trap for interactions with a gas target

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

Allen, F.I.; Biedermann, C.; Radtke, R.

2006-03-15

Highly charged ions are extracted from the Berlin Electron Beam Ion Trap for investigations of charge exchange with a gas target. The classical over-the-barrier model for slow highly charged ions describes this process, whereby one or more electrons are captured from the target into Rydberg states of the ion. The excited state relaxes via a radiative cascade of the electron to ground energy. The cascade spectra are characteristic of the capture state. We investigate x-ray photons emitted as a result of interactions between Ar{sup 17+} ions at energies {<=}5q keV with Ar atoms. Of particular interest is the velocity dependencemore » of the angular momentum capture state l{sub c}.« less

A Comparison of Kinetic Energy and Momentum in Special Relativity and Classical Mechanics

ERIC Educational Resources Information Center

Riggs, Peter J.

2016-01-01

Kinetic energy and momentum are indispensable dynamical quantities in both the special theory of relativity and in classical mechanics. Although momentum and kinetic energy are central to understanding dynamics, the differences between their relativistic and classical notions have not always received adequate treatment in undergraduate teaching.…

THz frequency spectrum of protein-solvent interaction energy using a recurrence plot-based Wiener-Khinchin method.

PubMed

Karain, Wael

2016-10-01

The dynamics of a protein and the water surrounding it are coupled via nonbonded energy interactions. This coupling can exhibit a complex, nonlinear, and nonstationary nature. The THz frequency spectrum for this interaction energy characterizes both the vibration spectrum of the water hydrogen bond network, and the frequency range of large amplitude modes of proteins. We use a Recurrence Plot based Wiener-Khinchin method RPWK to calculate this spectrum, and the results are compared to those determined using the classical auto-covariance-based Wiener-Khinchin method WK. The frequency spectra for the total nonbonded interaction energy extracted from molecular dynamics simulations between the β-Lactamase Inhibitory Protein BLIP, and water molecules within a 10 Å distance from the protein surface, are calculated at 150, 200, 250, and 310 K, respectively. Similar calculations are also performed for the nonbonded interaction energy between the residues 49ASP, 53TYR, and 142PHE in BLIP, with water molecules within 10 Å from each residue respectively at 150, 200, 250, and 310 K. A comparison of the results shows that RPWK performs better than WK, and is able to detect some frequency data points that WK fails to detect. This points to the importance of using methods capable of taking the complex nature of the protein-solvent energy landscape into consideration, and not to rely on standard linear methods. In general, RPWK can be a valuable addition to the analysis tools for protein molecular dynamics simulations. Proteins 2016; 84:1549-1557. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Are Anion/π Interactions Actually a Case of Simple Charge–Dipole Interactions?†

PubMed Central

Wheeler, Steven E.; Houk, K. N.

2011-01-01

Substituent effects in Cl− ••• C6H6−nXn complexes, models for anion/π interactions, have been examined using density functional theory and robust ab initio methods paired with large basis sets. Predicted interaction energies for 83 model Cl− ••• C6H6−nXn complexes span almost 40 kcal mol−1 and show an excellent correlation (r = 0.99) with computed electrostatic potentials. In contrast to prevailing models of anion/π interactions, which rely on substituent-induced changes in the aryl π-system, it is shown that substituent effects in these systems are due mostly to direct interactions between the anion and the substituents. Specifically, interaction energies for Cl− ••• C6H6−nXn complexes are recovered using a model system in which the substituents are isolated from the aromatic ring and π-resonance effects are impossible. Additionally, accurate potential energy curves for Cl− interacting with prototypical anion-binding arenes can be qualitatively reproduced by adding a classical charge–dipole interaction to the Cl− ••• C6H6 interaction potential. In substituted benzenes, binding of anions arises primarily from interactions of the anion with the local dipoles induced by the substituents, not changes in the interaction with the aromatic ring itself. When designing anion-binding motifs, phenyl rings should be viewed as a scaffold upon which appropriate substituents can be placed, because there are no attractive interactions between anions and the aryl π-system of substituted benzenes. PMID:20433187

Elastic interactions between two-dimensional geometric defects

NASA Astrophysics Data System (ADS)

Moshe, Michael; Sharon, Eran; Kupferman, Raz

2015-12-01

In this paper, we introduce a methodology applicable to a wide range of localized two-dimensional sources of stress. This methodology is based on a geometric formulation of elasticity. Localized sources of stress are viewed as singular defects—point charges of the curvature associated with a reference metric. The stress field in the presence of defects can be solved using a scalar stress function that generalizes the classical Airy stress function to the case of materials with nontrivial geometry. This approach allows the calculation of interaction energies between various types of defects. We apply our methodology to two physical systems: shear-induced failure of amorphous materials and the mechanical interaction between contracting cells.

Toward chemical accuracy in the description of ion-water interactions through many-body representations. Alkali-water dimer potential energy surfaces

NASA Astrophysics Data System (ADS)

Riera, Marc; Mardirossian, Narbe; Bajaj, Pushp; Götz, Andreas W.; Paesani, Francesco

2017-10-01

This study presents the extension of the MB-nrg (Many-Body energy) theoretical/computational framework of transferable potential energy functions (PEFs) for molecular simulations of alkali metal ion-water systems. The MB-nrg PEFs are built upon the many-body expansion of the total energy and include the explicit treatment of one-body, two-body, and three-body interactions, with all higher-order contributions described by classical induction. This study focuses on the MB-nrg two-body terms describing the full-dimensional potential energy surfaces of the M+(H2O) dimers, where M+ = Li+, Na+, K+, Rb+, and Cs+. The MB-nrg PEFs are derived entirely from "first principles" calculations carried out at the explicitly correlated coupled-cluster level including single, double, and perturbative triple excitations [CCSD(T)-F12b] for Li+ and Na+ and at the CCSD(T) level for K+, Rb+, and Cs+. The accuracy of the MB-nrg PEFs is systematically assessed through an extensive analysis of interaction energies, structures, and harmonic frequencies for all five M+(H2O) dimers. In all cases, the MB-nrg PEFs are shown to be superior to both polarizable force fields and ab initio models based on density functional theory. As previously demonstrated for halide-water dimers, the MB-nrg PEFs achieve higher accuracy by correctly describing short-range quantum-mechanical effects associated with electron density overlap as well as long-range electrostatic many-body interactions.

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Classical dimer model with anisotropic interactions on the square lattice

NASA Astrophysics Data System (ADS)

Otsuka, Hiromi

2009-07-01

We discuss phase transitions and the phase diagram of a classical dimer model with anisotropic interactions defined on a square lattice. For the attractive region, the perturbation of the orientational order parameter introduced by the anisotropy causes the Berezinskii-Kosterlitz-Thouless transitions from a dimer-liquid to columnar phases. According to the discussion by Nomura and Okamoto for a quantum-spin chain system [J. Phys. A 27, 5773 (1994)], we proffer criteria to determine transition points and also universal level-splitting conditions. Subsequently, we perform numerical diagonalization calculations of the nonsymmetric real transfer matrices up to linear dimension specified by L=20 and determine the global phase diagram. For the repulsive region, we find the boundary between the dimer-liquid and the strong repulsion phases. Based on the dispersion relation of the one-string motion, which exhibits a twofold “zero-energy flat band” in the strong repulsion limit, we give an intuitive account for the property of the strong repulsion phase.

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

Yoo, Soohaeng; Xantheas, Sotiris S.

Water's function as a universal solvent and its role in mediating several biological functions that are responsible for sustaining life has created tremendous interest in the understanding of its structure at the molecular level.1 Due to the size of the simulation cells and the sampling time needed to compute many macroscopic properties, most of the initial simulations are performed using a classical force field whereas several processes that involve chemistry are subsequently probed with electronic structure based methods. A significant effort has therefore been devoted towards the development of classical force fields for water.2 Clusters of water molecules are usefulmore » in probing the intermolecular interactions at the microscopic level as well as providing information about the subtle energy differences that are associated with different bonding arrangements within a hydrogen bonded network. They moreover render a quantitative picture of the nature and magnitude of the various components of the intermolecular interactions such as exchange, dispersion, induction etc. They can finally serve as a vehicle for the study of the convergence of properties with increasing size.« less

Understanding decomposition and encapsulation energies of structure I and II clathrate hydrates

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ohmura, Ryo

2016-10-01

When compressed with water or ice under high pressure and low temperature conditions, some gases form solid gas hydrate inclusion compounds which have higher melting points than ice under those pressures. In this work, we study the balance of the guest-water and water-water interaction energies that lead to the formation of the clathrate hydrate phases. In particular, molecular dynamics simulations with accurate water potentials are used to study the energetics of the formation of structure I (sI) and II (sII) clathrate hydrates of methane, ethane, and propane. The dissociation enthalpy of the clathrate hydrate phases, the encapsulation enthalpy of methane, ethane, and propane guests in the corresponding phases, and the average bonding enthalpy of water molecules are calculated and compared with accurate calorimetric measurements and previous classical and quantum mechanical calculations, when available. The encapsulation energies of methane, ethane, and propane guests stabilize the small and large sI and sII hydrate cages, with the larger molecules giving larger encapsulation energies. The average water-water interactions are weakened in the sI and sII phases compared to ice. The relative magnitudes of the van der Waals potential energy in ice and the hydrate phases are similar, but in the ice phase, the electrostatic interactions are stronger. The stabilizing guest-water "hydrophobic" interactions compensate for the weaker water-water interactions and stabilize the hydrate phases. A number of common assumptions regarding the guest-cage water interactions are used in the van der Waals-Platteeuw statistical mechanical theory to predict the clathrate hydrate phase stability under different pressure-temperature conditions. The present calculations show that some of these assumptions may not accurately reflect the physical nature of the interactions between guest molecules and the lattice waters.

Understanding decomposition and encapsulation energies of structure I and II clathrate hydrates.

PubMed

Alavi, Saman; Ohmura, Ryo

2016-10-21

When compressed with water or ice under high pressure and low temperature conditions, some gases form solid gas hydrate inclusion compounds which have higher melting points than ice under those pressures. In this work, we study the balance of the guest-water and water-water interaction energies that lead to the formation of the clathrate hydrate phases. In particular, molecular dynamics simulations with accurate water potentials are used to study the energetics of the formation of structure I (sI) and II (sII) clathrate hydrates of methane, ethane, and propane. The dissociation enthalpy of the clathrate hydrate phases, the encapsulation enthalpy of methane, ethane, and propane guests in the corresponding phases, and the average bonding enthalpy of water molecules are calculated and compared with accurate calorimetric measurements and previous classical and quantum mechanical calculations, when available. The encapsulation energies of methane, ethane, and propane guests stabilize the small and large sI and sII hydrate cages, with the larger molecules giving larger encapsulation energies. The average water-water interactions are weakened in the sI and sII phases compared to ice. The relative magnitudes of the van der Waals potential energy in ice and the hydrate phases are similar, but in the ice phase, the electrostatic interactions are stronger. The stabilizing guest-water "hydrophobic" interactions compensate for the weaker water-water interactions and stabilize the hydrate phases. A number of common assumptions regarding the guest-cage water interactions are used in the van der Waals-Platteeuw statistical mechanical theory to predict the clathrate hydrate phase stability under different pressure-temperature conditions. The present calculations show that some of these assumptions may not accurately reflect the physical nature of the interactions between guest molecules and the lattice waters.

Product-State Approximations to Quantum States

NASA Astrophysics Data System (ADS)

Brandão, Fernando G. S. L.; Harrow, Aram W.

2016-02-01

We show that for any many-body quantum state there exists an unentangled quantum state such that most of the two-body reduced density matrices are close to those of the original state. This is a statement about the monogamy of entanglement, which cannot be shared without limit in the same way as classical correlation. Our main application is to Hamiltonians that are sums of two-body terms. For such Hamiltonians we show that there exist product states with energy that is close to the ground-state energy whenever the interaction graph of the Hamiltonian has high degree. This proves the validity of mean-field theory and gives an explicitly bounded approximation error. If we allow states that are entangled within small clusters of systems but product across clusters then good approximations exist when the Hamiltonian satisfies one or more of the following properties: (1) high degree, (2) small expansion, or (3) a ground state where the blocks in the partition have sublinear entanglement. Previously this was known only in the case of small expansion or in the regime where the entanglement was close to zero. Our approximations allow an extensive error in energy, which is the scale considered by the quantum PCP (probabilistically checkable proof) and NLTS (no low-energy trivial-state) conjectures. Thus our results put restrictions on the possible Hamiltonians that could be used for a possible proof of the qPCP or NLTS conjectures. By contrast the classical PCP constructions are often based on constraint graphs with high degree. Likewise we show that the parallel repetition that is possible with classical constraint satisfaction problems cannot also be possible for quantum Hamiltonians, unless qPCP is false. The main technical tool behind our results is a collection of new classical and quantum de Finetti theorems which do not make any symmetry assumptions on the underlying states.

Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

PubMed

Graziani, F R; Bauer, J D; Murillo, M S

2014-09-01

Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations.

Experimental and theoretical study of rotationally inelastic diffraction of H{sub 2}(D{sub 2}) from methyl-terminated Si(111)

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

Nihill, Kevin J.; Hund, Zachary M.; Sibener, S. J., E-mail: s-sibener@uchicago.edu

2016-08-28

Fundamental details concerning the interaction between H{sub 2} and CH{sub 3}–Si(111) have been elucidated by the combination of diffractive scattering experiments and electronic structure and scattering calculations. Rotationally inelastic diffraction (RID) of H{sub 2} and D{sub 2} from this model hydrocarbon-decorated semiconductor interface has been confirmed for the first time via both time-of-flight and diffraction measurements, with modest j = 0 → 2 RID intensities for H{sub 2} compared to the strong RID features observed for D{sub 2} over a large range of kinematic scattering conditions along two high-symmetry azimuthal directions. The Debye-Waller model was applied to the thermal attenuationmore » of diffraction peaks, allowing for precise determination of the RID probabilities by accounting for incoherent motion of the CH{sub 3}–Si(111) surface atoms. The probabilities of rotationally inelastic diffraction of H{sub 2} and D{sub 2} have been quantitatively evaluated as a function of beam energy and scattering angle, and have been compared with complementary electronic structure and scattering calculations to provide insight into the interaction potential between H{sub 2} (D{sub 2}) and hence the surface charge density distribution. Specifically, a six-dimensional potential energy surface (PES), describing the electronic structure of the H{sub 2}(D{sub 2})/CH{sub 3}−Si(111) system, has been computed based on interpolation of density functional theory energies. Quantum and classical dynamics simulations have allowed for an assessment of the accuracy of the PES, and subsequently for identification of the features of the PES that serve as classical turning points. A close scrutiny of the PES reveals the highly anisotropic character of the interaction potential at these turning points. This combination of experiment and theory provides new and important details about the interaction of H{sub 2} with a hybrid organic-semiconductor interface, which can be used to further investigate energy flow in technologically relevant systems.« less

A Prediction Method of Binding Free Energy of Protein and Ligand

NASA Astrophysics Data System (ADS)

Yang, Kun; Wang, Xicheng

2010-05-01

Predicting the binding free energy is an important problem in bimolecular simulation. Such prediction would be great benefit in understanding protein functions, and may be useful for computational prediction of ligand binding strengths, e.g., in discovering pharmaceutical drugs. Free energy perturbation (FEP)/thermodynamics integration (TI) is a classical method to explicitly predict free energy. However, this method need plenty of time to collect datum, and that attempts to deal with some simple systems and small changes of molecular structures. Another one for estimating ligand binding affinities is linear interaction energy (LIE) method. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. However, it also is time-consuming work. In this paper, a new prediction method based on steered molecular dynamics (SMD) with direction optimization is developed to compute binding free energy. Jarzynski's equality is used to derive the PMF or free-energy. The results for two numerical examples are presented, showing that the method has good accuracy and efficiency. The novel method can also simulate whole binding proceeding and give some important structural information about development of new drugs.

Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car Parrinello) molecular dynamics

NASA Astrophysics Data System (ADS)

Hammond, Philip S.; Wu, Yudong; Harris, Rebecca; Minehardt, Todd J.; Car, Roberto; Schmitt, Jeffrey D.

2005-01-01

A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

Dielectric properties of classical and quantized ionic fluids.

PubMed

Høye, Johan S

2010-06-01

We study time-dependent correlation functions of classical and quantum gases using methods of equilibrium statistical mechanics for systems of uniform as well as nonuniform densities. The basis for our approach is the path integral formalism of quantum mechanical systems. With this approach the statistical mechanics of a quantum mechanical system becomes the equivalent of a classical polymer problem in four dimensions where imaginary time is the fourth dimension. Several nontrivial results for quantum systems have been obtained earlier by this analogy. Here, we will focus upon the presence of a time-dependent electromagnetic pair interaction where the electromagnetic vector potential that depends upon currents, will be present. Thus both density and current correlations are needed to evaluate the influence of this interaction. Then we utilize that densities and currents can be expressed by polarizations by which the ionic fluid can be regarded as a dielectric one for which a nonlocal susceptibility is found. This nonlocality has as a consequence that we find no contribution from a possible transverse electric zero-frequency mode for the Casimir force between metallic plates. Further, we establish expressions for a leading correction to ab initio calculations for the energies of the quantized electrons of molecules where now retardation effects also are taken into account.

Dynamics of tripartite quantum entanglement and discord under a classical dephasing random telegraph noise

NASA Astrophysics Data System (ADS)

Kenfack, Lionel Tenemeza; Tchoffo, Martin; Fai, Lukong Cornelius

2017-02-01

We address the dynamics of quantum correlations, including entanglement and quantum discord of a three-qubit system interacting with a classical pure dephasing random telegraph noise (RTN) in three different physical environmental situations (independent, mixed and common environments). Two initial entangled states of the system are examined, namely the Greenberger-Horne-Zeilinger (GHZ)- and Werner (W)-type states. The classical noise is introduced as a stochastic process affecting the energy splitting of the qubits. With the help of suitable measures of tripartite entanglement (entanglement witnesses and lower bound of concurrence) and quantum discord (global quantum discord and quantum dissension), we show that the evolution of quantum correlations is not only affected by the type of the system-environment interaction but also by the input configuration of the qubits and the memory properties of the environmental noise. Indeed, depending on the memory properties of the environmental noise and the initial state considered, we find that independent, common and mixed environments can play opposite roles in preserving quantum correlations, and that the sudden death and revival phenomena or the survival of quantum correlations may occur. On the other hand, we also show that the W-type state has strong dynamics under this noise than the GHZ-type ones.

Investigating the foil-generated deuteron beam interaction with a DT target in degenerate and classical plasma

NASA Astrophysics Data System (ADS)

Mehrangiz, M.; Ghasemizad, A.

2017-06-01

Deuteron fast ignition of a conically guided pre-compressed DT fuel is investigated. For this purpose, the acceleration of the deuterated thin foil by the intense laser beam is evaluated. The acceleration values and the number of foil-generated deuterons are calculated in terms of the laser pulse duration. Using the created deuterons as the fast ignitors, we investigate the fast ignition scheme by comparing fully degenerate, partial degenerate and classical types of DT plasma. The total energy gain of deuterons "beam fusion" is calculated to show the efficiency of beam reactions in increasing fusion rate. Besides, the stopping time and stopping range of incident deuterons are evaluated. Our numerical results indicate that degeneracy increases the beam-target collisions. Thus, it prepares the ignition situation sooner than the classical plasma. Moreover, the number of generated deuterons and their acceleration depend on the foil thickness and laser parameters. We show that when a 4ps laser with intensity of 10^{19} W/cm^2 focused onto a 20μm foil, 35× 10^{15} deuterons are generated. Moreover, under our analysis, in order to have a practicable fast ignition, 18% of the laser energy is necessary to convert into a deuteron driver.

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

PubMed Central

2016-01-01

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

Nonadiabatic Molecular Dynamics and Orthogonality Constrained Density Functional Theory

NASA Astrophysics Data System (ADS)

Shushkov, Philip Georgiev

The exact quantum dynamics of realistic, multidimensional systems remains a formidable computational challenge. In many chemical processes, however, quantum effects such as tunneling, zero-point energy quantization, and nonadiabatic transitions play an important role. Therefore, approximate approaches that improve on the classical mechanical framework are of special practical interest. We propose a novel ring polymer surface hopping method for the calculation of chemical rate constants. The method blends two approaches, namely ring polymer molecular dynamics that accounts for tunneling and zero-point energy quantization, and surface hopping that incorporates nonadiabatic transitions. We test the method against exact quantum mechanical calculations for a one-dimensional, two-state model system. The method reproduces quite accurately the tunneling contribution to the rate and the distribution of reactants between the electronic states for this model system. Semiclassical instanton theory, an approach related to ring polymer molecular dynamics, accounts for tunneling by the use of periodic classical trajectories on the inverted potential energy surface. We study a model of electron transfer in solution, a chemical process where nonadiabatic events are prominent. By representing the tunneling electron with a ring polymer, we derive Marcus theory of electron transfer from semiclassical instanton theory after a careful analysis of the tunneling mode. We demonstrate that semiclassical instanton theory can recover the limit of Fermi's Golden Rule rate in a low-temperature, deep-tunneling regime. Mixed quantum-classical dynamics treats a few important degrees of freedom quantum mechanically, while classical mechanics describes affordably the rest of the system. But the interface of quantum and classical description is a challenging theoretical problem, especially for low-energy chemical processes. We therefore focus on the semiclassical limit of the coupled nuclear-electronic dynamics. We show that the time-dependent Schrodinger equation for the electrons employed in the widely used fewest switches surface hopping method is applicable only in the limit of nearly identical classical trajectories on the different potential energy surfaces. We propose a short-time decoupling algorithm that restricts the use of the Schrodinger equation only to the interaction regions. We test the short-time approximation on three model systems against exact quantum-mechanical calculations. The approximation improves the performance of the surface hopping approach. Nonadiabatic molecular dynamics simulations require the efficient and accurate computation of ground and excited state potential energy surfaces. Unlike the ground state calculations where standard methods exist, the computation of excited state properties is a challenging task. We employ time-independent density functional theory, in which the excited state energy is represented as a functional of the total density. We suggest an adiabatic-like approximation that simplifies the excited state exchange-correlation functional. We also derive a set of minimal conditions to impose exactly the orthogonality of the excited state Kohn-Sham determinant to the ground state determinant. This leads to an efficient, variational algorithm for the self-consistent optimization of the excited state energy. Finally, we assess the quality of the excitation energies obtained by the new method on a set of 28 organic molecules. The new approach provides results of similar accuracy to time-dependent density functional theory.

Experimental Preparation and Measurement of Quantum States of Motion of a Trapped Atom

DTIC Science & Technology

1997-01-01

trapped atom are quantum harmonic oscillators, their couplings to internal atomic levels (described by the Jaynes - Cummings model (JCM) [ l , 21) are... wave approximation in a frame rotating with WO, where hwo is the energy difference of the two internal levels, the interaction of the classical laser... Jaynes - Cummings model , the system is suited to realizing many proposals originally introduced in the realm of quantum optics and cavity quantum

The impact of symmetric modes on intramolecular electron transfer: A semi-classical approach

NASA Astrophysics Data System (ADS)

Coropceanu, Veaceslav; Boldyrev, Sergei I.; Risko, Chad; Brédas, Jean-Luc

2006-07-01

We have generalized the Hush equations developed for the analysis of intervalence charge-transfer bands by including into the model the interaction with symmetric vibrations. Our results indicate that in symmetric class-II systems the maximum of the intervalence charge-transfer band is equal to the reorganization energy λ related to the antisymmetric vibrations as is the case in the conventional Hush model. In contrast, the corresponding transition dipole moment and the activation barrier for thermal electron transfer, in addition to their dependence on λ, also depend on the reorganization energy L related to symmetric vibrational modes. We show that the interaction with symmetric vibrational modes reduces the activation barrier and that the thermal electron-transfer rates derived on the basis of a Hush-type analysis of the optical data are generally underestimated.

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

PubMed

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

2017-11-01

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

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

PubMed Central

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

2018-01-01

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

Intermolecular orbital interaction in π systems

NASA Astrophysics Data System (ADS)

Zhao, Rundong; Zhang, Rui-Qin

2018-04-01

Intermolecular interactions, in regard to which people tend to emphasise the noncovalent van der Waals (vdW) forces when conducting investigations throughout chemistry, can influence the structure, stability and function of molecules and materials. Despite the ubiquitous nature of vdW interactions, a simplified electrostatic model has been popularly adopted to explain common intermolecular interactions, especially those existing in π-involved systems. However, this classical model has come under fire in revealing specific issues such as substituent effects, due to its roughness; and it has been followed in past decades by sundry explanations which sometimes bring in nebulous descriptions. In this account, we try to summarise and present a unified model for describing and analysing the binding mechanism of such systems from the viewpoint of energy decomposition. We also emphasise a commonly ignored factor - orbital interaction, pointing out that the noncovalent intermolecular orbital interactions actually exhibit similar bonding and antibonding phenomena as those in covalent bonds.

Hydrogen adsorption in HKUST-1: a combined inelastic neutron scattering and first-principles study.

PubMed

Brown, Craig M; Liu, Yun; Yildirim, Taner; Peterson, Vanessa K; Kepert, Cameron J

2009-05-20

Hydrogen adsorption in high surface area nanoporous coordination polymers has attracted a great deal of interest in recent years due to the potential applications in energy storage. Here we present combined inelastic neutron scattering measurements and detailed first-principles calculations aimed at unraveling the nature of hydrogen adsorption in HKUST-1 (Cu3(1,3,5-benzenetricarboxylate)2), a metal-organic framework (MOF) with unsaturated metal centers. We reveal that, in this system, the major contribution to the overall binding comes from the classical Coulomb interaction which is not screened due to the open metal site; this explains the relatively high binding energies and short H2-metal distances observed in MOFs with exposed metal sites as compared to traditional ones. Despite the short distances, there is no indication of an elongation of the H-H bond for the bound H2 molecule at the metal site. We find that both the phonon and rotational energy levels of the hydrogen molecule are closely similar, making the interpretation of the inelastic neutron scattering data difficult. Finally, we show that the orientation of H2 has a surprisingly large effect on the binding potential, reducing the classical binding energy by almost 30%. The implication of these results for the development of MOF materials for better hydrogen storage is discussed.

Hydrogen adsorption in HKUST-1: a combined inelastic neutron scattering and first-principles study

NASA Astrophysics Data System (ADS)

Brown, Craig M.; Liu, Yun; Yildirim, Taner; Peterson, Vanessa K.; Kepert, Cameron J.

2009-05-01

Hydrogen adsorption in high surface area nanoporous coordination polymers has attracted a great deal of interest in recent years due to the potential applications in energy storage. Here we present combined inelastic neutron scattering measurements and detailed first-principles calculations aimed at unraveling the nature of hydrogen adsorption in HKUST-1 (Cu3(1,3,5-benzenetricarboxylate)2), a metal-organic framework (MOF) with unsaturated metal centers. We reveal that, in this system, the major contribution to the overall binding comes from the classical Coulomb interaction which is not screened due to the open metal site; this explains the relatively high binding energies and short H2-metal distances observed in MOFs with exposed metal sites as compared to traditional ones. Despite the short distances, there is no indication of an elongation of the H-H bond for the bound H2 molecule at the metal site. We find that both the phonon and rotational energy levels of the hydrogen molecule are closely similar, making the interpretation of the inelastic neutron scattering data difficult. Finally, we show that the orientation of H2 has a surprisingly large effect on the binding potential, reducing the classical binding energy by almost 30%. The implication of these results for the development of MOF materials for better hydrogen storage is discussed.

Electric-field-induced modification in Curie temperature of Co monolayer on Pt(111)

NASA Astrophysics Data System (ADS)

Nakamura, Kohji; Oba, Mikito; Akiyama, Toru; Ito, Tomonori; Weinert, Michael

2015-03-01

Magnetism induced by an external electric field (E-field) has received much attention as a potential approach for controlling magnetism at the nano-scale with the promise of ultra-low energy power consumption. Here, the E-field-induced modification of the Curie temperature for a prototypical transition-metal thin layer of a Co monolayer on Pt(111) is investigated by first-principles calculations by using the full-potential linearized augmented plane wave method that treats spin-spiral structures in an E-field. An applied E-field modifies the magnon (spin-spiral formation) energies by a few meV, which leads to a modification of the exchange pair interaction parameters within the classical Heisenberg model. With inclusion of the spin-orbit coupling (SOC), the magnetocrystalline anisotropy and the Dzyaloshinskii-Morita interaction are obtained by the second variation SOC method. An E-field-induced modification of the Curie temperature is demonstrated by Monte Carlo simulations, in which a change in the exchange interaction is found to play a key role.

Predicting Multicomponent Adsorption Isotherms in Open-Metal Site Materials Using Force Field Calculations Based on Energy Decomposed Density Functional Theory.

PubMed

Heinen, Jurn; Burtch, Nicholas C; Walton, Krista S; Fonseca Guerra, Célia; Dubbeldam, David

2016-12-12

For the design of adsorptive-separation units, knowledge is required of the multicomponent adsorption behavior. Ideal adsorbed solution theory (IAST) breaks down for olefin adsorption in open-metal site (OMS) materials due to non-ideal donor-acceptor interactions. Using a density-function-theory-based energy decomposition scheme, we develop a physically justifiable classical force field that incorporates the missing orbital interactions using an appropriate functional form. Our first-principles derived force field shows greatly improved quantitative agreement with the inflection points, initial uptake, saturation capacity, and enthalpies of adsorption obtained from our in-house adsorption experiments. While IAST fails to make accurate predictions, our improved force field model is able to correctly predict the multicomponent behavior. Our approach is also transferable to other OMS structures, allowing the accurate study of their separation performances for olefins/paraffins and further mixtures involving complex donor-acceptor interactions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Particle Acceleration and Fractional Transport in Turbulent Reconnection

NASA Astrophysics Data System (ADS)

Isliker, Heinz; Pisokas, Theophilos; Vlahos, Loukas; Anastasiadis, Anastasios

2017-11-01

We consider a large-scale environment of turbulent reconnection that is fragmented into a number of randomly distributed unstable current sheets (UCSs), and we statistically analyze the acceleration of particles within this environment. We address two important cases of acceleration mechanisms when particles interact with the UCS: (a) electric field acceleration and (b) acceleration by reflection at contracting islands. Electrons and ions are accelerated very efficiently, attaining an energy distribution of power-law shape with an index 1-2, depending on the acceleration mechanism. The transport coefficients in energy space are estimated from test-particle simulation data, and we show that the classical Fokker-Planck (FP) equation fails to reproduce the simulation results when the transport coefficients are inserted into it and it is solved numerically. The cause for this failure is that the particles perform Levy flights in energy space, while the distributions of the energy increments exhibit power-law tails. We then use the fractional transport equation (FTE) derived by Isliker et al., whose parameters and the order of the fractional derivatives are inferred from the simulation data, and solving the FTE numerically, we show that the FTE successfully reproduces the kinetic energy distribution of the test particles. We discuss in detail the analysis of the simulation data and the criteria that allow one to judge the appropriateness of either an FTE or a classical FP equation as a transport model.

Complexity of Quantum Impurity Problems

NASA Astrophysics Data System (ADS)

Bravyi, Sergey; Gosset, David

2017-12-01

We give a quasi-polynomial time classical algorithm for estimating the ground state energy and for computing low energy states of quantum impurity models. Such models describe a bath of free fermions coupled to a small interacting subsystem called an impurity. The full system consists of n fermionic modes and has a Hamiltonian {H=H_0+H_{imp}}, where H 0 is quadratic in creation-annihilation operators and H imp is an arbitrary Hamiltonian acting on a subset of O(1) modes. We show that the ground energy of H can be approximated with an additive error {2^{-b}} in time {n^3 \\exp{[O(b^3)]}}. Our algorithm also finds a low energy state that achieves this approximation. The low energy state is represented as a superposition of {\\exp{[O(b^3)]}} fermionic Gaussian states. To arrive at this result we prove several theorems concerning exact ground states of impurity models. In particular, we show that eigenvalues of the ground state covariance matrix decay exponentially with the exponent depending very mildly on the spectral gap of H 0. A key ingredient of our proof is Zolotarev's rational approximation to the {√{x}} function. We anticipate that our algorithms may be used in hybrid quantum-classical simulations of strongly correlated materials based on dynamical mean field theory. We implemented a simplified practical version of our algorithm and benchmarked it using the single impurity Anderson model.

Particle Acceleration and Fractional Transport in Turbulent Reconnection

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

Isliker, Heinz; Pisokas, Theophilos; Vlahos, Loukas

We consider a large-scale environment of turbulent reconnection that is fragmented into a number of randomly distributed unstable current sheets (UCSs), and we statistically analyze the acceleration of particles within this environment. We address two important cases of acceleration mechanisms when particles interact with the UCS: (a) electric field acceleration and (b) acceleration by reflection at contracting islands. Electrons and ions are accelerated very efficiently, attaining an energy distribution of power-law shape with an index 1–2, depending on the acceleration mechanism. The transport coefficients in energy space are estimated from test-particle simulation data, and we show that the classical Fokker–Planckmore » (FP) equation fails to reproduce the simulation results when the transport coefficients are inserted into it and it is solved numerically. The cause for this failure is that the particles perform Levy flights in energy space, while the distributions of the energy increments exhibit power-law tails. We then use the fractional transport equation (FTE) derived by Isliker et al., whose parameters and the order of the fractional derivatives are inferred from the simulation data, and solving the FTE numerically, we show that the FTE successfully reproduces the kinetic energy distribution of the test particles. We discuss in detail the analysis of the simulation data and the criteria that allow one to judge the appropriateness of either an FTE or a classical FP equation as a transport model.« less

Calculations on Isotope Separation by Laser Induced Photodissociation of Polyatomic Molecules. Final Report

DOE R&D Accomplishments Database

Lamb, W. E. Jr.

1978-11-01

This report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. Newton`s equations of motion were integrated for the atoms of the SF{sub 6} molecule including the laser field interaction. The first year`s work has been largely dedicated to obtaining a suitable interatomic potential valid for arbitrary configurations of the seven particles. This potential gives the correct symmetry of the molecule, the equilibrium configuration, the frequencies of the six distinct normal modes of oscillation and the correct (or assumed) value of the total potential energy of the molecule. Other conditions can easily be imposed in order to obtain a more refined potential energy function, for example, by making allowance for anharmonicity data. A suitable expression was also obtained for the interaction energy between a laser field and the polyatomic molecule. The electromagnetic field is treated classically, and it would be easily possible to treat the cases of time dependent pulses, frequency modulation and noise.

Thermodynamics of an ideal generalized gas: I. Thermodynamic laws.

PubMed

Lavenda, B H

2005-11-01

The equations of state for an ideal relativistic, or generalized, gas, like an ideal quantum gas, are expressed in terms of power laws of the temperature. In contrast to an ideal classical gas, the internal energy is a function of volume at constant temperature, implying that the ideal generalized gas will show either attractive or repulsive interactions. This is a necessary condition in order that the third law be obeyed and for matter to have an electromagnetic origin. The transition from an ideal generalized to a classical gas occurs when the two independent solutions of the subsidiary equation to Lagrange's equation coalesce. The equation of state relating the pressure to the internal energy encompasses the full range of cosmological scenarios, from the radiation to the matter dominated universes and finally to the vacuum energy, enabling the coefficient of proportionality, analogous to the Grüeisen ratio, to be interpreted in terms of the degrees of freedom related to the temperature exponents of the internal energy and the absolute temperature expressed in terms of a power of the empirical temperature. The limit where these exponents merge is shown to be the ideal classical gas limit. A corollary to Carnot's theorem is proved, asserting that the ratio of the work done over a cycle to the heat absorbed to increase the temperature at constant volume is the same for all bodies at the same volume. As power means, the energy and entropy are incomparable, and a new adiabatic potential is introduced by showing that the volume raised to a characteristic exponent is also the integrating factor for the quantity of heat so that the second law can be based on the property that power means are monotonically increasing functions of their order. The vanishing of the chemical potential in extensive systems implies that energy cannot be transported without matter and is equivalent to the condition that Clapeyron's equation be satisfied.

Transition from metal-ligand bonding to halogen bonding involving a metal as halogen acceptor a study of Cu, Ag, Au, Pt, and Hg complexes

NASA Astrophysics Data System (ADS)

Oliveira, Vytor; Cremer, Dieter

2017-08-01

Utilizing all-electron Dirac-exact relativistic calculations with the Normalized Elimination of the Small Component (NESC) method and the local vibrational mode approach, the transition from metal-halide to metal halogen bonding is determined for Au-complexes interacting with halogen-donors. The local stretching force constants of the metal-halogen interactions reveal a smooth transition from weak non-covalent halogen bonding to non-classical 3-center-4-electron bonding and finally covalent metal-halide bonding. The strongest halogen bonds are found for dialkylaurates interacting with Cl2 or FCl. Differing trends in the intrinsic halogen-metal bond strength, the binding energy, and the electrostatic potential are explained.

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.

PubMed

Horn, Hans W; Swope, William C; Pitera, Jed W

2005-11-15

The liquid-vapor-phase equilibrium properties of the previously developed TIP4P-Ew water model have been studied using thermodynamic integration free-energy simulation techniques in the temperature range of 274-400 K. We stress that free-energy results from simulations need to be corrected in order to be compared to the experiment. This is due to the fact that the thermodynamic end states accessible through simulations correspond to fictitious substances (classical rigid liquids and classical rigid ideal gases) while experiments operate on real substances (liquids and real gases, with quantum effects). After applying analytical corrections the vapor pressure curve obtained from simulated free-energy changes is in excellent agreement with the experimental vapor pressure curve. The boiling point of TIP4P-Ew water under ambient pressure is found to be at 370.3+/-1.9 K, about 7 K higher than the boiling point of TIP4P water (363.7+/-5.1 K; from simulations that employ finite range treatment of electrostatic and Lennard-Jones interactions). This is in contrast to the approximately +15 K by which the temperature of the density maximum and the melting temperature of TIP4P-Ew are shifted relative to TIP4P, indicating that the temperature range over which the liquid phase of TIP4P-Ew is stable is narrower than that of TIP4P and resembles more that of real water. The quality of the vapor pressure results highlights the success of TIP4P-Ew in describing the energetic and entropic aspects of intermolecular interactions in liquid water.

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

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

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

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

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

DOE PAGES

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

2016-11-17

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

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

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

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

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

Quantum-mechanical transport equation for atomic systems.

NASA Technical Reports Server (NTRS)

Berman, P. R.

1972-01-01

A quantum-mechanical transport equation (QMTE) is derived which should be applicable to a wide range of problems involving the interaction of radiation with atoms or molecules which are also subject to collisions with perturber atoms. The equation follows the time evolution of the macroscopic atomic density matrix elements of atoms located at classical position R and moving with classical velocity v. It is quantum mechanical in the sense that all collision kernels or rates which appear have been obtained from a quantum-mechanical theory and, as such, properly take into account the energy-level variations and velocity changes of the active (emitting or absorbing) atom produced in collisions with perturber atoms. The present formulation is better suited to problems involving high-intensity external fields, such as those encountered in laser physics.

SIM(1)-VSR Maxwell-Chern-Simons electrodynamics

NASA Astrophysics Data System (ADS)

Bufalo, R.

2016-06-01

In this paper we propose a very special relativity (VSR)-inspired generalization of the Maxwell-Chern-Simons (MCS) electrodynamics. This proposal is based upon the construction of a proper study of the SIM (1)-VSR gauge-symmetry. It is shown that the VSR nonlocal effects present a significant and healthy departure from the usual MCS theory. The classical dynamics is analysed in full detail, by studying the solution for the electric field and static energy for this configuration. Afterwards, the interaction energy between opposite charges is derived and we show that the VSR effects play an important part in obtaining a (novel) finite expression for the static potential.

Optical Realization of Double-Continuum Fano Interference and Coherent Control in Plasmonic Metasurfaces

NASA Astrophysics Data System (ADS)

Arju, Nihal; Ma, Tzuhsuan; Khanikaev, Alexander; Purtseladze, David; Shvets, Gennady

2015-06-01

Classical realization of a ubiquitous quantum mechanical phenomenon of double-continuum Fano interference using metasurfaces is experimentally demonstrated by engineering the near-field interaction between two bright and one dark plasmonic modes. The competition between the bright modes, one of them effectively suppressing the Fano interference for the orthogonal light polarization, is discovered. Coherent control of optical energy concentration and light absorption by the ellipticity of the incident light is theoretically predicted.

Illustrated study of the semiholographic nonperturbative framework

NASA Astrophysics Data System (ADS)

Banerjee, Souvik; Gaddam, Nava; Mukhopadhyay, Ayan

2017-03-01

Semiholography has been proposed as an effective nonperturbative framework which can consistently combine perturbative and nonperturbative effects for theories like QCD. It is postulated that the strongly coupled nonperturbative sector has a holographic dual in the form of a classical gravity theory in the large N limit, and the perturbative fields determine the gravitational boundary conditions. In this work, we pursue a fundamental derivation of this framework particularly showing how perturbative physics by itself can determine the holographic dual of the infrared, and also the interactions between the perturbative and the holographic sectors. We firstly demonstrate that the interactions between the two sectors can be constrained through the existence of a conserved local energy-momentum tensor for the full system up to hard-soft coupling constants. As an illustration, we set up a biholographic toy theory where both the UV and IR sectors are strongly coupled and holographic with distinct classical gravity duals. In this construction, the requirement that an appropriate gluing can cure the singularities (geodetic incompleteness) of the respective geometries leads us to determine the parameters of the IR theory and the hard-soft couplings in terms of those of the UV theory. The high energy scale behavior of the hard-soft couplings is state-independent but their runnings turn out to be state-dependent. We discuss how our approach can be adapted to the construction of the semiholographic framework for QCD.

Electron capture and excitation processes in H+-H collisions in dense quantum plasmas

NASA Astrophysics Data System (ADS)

Jakimovski, D.; Markovska, N.; Janev, R. K.

2016-10-01

Electron capture and excitation processes in proton-hydrogen atom collisions taking place in dense quantum plasmas are studied by employing the two-centre atomic orbital close-coupling (TC-AOCC) method. The Debye-Hückel cosine (DHC) potential is used to describe the plasma screening effects on the Coulomb interaction between charged particles. The properties of a hydrogen atom with DHC potential are investigated as a function of the screening strength of the potential. It is found that the decrease in binding energy of nl levels with increasing screening strength is considerably faster than in the case of the Debye-Hückel (DH) screening potential, appropriate for description of charged particle interactions in weakly coupled classical plasmas. This results in a reduction in the number of bound states in the DHC potential with respect to that in the DH potential for the same plasma screening strength, and is reflected in the dynamics of excitation and electron capture processes for the two screened potentials. The TC-AOCC cross sections for total and state-selective electron capture and excitation cross sections with the DHC potential are calculated for a number of representative screening strengths in the 1-300 keV energy range and compared with those for the DH and pure Coulomb potential. The total capture cross sections for a selected number of screening strengths are compared with the available results from classical trajectory Monte Carlo calculations.

Comparison of Quantum and Classical Monte Carlo on a Simple Model Phase Transition

NASA Astrophysics Data System (ADS)

Cohen, D. E.; Cohen, R. E.

2005-12-01

Most simulations of phase transitions in minerals use classical molecular dynamics or classical Monte Carlo. However, it is known that in some cases, quantum effects are quite large, even for perovskite oxides [1]. We have studied the simplest model of a phase transition where this can be tested, that of interacting of double wells with an infinite- range interaction. The energy is E = ∑i (-A xi2 + B xi4 + ξ xi) . We used the same parameters used in a study of vibrational spectra and soft- mode behavior [4], A=0.01902, B=0.14294, ξ=0.025 in Hartree atomic units. This gives Tc of about 400 K. We varied the oscillator mass from 18 to 100. Classical Monte Carlo and path integral Monte Carlo (PIMC) were performed on this model. The maximum effect was for the lightest mass, in which PIMC gave a 75K lower Tc than the classical simulation. This is similar to the reduction in Tc observed in PIMC simulations for BaTiO3 at zero pressure [1]. We will explore the effects of varying the well depths. Shallower wells would show a greater quantum effect, as was seen in the high pressure BaTiO3 simulations, since pressure reduces the double well depths [5]. [1] Iniguez, J. & Vanderbilt, D. First-principles study of the temperature-pressure phase diagram of BaTiO3. Phys. Rev. Lett. 89, 115503 (2002). [2] Gillis, N. S. & Koehler, T. R. Phase transitions in a simple model ferroelectric-- -comparison of exact and variational treatments of a molecular-field Hamiltonian. Phys. Rev. B 9, 3806 (1974). [3] Koehler, T. R. & Gillis, N. S. Phase Transitions in a Model of Interacting Anharmonic Oscillators. Phys. Rev. B 7, 4980 (1973). [4] Flocken, J. W., Guenther, R. A., Hardy, J. R. & Boyer, L. L. Dielectric response spectrum of a damped one-dimensional double-well oscillator. Phys. Rev. B 40, 11496-11501 (1989). [5] Cohen, R. E. Origin of ferroelectricity in oxide ferroelectrics and the difference in ferroelectric behavior of BaTiO3 and PbTiO3. Nature 358, 136-138 (1992).

Early Time Dynamics of Gluon Fields in High Energy Nuclear Collisions

NASA Astrophysics Data System (ADS)

Kapusta, Joseph I.; Chen, Guangyao; Fries, Rainer J.; Li, Yang

2016-12-01

Nuclei colliding at very high energy create a strong, quasi-classical gluon field during the initial phase of their interaction. We present an analytic calculation of the initial space-time evolution of this field in the limit of very high energies using a formal recursive solution of the Yang-Mills equations. We provide analytic expressions for the initial chromo-electric and chromo-magnetic fields and for their energy-momentum tensor. In particular, we discuss event-averaged results for energy density and energy flow as well as for longitudinal and transverse pressure of this system. Our results are generally applicable if τ < 1 /Qs. The transverse energy flow of the gluon field exhibits hydrodynamic-like contributions that follow transverse gradients of the energy density. In addition, a rapidity-odd energy flow also emerges from the non-abelian analog of Gauss' Law and generates non-vanishing angular momentum of the field. We will discuss the space-time picture that emerges from our analysis and its implications for observables in heavy ion collisions.

In tight junctions, claudins regulate the interactions between occludin, tricellulin and marvelD3, which, inversely, modulate claudin oligomerization.

PubMed

Cording, Jimmi; Berg, Johanna; Käding, Nadja; Bellmann, Christian; Tscheik, Christian; Westphal, Julie K; Milatz, Susanne; Günzel, Dorothee; Wolburg, Hartwig; Piontek, Jörg; Huber, Otmar; Blasig, Ingolf Ernst

2013-01-15

Tight junctions seal the paracellular cleft of epithelia and endothelia, form vital barriers between tissue compartments and consist of tight-junction-associated marvel proteins (TAMPs) and claudins. The function of TAMPs and the interaction with claudins are not understood. We therefore investigated the binding between the TAMPs occludin, tricellulin, and marvelD3 and their interaction with claudins in living tight-junction-free human embryonic kidney-293 cells. In contrast to claudins and occludin, tricellulin and marvelD3 showed no enrichment at cell-cell contacts indicating lack of homophilic trans-interaction between two opposing cell membranes. However, occludin, marvelD3 and tricellulin exhibited homophilic cis-interactions, along one plasma membrane, as measured by fluorescence resonance energy transfer. MarvelD3 also cis-interacted with occludin and tricellulin heterophilically. Classic claudins, such as claudin-1 to -5 may show cis-oligomerization with TAMPs, whereas the non-classic claudin-11 did not. Claudin-1 and -5 improved enrichment of occludin and tricellulin at cell-cell contacts. The low mobile claudin-1 reduced the membrane mobility of the highly mobile occludin and tricellulin, as studied by fluorescence recovery after photobleaching. Co-transfection of claudin-1 with TAMPs led to changes of the tight junction strand network of this claudin to a more physiological morphology, depicted by freeze-fracture electron microscopy. The results demonstrate multilateral interactions between the tight junction proteins, in which claudins determine the function of TAMPs and vice versa, and provide deeper insights into the tight junction assembly.

Parametric excitation and squeezing in a many-body spinor condensate

PubMed Central

Hoang, T. M.; Anquez, M.; Robbins, B. A.; Yang, X. Y.; Land, B. J.; Hamley, C. D.; Chapman, M. S.

2016-01-01

Atomic spins are usually manipulated using radio frequency or microwave fields to excite Rabi oscillations between different spin states. These are single-particle quantum control techniques that perform ideally with individual particles or non-interacting ensembles. In many-body systems, inter-particle interactions are unavoidable; however, interactions can be used to realize new control schemes unique to interacting systems. Here we demonstrate a many-body control scheme to coherently excite and control the quantum spin states of an atomic Bose gas that realizes parametric excitation of many-body collective spin states by time varying the relative strength of the Zeeman and spin-dependent collisional interaction energies at multiples of the natural frequency of the system. Although parametric excitation of a classical system is ineffective from the ground state, we show that in our experiment, parametric excitation from the quantum ground state leads to the generation of quantum squeezed states. PMID:27044675

Parametric excitation and squeezing in a many-body spinor condensate

NASA Astrophysics Data System (ADS)

Hoang, T. M.; Anquez, M.; Robbins, B. A.; Yang, X. Y.; Land, B. J.; Hamley, C. D.; Chapman, M. S.

2016-04-01

Atomic spins are usually manipulated using radio frequency or microwave fields to excite Rabi oscillations between different spin states. These are single-particle quantum control techniques that perform ideally with individual particles or non-interacting ensembles. In many-body systems, inter-particle interactions are unavoidable; however, interactions can be used to realize new control schemes unique to interacting systems. Here we demonstrate a many-body control scheme to coherently excite and control the quantum spin states of an atomic Bose gas that realizes parametric excitation of many-body collective spin states by time varying the relative strength of the Zeeman and spin-dependent collisional interaction energies at multiples of the natural frequency of the system. Although parametric excitation of a classical system is ineffective from the ground state, we show that in our experiment, parametric excitation from the quantum ground state leads to the generation of quantum squeezed states.

Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach.

PubMed

Rubinstein, Alexander; Sherman, Simon

The dielectric properties of the polar solvent on the protein-solvent interface at small intercharge distances are still poorly explored. To deconvolute this problem and to evaluate the pair-wise electrostatic interaction (PEI) energies of the point charges located at the protein-solvent interface we used a nonlocal (NL) electrostatic approach along with a static NL dielectric response function of water. The influence of the aqueous solvent microstructure (determined by a strong nonelectrostatic correlation effect between water dipoles within the orientational Debye polarization mode) on electrostatic interactions at the interface was studied in our work. It was shown that the PEI energies can be significantly higher than the energies evaluated by the classical (local) consideration, treating water molecules as belonging to the bulk solvent with a high dielectric constant. Our analysis points to the existence of a rather extended, effective low-dielectric interfacial water shell on the protein surface. The main dielectric properties of this shell (effective thickness together with distance- and orientation-dependent dielectric permittivity function) were evaluated. The dramatic role of this shell was demonstrated when estimating the protein association rate constants.

Search for Astrophysical Sources of Neutrinos Using Cascade Events in IceCube

NASA Astrophysics Data System (ADS)

Aartsen, M. G.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Ahrens, M.; Samarai, I. Al; Altmann, D.; Andeen, K.; Anderson, T.; Ansseau, I.; Anton, G.; Argüelles, C.; Auffenberg, J.; Axani, S.; Bagherpour, H.; Bai, X.; Barwick, S. W.; Baum, V.; Bay, R.; Beatty, J. J.; Becker Tjus, J.; Becker, K.-H.; BenZvi, S.; Berley, D.; Bernardini, E.; Besson, D. Z.; Binder, G.; Bindig, D.; Blaufuss, E.; Blot, S.; Bohm, C.; Börner, M.; Bos, F.; Bose, D.; Böser, S.; Botner, O.; Bourbeau, J.; Bradascio, F.; Braun, J.; Brayeur, L.; Brenzke, M.; Bretz, H.-P.; Bron, S.; Burgman, A.; Carver, T.; Casey, J.; Casier, M.; Cheung, E.; Chirkin, D.; Christov, A.; Clark, K.; Classen, L.; Coenders, S.; Collin, G. H.; Conrad, J. M.; Cowen, D. F.; Cross, R.; Day, M.; de André, J. P. A. M.; De Clercq, C.; DeLaunay, J. J.; Dembinski, H.; De Ridder, S.; Desiati, P.; de Vries, K. D.; de Wasseige, G.; de With, M.; DeYoung, T.; Díaz-Vélez, J. C.; di Lorenzo, V.; Dujmovic, H.; Dumm, J. P.; Dunkman, M.; Eberhardt, B.; Ehrhardt, T.; Eichmann, B.; Eller, P.; Evenson, P. A.; Fahey, S.; Fazely, A. R.; Felde, J.; Filimonov, K.; Finley, C.; Flis, S.; Franckowiak, A.; Friedman, E.; Fuchs, T.; Gaisser, T. K.; Gallagher, J.; Gerhardt, L.; Ghorbani, K.; Giang, W.; Glauch, T.; Glüsenkamp, T.; Goldschmidt, A.; Gonzalez, J. G.; Grant, D.; Griffith, Z.; Haack, C.; Hallgren, A.; Halzen, F.; Hanson, K.; Hebecker, D.; Heereman, D.; Helbing, K.; Hellauer, R.; Hickford, S.; Hignight, J.; Hill, G. C.; Hoffman, K. D.; Hoffmann, R.; Hokanson-Fasig, B.; Hoshina, K.; Huang, F.; Huber, M.; Hultqvist, K.; In, S.; Ishihara, A.; Jacobi, E.; Japaridze, G. S.; Jeong, M.; Jero, K.; Jones, B. J. P.; Kalacynski, P.; Kang, W.; Kappes, A.; Karg, T.; Karle, A.; Katz, U.; Kauer, M.; Keivani, A.; Kelley, J. L.; Kheirandish, A.; Kim, J.; Kim, M.; Kintscher, T.; Kiryluk, J.; Kittler, T.; Klein, S. R.; Kohnen, G.; Koirala, R.; Kolanoski, H.; Köpke, L.; Kopper, C.; Kopper, S.; Koschinsky, J. P.; Koskinen, D. J.; Kowalski, M.; Krings, K.; Kroll, M.; Krückl, G.; Kunnen, J.; Kunwar, S.; Kurahashi, N.; Kuwabara, T.; Kyriacou, A.; Labare, M.; Lanfranchi, J. L.; Larson, M. J.; Lauber, F.; Lennarz, D.; Lesiak-Bzdak, M.; Leuermann, M.; Liu, Q. R.; Lu, L.; Lünemann, J.; Luszczak, W.; Madsen, J.; Maggi, G.; Mahn, K. B. M.; Mancina, S.; Maruyama, R.; Mase, K.; Maunu, R.; McNally, F.; Meagher, K.; Medici, M.; Meier, M.; Menne, T.; Merino, G.; Meures, T.; Miarecki, S.; Micallef, J.; Momenté, G.; Montaruli, T.; Moulai, M.; Nahnhauer, R.; Nakarmi, P.; Naumann, U.; Neer, G.; Niederhausen, H.; Nowicki, S. C.; Nygren, D. R.; Obertacke Pollmann, A.; Olivas, A.; O'Murchadha, A.; Palczewski, T.; Pandya, H.; Pankova, D. V.; Peiffer, P.; Pepper, J. A.; Pérez de los Heros, C.; Pieloth, D.; Pinat, E.; Plum, M.; Price, P. B.; Przybylski, G. T.; Raab, C.; Rädel, L.; Rameez, M.; Rawlins, K.; Reimann, R.; Relethford, B.; Relich, M.; Resconi, E.; Rhode, W.; Richman, M.; Riedel, B.; Robertson, S.; Rongen, M.; Rott, C.; Ruhe, T.; Ryckbosch, D.; Rysewyk, D.; Sälzer, T.; Sanchez Herrera, S. E.; Sandrock, A.; Sandroos, J.; Sarkar, S.; Sarkar, S.; Satalecka, K.; Schlunder, P.; Schmidt, T.; Schneider, A.; Schoenen, S.; Schöneberg, S.; Schumacher, L.; Seckel, D.; Seunarine, S.; Soldin, D.; Song, M.; Spiczak, G. M.; Spiering, C.; Stachurska, J.; Stanev, T.; Stasik, A.; Stettner, J.; Steuer, A.; Stezelberger, T.; Stokstad, R. G.; Stößl, A.; Strotjohann, N. L.; Sullivan, G. W.; Sutherland, M.; Taboada, I.; Tatar, J.; Tenholt, F.; Ter-Antonyan, S.; Terliuk, A.; Tešić, G.; Tilav, S.; Toale, P. A.; Tobin, M. N.; Toscano, S.; Tosi, D.; Tselengidou, M.; Tung, C. F.; Turcati, A.; Turley, C. F.; Ty, B.; Unger, E.; Usner, M.; Vandenbroucke, J.; Van Driessche, W.; van Eijndhoven, N.; Vanheule, S.; van Santen, J.; Vehring, M.; Vogel, E.; Vraeghe, M.; Walck, C.; Wallace, A.; Wallraff, M.; Wandkowsky, N.; Waza, A.; Weaver, C.; Weiss, M. J.; Wendt, C.; Westerhoff, S.; Whelan, B. J.; Wickmann, S.; Wiebe, K.; Wiebusch, C. H.; Wille, L.; Williams, D. R.; Wills, L.; Wolf, M.; Wood, J.; Wood, T. R.; Woolsey, E.; Woschnagg, K.; Xu, D. L.; Xu, X. W.; Xu, Y.; Yanez, J. P.; Yodh, G.; Yoshida, S.; Yuan, T.; Zoll, M.; IceCube Collaboration

2017-09-01

The IceCube neutrino observatory has established the existence of a flux of high-energy astrophysical neutrinos, which is inconsistent with the expectation from atmospheric backgrounds at a significance greater than 5σ. This flux has been observed in analyses of both track events from muon neutrino interactions and cascade events from interactions of all neutrino flavors. Searches for astrophysical neutrino sources have focused on track events due to the significantly better angular resolution of track reconstructions. To date, no such sources have been confirmed. Here we present the first search for astrophysical neutrino sources using cascades interacting in IceCube with deposited energies as small as 1 TeV. No significant clustering was observed in a selection of 263 cascades collected from 2010 May to 2012 May. We show that compared to the classic approach using tracks, this statistically independent search offers improved sensitivity to sources in the southern sky, especially if the emission is spatially extended or follows a soft energy spectrum. This enhancement is due to the low background from atmospheric neutrinos forming cascade events and the additional veto of atmospheric neutrinos at declinations ≲-30°.

Search for Astrophysical Sources of Neutrinos Using Cascade Events in IceCube

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

Aartsen, M. G.; Ackermann, M.; Adams, J.

The IceCube neutrino observatory has established the existence of a flux of high-energy astrophysical neutrinos, which is inconsistent with the expectation from atmospheric backgrounds at a significance greater than 5 σ . This flux has been observed in analyses of both track events from muon neutrino interactions and cascade events from interactions of all neutrino flavors. Searches for astrophysical neutrino sources have focused on track events due to the significantly better angular resolution of track reconstructions. To date, no such sources have been confirmed. Here we present the first search for astrophysical neutrino sources using cascades interacting in IceCube withmore » deposited energies as small as 1 TeV. No significant clustering was observed in a selection of 263 cascades collected from 2010 May to 2012 May. We show that compared to the classic approach using tracks, this statistically independent search offers improved sensitivity to sources in the southern sky, especially if the emission is spatially extended or follows a soft energy spectrum. This enhancement is due to the low background from atmospheric neutrinos forming cascade events and the additional veto of atmospheric neutrinos at declinations ≲−30°.« less

Tunable heat conduction through coupled Fermi-Pasta-Ulam chains

NASA Astrophysics Data System (ADS)

Su, Ruixia; Yuan, Zongqiang; Wang, Jun; Zheng, Zhigang

2015-01-01

We conduct a study on heat conduction through coupled Fermi-Pasta-Ulam (FPU) chains by using classical molecular dynamics simulations. Our attention is dedicated to showing how the phonon transport is affected by the interchain coupling. It has been well accepted that the heat conduction could be impeded by the interchain interaction due to the interface phonon scattering. However, recent theoretical and experimental studies suggest that the thermal conductivity of nanoscale materials can be counterintuitively enhanced by the interaction with the substrate. In the present paper, by consecutively varying the interchain coupling intensity, we observed both enhancement and suppression of thermal transport through the coupled FPU chains. For weak interchain couplings, it is found that the heat flux increases with the coupling intensity, whereas in the case of strong interchain couplings, the energy transport is found to be suppressed by the interchain interaction. Based on the phonon spectral energy density method, we attribute the enhancement of the energy transport to the excited phonon modes (in addition to the intrinsic phonon modes), while the upward shift of the high-frequency phonon branch and the interface phonon-phonon scattering account for the suppressed heat conduction.

A comparative study based on docking and molecular dynamics simulations over HDAC-tubulin dual inhibitors.

PubMed

Hassanzadeh, Malihe; Bagherzadeh, Kowsar; Amanlou, Massoud

2016-11-01

Nowadays the ability to prediction of complex behavior rationally based on the computational approaches has been a successful technique in drug discovery. In the present study interactions of a new series of hybrids, which were made by linking colchicine as a tubulin inhibitor and suberoylanilide hydroxamic acid (SAHA) as a HDAC inhibitor, with HDAC8 and HDAC1 were investigated and compared. This research has been facilitated by the availability of experimental information besides employing docking methodology as well as classical molecular dynamics simulations and binding free energy calculation were performed. The obtained findings indicate different modes of interactions and inhibition strengths of the studied inhibitors for HDAC8 and HDAC1. HDAC8 binding free energies (-34.35 to -26.27kcal/mol) revealed higher binding affinity to HDAC8 compared to HDAC1 (-33.17 to -7.99kcal/mol). The binding energy contribution of each residue with the hybrid compounds 4a-4e within the active site of HDAC1 and HDAC8 was analyzed and the results confirmed the rule of key amino acids in interaction with the hybrid compounds. Copyright © 2016 Elsevier Inc. All rights reserved.

Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

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

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2014-01-14

The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei (CCN), and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems.more » The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics (PIMD) method at the density functional theory (DFT) level of theory. We observe a small zero-point effect on the the equilibrium structures of certain clusters. One configuration is found to display a bimodal behaviour at 300 K in contrast to the stable ionised state suggested from a zero temperature classical geometry optimisation. The general effect of zero-point motion is to promote the extent of proton transfer with respect to classical behaviour. We thank Prof. Angelos Michaelides and his group in University College London (UCL) for practical advice and helpful discussions. This work benefited from interactions with the Thomas Young Centre through seminar and discussions involving the PIMD method. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. JLS and IJF were supported by the IMPACT scheme at UCL and by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. We are grateful for use of the UCL Legion High Performance Computing Facility and the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy, Office of Science of the under Contract No. DE-AC02-05CH11231.« less

Four Weeks of Classical Altitude Training Increases Resting Metabolic Rate in Highly Trained Middle-Distance Runners.

PubMed

Woods, Amy L; Sharma, Avish P; Garvican-Lewis, Laura A; Saunders, Philo U; Rice, Anthony J; Thompson, Kevin G

2017-02-01

High altitude exposure can increase resting metabolic rate (RMR) and induce weight loss in obese populations, but there is a lack of research regarding RMR in athletes at moderate elevations common to endurance training camps. The present study aimed to determine whether 4 weeks of classical altitude training affects RMR in middle-distance runners. Ten highly trained athletes were recruited for 4 weeks of endurance training undertaking identical programs at either 2200m in Flagstaff, Arizona (ALT, n = 5) or 600m in Canberra, Australia (CON, n = 5). RMR, anthropometry, energy intake, and hemoglobin mass (Hb mass ) were assessed pre- and posttraining. Weekly run distance during the training block was: ALT 96.8 ± 18.3km; CON 103.1 ± 5.6km. A significant interaction for Time*Group was observed for absolute (kJ.day -1 ) (F-statistic, p-value: F (1,8) =13.890, p = .01) and relative RMR (F (1,8) =653.453, p = .003) POST-training. No significant changes in anthropometry were observed in either group. Energy intake was unchanged (mean ± SD of difference, ALT: 195 ± 3921kJ, p = .25; CON: 836 ± 7535kJ, p = .75). A significant main effect for time was demonstrated for total Hb mass (g) (F (1,8) =13.380, p = .01), but no significant interactions were observed for either variable [Total Hb mass (g): F (1,8) =1.706, p = .23; Relative Hb mass (g.kg -1 ): F (1,8) =0.609, p = .46]. These novel findings have important practical application to endurance athletes routinely training at moderate altitude, and those seeking to optimize energy management without compromising training adaptation. Altitude exposure may increase RMR and enhance training adaptation,. During training camps at moderate altitude, an increased energy intake is likely required to support an increased RMR and provide sufficient energy for training and performance.

Vacuum polarization and Hawking radiation

NASA Astrophysics Data System (ADS)

Rahmati, Shohreh

Quantum gravity is one of the interesting fields in contemporary physics which is still in progress. The purpose of quantum gravity is to present a quantum description for spacetime at 10-33cm or find the 'quanta' of gravitational interaction.. At present, the most viable theory to describe gravitational interaction is general relativity which is a classical theory. Semi-classical quantum gravity or quantum field theory in curved spacetime is an approximation to a full quantum theory of gravity. This approximation considers gravity as a classical field and matter fields are quantized. One interesting phenomena in semi-classical quantum gravity is Hawking radiation. Hawking radiation was derived by Stephen Hawking as a thermal emission of particles from the black hole horizon. In this thesis we obtain the spectrum of Hawking radiation using a new method. Vacuum is defined as the possible lowest energy state which is filled with pairs of virtual particle-antiparticle. Vacuum polarization is a consequence of pair creation in the presence of an external field such as an electromagnetic or gravitational field. Vacuum polarization in the vicinity of a black hole horizon can be interpreted as the cause of the emission from black holes known as Hawking radiation. In this thesis we try to obtain the Hawking spectrum using this approach. We re-examine vacuum polarization of a scalar field in a quasi-local volume that includes the horizon. We study the interaction of a scalar field with the background gravitational field of the black hole in the desired quasi-local region. The quasi-local volume is a hollow cylinder enclosed by two membranes, one inside the horizon and one outside the horizon. The net rate of particle emission can be obtained as the difference of the vacuum polarization from the outer boundary and inner boundary of the cylinder. Thus we found a new method to derive Hawking emission which is unitary and well defined in quantum field theory.

Experimental Evidence of Radiation Reaction in the Collision of a High-Intensity Laser Pulse with a Laser-Wakefield Accelerated Electron Beam

NASA Astrophysics Data System (ADS)

Cole, J. M.; Behm, K. T.; Gerstmayr, E.; Blackburn, T. G.; Wood, J. C.; Baird, C. D.; Duff, M. J.; Harvey, C.; Ilderton, A.; Joglekar, A. S.; Krushelnick, K.; Kuschel, S.; Marklund, M.; McKenna, P.; Murphy, C. D.; Poder, K.; Ridgers, C. P.; Samarin, G. M.; Sarri, G.; Symes, D. R.; Thomas, A. G. R.; Warwick, J.; Zepf, M.; Najmudin, Z.; Mangles, S. P. D.

2018-02-01

The dynamics of energetic particles in strong electromagnetic fields can be heavily influenced by the energy loss arising from the emission of radiation during acceleration, known as radiation reaction. When interacting with a high-energy electron beam, today's lasers are sufficiently intense to explore the transition between the classical and quantum radiation reaction regimes. We present evidence of radiation reaction in the collision of an ultrarelativistic electron beam generated by laser-wakefield acceleration (ɛ >500 MeV ) with an intense laser pulse (a0>10 ). We measure an energy loss in the postcollision electron spectrum that is correlated with the detected signal of hard photons (γ rays), consistent with a quantum description of radiation reaction. The generated γ rays have the highest energies yet reported from an all-optical inverse Compton scattering scheme, with critical energy ɛcrit>30 MeV .

Impact of charge carrier injection on single-chain photophysics of conjugated polymers

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

Hofmann, Felix J.; Vogelsang, Jan, E-mail: jan.vogelsang@physik.uni-regensburg.de; Lupton, John M.

Charges in conjugated polymer materials have a strong impact on the photophysics and their interaction with the primary excited state species has to be taken into account in understanding device properties. Here, we employ single-molecule spectroscopy to unravel the influence of charges on several photoluminescence (PL) observables. The charges are injected either stochastically by a photochemical process or deterministically in a hole-injection sandwich device configuration. We find that upon charge injection, besides a blue-shift of the PL emission and a shortening of the PL lifetime due to quenching and blocking of the lowest-energy chromophores, the non-classical photon arrival time distributionmore » of the multichromophoric chain is modified towards a more classical distribution. Surprisingly, the fidelity of photon antibunching deteriorates upon charging, whereas one would actually expect the opposite: the number of chromophores to be reduced. A qualitative model is presented to explain the observed PL changes. The results are of interest to developing a microscopic understanding of the intrinsic charge-exciton quenching interaction in devices.« less

The physics of quantum materials

NASA Astrophysics Data System (ADS)

Keimer, B.; Moore, J. E.

2017-11-01

The physical description of all materials is rooted in quantum mechanics, which describes how atoms bond and electrons interact at a fundamental level. Although these quantum effects can in many cases be approximated by a classical description at the macroscopic level, in recent years there has been growing interest in material systems where quantum effects remain manifest over a wider range of energy and length scales. Such quantum materials include superconductors, graphene, topological insulators, Weyl semimetals, quantum spin liquids, and spin ices. Many of them derive their properties from reduced dimensionality, in particular from confinement of electrons to two-dimensional sheets. Moreover, they tend to be materials in which electrons cannot be considered as independent particles but interact strongly and give rise to collective excitations known as quasiparticles. In all cases, however, quantum-mechanical effects fundamentally alter properties of the material. This Review surveys the electronic properties of quantum materials through the prism of the electron wavefunction, and examines how its entanglement and topology give rise to a rich variety of quantum states and phases; these are less classically describable than conventional ordered states also driven by quantum mechanics, such as ferromagnetism.

Evaluation of the mathematical and economic basis for conversion processes in the LEAP energy-economy model

NASA Astrophysics Data System (ADS)

Oblow, E. M.

1982-10-01

An evaluation was made of the mathematical and economic basis for conversion processes in the Long-term Energy Analysis Program (LEAP) energy economy model. Conversion processes are the main modeling subunit in LEAP used to represent energy conversion industries and are supposedly based on the classical economic theory of the firm. Questions about uniqueness and existence of LEAP solutions and their relation to classical equilibrium economic theory prompted the study. An analysis of classical theory and LEAP model equations was made to determine their exact relationship. The conclusions drawn from this analysis were that LEAP theory is not consistent with the classical theory of the firm. Specifically, the capacity factor formalism used by LEAP does not support a classical interpretation in terms of a technological production function for energy conversion processes. The economic implications of this inconsistency are suboptimal process operation and short term negative profits in years where plant operation should be terminated. A new capacity factor formalism, which retains the behavioral features of the original model, is proposed to resolve these discrepancies.

Using qubits to reveal quantum signatures of an oscillator

NASA Astrophysics Data System (ADS)

Agarwal, Shantanu

In this thesis, we seek to study the qubit-oscillator system with the aim to identify and quantify inherent quantum features of the oscillator. We show that the quantum signatures of the oscillator get imprinted on the dynamics of the joint system. The two key features which we explore are the quantized energy spectrum of the oscillator and the non-classicality of the oscillator's wave function. To investigate the consequences of the oscillator's discrete energy spectrum, we consider the qubit to be coupled to the oscillator through the Rabi Hamiltonian. Recent developments in fabrication technology have opened up the possibility to explore parameter regimes which were conventionally inaccessible. Motivated by these advancements, we investigate in this thesis a parameter space where the qubit frequency is much smaller than the oscillator frequency and the Rabi frequency is allowed to be an appreciable fraction of the bare frequency of the oscillator. We use the adiabatic approximation to understand the dynamics in this quasi-degenerate qubit regime. By deriving a dressed master equation, we systematically investigate the effects of the environment on the system dynamics. We develop a spectroscopic technique, using which one can probe the steady state response of the driven and damped system. The spectroscopic signal clearly reveals the quantized nature of the oscillator's energy spectrum. We extend the adiabatic approximation, earlier developed only for the single qubit case, to a scenario where multiple qubits interact with the oscillator. Using the extended adiabatic approximation, we study the collapse and revival of multi-qubit observables. We develop analytic expressions for the revival signals which are in good agreement with the numerically evaluated results. Within the quantum restriction imposed by Heisenberg's uncertainty principle, the uncertainty in the position and momentum of an oscillator is minimum and shared equally when the oscillator is prepared in a coherent state. For this reason, coherent states and states which can be thought of as a statistical mixture of coherent states are categorized as classical; whereas states which are not valid coherent state mixtures are classified as non-classical. In this thesis, we propose a new non-classicality witness operation which does not require a tomography of the oscillator's state. We show that by coupling a qubit longitudinally to the oscillator, one can infer about the non-classical nature of the initial state of the oscillator. Using a qubit observable, we derive a non-classicality witness inequality, a violation of which definitively indicates the non-classical nature of an oscillator's state.

Matter, energy, and heat transfer in a classical ballistic atom pump.

PubMed

Byrd, Tommy A; Das, Kunal K; Mitchell, Kevin A; Aubin, Seth; Delos, John B

2014-11-01

A ballistic atom pump is a system containing two reservoirs of neutral atoms or molecules and a junction connecting them containing a localized time-varying potential. Atoms move through the pump as independent particles. Under certain conditions, these pumps can create net transport of atoms from one reservoir to the other. While such systems are sometimes called "quantum pumps," they are also models of classical chaotic transport, and their quantum behavior cannot be understood without study of the corresponding classical behavior. Here we examine classically such a pump's effect on energy and temperature in the reservoirs, in addition to net particle transport. We show that the changes in particle number, of energy in each reservoir, and of temperature in each reservoir vary in unexpected ways as the incident particle energy is varied.

Resource Letter NSM-1: New insights into the nuclear shell model

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

Dean, David Jarvis; Hamilton, J. H.

2011-01-01

This Resource Letter provides a guide to the literature on the spherical shell model as applied to nuclei. The nuclear shell model describes the structure of nuclei starting with a nuclear core developed by the classical neutron and proton magic numbers N,Z=2,8,20,28,50,82, 126, where gaps occur in the single-particle energies as a shell is filled, and the interactions of valence nucleons that reside beyond that core. Various modern extensions of this model for spherical nuclei are likewise described. Significant extensions of the nuclear shell model include new magic numbers for spherical nuclei and now for deformed nuclei as well. Whenmore » both protons and neutrons have shell gaps at the same spherical or deformed shapes, they can reinforce each other to give added stability to that shape and lead to new magic numbers. The vanishings of the classical spherical shell model energy gaps and magic numbers in new neutron-rich nuclei are described. Spherical and deformed shell gaps are seen to be critical for the existence of elements with Z > 100.« less

Topological magnons in a kagome-lattice spin system with X X Z and Dzyaloshinskii-Moriya interactions

NASA Astrophysics Data System (ADS)

Seshadri, Ranjani; Sen, Diptiman

2018-04-01

We study the phases of a spin system on the kagome lattice with nearest-neighbor X X Z interactions with anisotropy ratio Δ and Dzyaloshinskii-Moriya interactions with strength D . In the classical limit where the spin S at each site is very large, we find a rich phase diagram of the ground state as a function of Δ and D . There are five distinct phases which correspond to different ground-state spin configurations in the classical limit. We use spin-wave theory to find the bulk energy bands of the magnons in some of these phases. We also study a strip of the system which has infinite length and finite width; we find states which are localized near one of the edges of the strip with energies which lie in the gaps of the bulk states. In the ferromagnetic phase in which all the spins point along the +z ̂ or -z ̂ direction, the bulk bands are separated from each other by finite energy gaps. This makes it possible to calculate the Berry curvature at all momenta, and hence the Chern numbers for every band; the number of edge states is related to the Chern numbers. Interestingly, we find that there are four different regions in this phase where the Chern numbers are different. Hence there are four distinct topological phases even though the ground-state spin configuration is identical in all these phases. We calculate the thermal Hall conductivity of the magnons as a function of the temperature in the above ferromagnetic phase; we find that this can distinguish between the various topological phases. These results are valid for all values of S . In the other phases, there are no gaps between the different bands; hence the edge states are not topologically protected.

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

NASA Astrophysics Data System (ADS)

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-01

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

Amino acid analogues bind to carbon nanotube via π-π interactions: comparison of molecular mechanical and quantum mechanical calculations.

PubMed

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-14

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

The Multiphoton Interaction of Lambda Model Atom and Two-Mode Fields

NASA Technical Reports Server (NTRS)

Liu, Tang-Kun

1996-01-01

The system of two-mode fields interacting with atom by means of multiphotons is addressed, and the non-classical statistic quality of two-mode fields with interaction is discussed. Through mathematical calculation, some new rules of non-classical effects of two-mode fields which evolue with time, are established.

How classical gluon fields generate odd azimuthal harmonics for the two-gluon correlation function in high-energy collisions

NASA Astrophysics Data System (ADS)

Kovchegov, Yuri V.; Skokov, Vladimir V.

2018-05-01

We show that, in the saturation/color glass condensate framework, odd azimuthal harmonics of the two-gluon correlation function with a long-range separation in rapidity are generated by the higher-order saturation corrections in the interactions with the projectile and the target. At the very least, the odd harmonics require three scatterings in the projectile and three scatterings in the target. We derive the leading-order expression for the two-gluon production cross section which generates odd harmonics: the expression includes all-order interactions with the target and three interactions with the projectile. We evaluate the obtained expression both analytically and numerically, confirming that the odd-harmonics contribution to the two-gluon production in the saturation framework is nonzero.

Higher-order electric multipole contributions to retarded non-additive three-body dispersion interaction energies between atoms: Equilateral triangle and collinear configurations

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

Salam, A., E-mail: salama@wfu.edu

2013-12-28

The theory of molecular quantum electrodynamics (QED) is used to calculate higher electric multipole contributions to the dispersion energy shift between three atoms or molecules arranged in a straight line or in an equilateral triangle configuration. As in two-body potentials, three-body dispersion interactions are viewed in the QED formalism to arise from exchange of virtual photons between coupled pairs of particles. By employing an interaction Hamiltonian that is quadratic in the electric displacement field means that third-order perturbation theory can be used to yield the energy shift for a particular combination of electric multipole polarizable species, with only six time-orderedmore » diagrams needing to be summed over. Specific potentials evaluated include dipole-dipole-quadrupole (DDQ), dipole-quadrupole-quadrupole (DQQ), and dipole-dipole-octupole (DDO) terms. For the geometries of interest, near-zone limiting forms are found to exhibit an R{sup −11} dependence on separation distance for the DDQ interaction, and an R{sup −13} behaviour for DQQ and DDO shifts, agreeing with an earlier semi-classical computation. Retardation weakens the potential in each case by R{sup −1} in the far-zone. It is found that by decomposing the octupole moment into its irreducible components of weights-1 and -3 that the former contribution to the DDO potential may be taken to be a higher-order correction to the leading triple dipole energy shift.« less

Gravitational-Wave Astronomy

NASA Technical Reports Server (NTRS)

Kelly, Bernard J.

2010-01-01

Einstein's General Theory of Relativity is our best classical description of gravity, and informs modern astronomy and astrophysics at all scales: stellar, galactic, and cosmological. Among its surprising predictions is the existence of gravitational waves -- ripples in space-time that carry energy and momentum away from strongly interacting gravitating sources. In my talk, I will give an overview of the properties of this radiation, recent breakthroughs in computational physics allowing us to calculate the waveforms from galactic mergers, and the prospect of direct observation with interferometric detectors such as LIGO and LISA.

The water dimer II: Theoretical investigations

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-05-01

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interactions in clusters and the condensed phases of water.

The Water Dimer II: Theoretical Investigations

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

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. Here in this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and the condensed phases of water.

The Water Dimer II: Theoretical Investigations

DOE PAGES

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-03-29

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. Here in this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and the condensed phases of water.

Ionic liquids-mediated interactions between nanorods

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

Yu, Zhou; Zhang, Fei; Huang, Jingsong

Surface forces mediated by room-temperature ionic liquids (RTILs) play an essential role in diverse applications including self-assembly, lubrication, and electrochemical energy storage. In this work, using molecular simulations we study the interactions between two nanorods immersed in model RTILs at rod-rod separations where both structural and double layer forces are important. The interaction force between neutral rods oscillates as the two rods approach each other, similar to the classical structural forces. Such oscillatory force originates from the density oscillation of RTILs near each rod and is affected by the packing constraints imposed by the neighboring rods. The oscillation period andmore » decay length of the oscillatory force are mainly dictated by the ion density distribution near isolated nanorods. When charges are introduced on the rods, the interaction force remains short-range and oscillatory, similar to the interactions between planar walls mediated by some protic RTILs reported earlier. Nevertheless, introducing net charges to the rods greatly changes the rod-rod interactions, e.g., by delaying the appearance of the first force trough and increasing the oscillation period and decay length of the interaction force. The oscillation period and decay length of the oscillatory force and free energy are commensurate with those of the space charge density near an isolated, charged rod. The free energy of rod-rod interactions reaches local minima (maxima) at rod-rod separations when the space charges near the two rods interfere constructively (destructively). Here, the insight on the short-range interactions between nanorods in RTILs helps guide the design of novel materials, e.g., crystalline ion gels based on rigid-rod polyanions and RTILs.« less

Ionic liquids-mediated interactions between nanorods

DOE PAGES

Yu, Zhou; Zhang, Fei; Huang, Jingsong; ...

2017-10-06

Surface forces mediated by room-temperature ionic liquids (RTILs) play an essential role in diverse applications including self-assembly, lubrication, and electrochemical energy storage. In this work, using molecular simulations we study the interactions between two nanorods immersed in model RTILs at rod-rod separations where both structural and double layer forces are important. The interaction force between neutral rods oscillates as the two rods approach each other, similar to the classical structural forces. Such oscillatory force originates from the density oscillation of RTILs near each rod and is affected by the packing constraints imposed by the neighboring rods. The oscillation period andmore » decay length of the oscillatory force are mainly dictated by the ion density distribution near isolated nanorods. When charges are introduced on the rods, the interaction force remains short-range and oscillatory, similar to the interactions between planar walls mediated by some protic RTILs reported earlier. Nevertheless, introducing net charges to the rods greatly changes the rod-rod interactions, e.g., by delaying the appearance of the first force trough and increasing the oscillation period and decay length of the interaction force. The oscillation period and decay length of the oscillatory force and free energy are commensurate with those of the space charge density near an isolated, charged rod. The free energy of rod-rod interactions reaches local minima (maxima) at rod-rod separations when the space charges near the two rods interfere constructively (destructively). Here, the insight on the short-range interactions between nanorods in RTILs helps guide the design of novel materials, e.g., crystalline ion gels based on rigid-rod polyanions and RTILs.« less

Picking a Fight with Water, and Water Lost ... an Electron

NASA Astrophysics Data System (ADS)

Herr, Jonathan D.

The global need for energy is increasing, as is the importance of producing energy by green and renewable methodologies. This document outlines a research program dedicated to investigating a possible source for this form of energy generation and storage: solar fuels. The photon-induced splitting of water into molecular hydrogen and oxygen is currently hindered by large overpotentials from the oxidation half-reaction of water-splitting. This study concentrated on fundamental models of water-spitting chemistry, using a physical and computational chemistry analysis. The oxidation was first explored via ab initio electronic structure calculations of bare cationic water clusters, comprised of 2 to 21 molecules, in order to determine key electronic interactions that facilitate oxidation. Deeper understanding of these interactions could serve as guides for the development of viable water oxidation catalysts (WOC) designed to reduce overpotentials. The cationic water cluster study was followed by an investigation into hydrated copper (I) clusters, which acted as precursor models for real WOCs. Analyzing how the copper ion perturbed the properties of water clusters led to important electronic considerations for the development of WOCs, such as copper-water interactions that go beyond simple electrostatics. The importance of diagnostic thermodynamic properties, as well as anharmonic characteristics being persistent throughout oxidized water clusters, necessitated the use of quantum and classical molecular dynamics (MD) routines. Therefore, two new methods for accelerating computationally demanding classical and quantum MD methods were developed to increase their accessibility. The first method utilized a new form of electronic extrapolation - a linear prediction routine incorporating a Burg minimization - to decrease the iterations required for solving the electronic equations throughout the dynamics. The second method utilized a multiple-timestepping description of the potential energy term in the path integral molecular dynamics (PIMD) formalism. This method led to reductions of computational time by allowing the use of less computationally laborious methods for portions of the simulation and resulted in negligible increase of error. The determination of the fundamental driving forces within water oxidation and the development of acceleration techniques for important electronic structure methods will help drive progress into fully solar-initiated water oxidation.

Configuration interaction in charge exchange spectra of tin and xenon

NASA Astrophysics Data System (ADS)

D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

2011-06-01

Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

Specific energy contributions from competing hydrogen-bonded structures in six polymorphs of phenobarbital.

PubMed

Gelbrich, Thomas; Braun, Doris E; Griesser, Ulrich J

2016-01-01

In solid state structures of organic molecules, identical sets of H-bond donor and acceptor functions can result in a range of distinct H-bond connectivity modes. Specifically, competing H-bond structures (HBSs) may differ in the quantitative proportion between one-point and multiple-point H-bond connections. For an assessment of such HBSs, the effects of their internal as well as external (packing) interactions need to be taken into consideration. The semi-classical density sums (SCDS-PIXEL) method, which enables the calculation of interaction energies for molecule-molecule pairs, was used to investigate six polymorphs of phenobarbital (Pbtl) with different quantitative proportions of one-point and two-point H-bond connections. The structures of polymorphs V and VI of Pbtl were determined from single crystal data. Two-point H-bond connections are inherently inflexible in their geometry and lie within a small PIXEL energy range (-45.7 to -49.7 kJ mol(-1)). One-point H-bond connections are geometrically less restricted and subsequently show large variations in their dispersion terms and total energies (-23.1 to -40.5 kJ mol(-1)). The comparison of sums of interaction energies in small clusters containing only the strongest intermolecular interactions showed an advantage for compact HBSs with multiple-point connections, whereas alternative HBSs based on one-point connections may enable more favourable overall packing interactions (i.e. V vs. III). Energy penalties associated with experimental intramolecular geometries relative to the global conformational energy minimum were calculated and used to correct total PIXEL energies. The estimated order of stabilities (based on PIXEL energies) is III > I > II > VI > X > V, with a difference of just 1.7 kJ mol(-1) between the three most stable forms. For an analysis of competing HBSs, one has to consider the contributions from internal H-bond and non-H-bond interactions, from the packing of multiple HBS instances and intramolecular energy penalties. A compact HBS based on multiple-point H-bond connections should typically lead to more packing alternatives and ultimately to a larger number of viable low-energy structures than a competing one-point HBS (i.e. dimer vs. catemer). Coulombic interaction energies associated with typical short intermolecular C-H···O contact geometries are small in comparison with dispersion effects associated with the packing complementary molecular shapes.Graphical abstractCompeting H-bond motifs can differ markedly in their energy contributions.

Plasmon-controlled fluorescence: a new paradigm in fluorescence spectroscopy

PubMed Central

Lakowicz, Joseph R.; Ray, Krishanu; Chowdhury, Mustafa; Szmacinski, Henryk; Fu, Yi; Zhang, Jian; Nowaczyk, Kazimierz

2009-01-01

Fluorescence spectroscopy is widely used in biological research. Until recently, essentially all fluorescence experiments were performed using optical energy which has radiated to the far-field. By far-field we mean at least several wavelengths from the fluorophore, but propagating far-field radiation is usually detected at larger macroscopic distances from the sample. In recent years there has been a growing interest in the interactions of fluorophores with metallic surfaces or particles. Near-field interactions are those occurring within a wavelength distance of an excited fluorophore. The spectral properties of fluorophores can be dramatically altered by near-field interactions with the electron clouds present in metals. These interactions modify the emission in ways not seen in classical fluorescence experiments. In this review we provide an intuitive description of the complex physics of plasmons and near-field interactions. Additionally, we summarize the recent work on metal–fluorophore interactions and suggest how these effects will result in new classes of experimental procedures, novel probes, bioassays and devices. PMID:18810279

Experimental study of three-wave interactions among capillary-gravity surface waves

NASA Astrophysics Data System (ADS)

Haudin, Florence; Cazaubiel, Annette; Deike, Luc; Jamin, Timothée; Falcon, Eric; Berhanu, Michael

2016-04-01

In propagating wave systems, three- or four-wave resonant interactions constitute a classical nonlinear mechanism exchanging energy between the different scales. Here we investigate three-wave interactions for gravity-capillary surface waves in a closed laboratory tank. We generate two crossing wave trains and we study their interaction. Using two optical methods, a local one (laser doppler vibrometry) and a spatiotemporal one (diffusive light photography), a third wave of smaller amplitude is detected, verifying the three-wave resonance conditions in frequency and in wave number. Furthermore, by focusing on the stationary regime and by taking into account viscous dissipation, we directly estimate the growth rate of the resonant mode. The latter is then compared to the predictions of the weakly nonlinear triadic resonance interaction theory. The obtained results confirm qualitatively and extend previous experimental results obtained only for collinear wave trains. Finally, we discuss the relevance of three-wave interaction mechanisms in recent experiments studying gravity-capillary turbulence.

Experimental study of three-wave interactions among capillary-gravity surface waves.

PubMed

Haudin, Florence; Cazaubiel, Annette; Deike, Luc; Jamin, Timothée; Falcon, Eric; Berhanu, Michael

2016-04-01

In propagating wave systems, three- or four-wave resonant interactions constitute a classical nonlinear mechanism exchanging energy between the different scales. Here we investigate three-wave interactions for gravity-capillary surface waves in a closed laboratory tank. We generate two crossing wave trains and we study their interaction. Using two optical methods, a local one (laser doppler vibrometry) and a spatiotemporal one (diffusive light photography), a third wave of smaller amplitude is detected, verifying the three-wave resonance conditions in frequency and in wave number. Furthermore, by focusing on the stationary regime and by taking into account viscous dissipation, we directly estimate the growth rate of the resonant mode. The latter is then compared to the predictions of the weakly nonlinear triadic resonance interaction theory. The obtained results confirm qualitatively and extend previous experimental results obtained only for collinear wave trains. Finally, we discuss the relevance of three-wave interaction mechanisms in recent experiments studying gravity-capillary turbulence.

Pauli structures arising from confined particles interacting via a statistical potential

NASA Astrophysics Data System (ADS)

Batle, Josep; Ciftja, Orion; Farouk, Ahmed; Alkhambashi, Majid; Abdalla, Soliman

2017-09-01

There have been suggestions that the Pauli exclusion principle alone can lead a non-interacting (free) system of identical fermions to form crystalline structures dubbed Pauli crystals. Single-shot imaging experiments for the case of ultra-cold systems of free spin-polarized fermionic atoms in a two-dimensional harmonic trap appear to show geometric arrangements that cannot be characterized as Wigner crystals. This work explores this idea and considers a well-known approach that enables one to treat a quantum system of free fermions as a system of classical particles interacting with a statistical interaction potential. The model under consideration, though classical in nature, incorporates the quantum statistics by endowing the classical particles with an effective interaction potential. The reasonable expectation is that possible Pauli crystal features seen in experiments may manifest in this model that captures the correct quantum statistics as a first order correction. We use the Monte Carlo simulated annealing method to obtain the most stable configurations of finite two-dimensional systems of confined particles that interact with an appropriate statistical repulsion potential. We consider both an isotropic harmonic and a hard-wall confinement potential. Despite minor differences, the most stable configurations observed in our model correspond to the reported Pauli crystals in single-shot imaging experiments of free spin-polarized fermions in a harmonic trap. The crystalline configurations observed appear to be different from the expected classical Wigner crystal structures that would emerge should the confined classical particles had interacted with a pair-wise Coulomb repulsion.

Internal proton transfer and H2 rotations in the H5(+) cluster: a marked influence on its thermal equilibrium state.

PubMed

de Tudela, Ricardo Pérez; Barragán, Patricia; Prosmiti, Rita; Villarreal, Pablo; Delgado-Barrio, Gerardo

2011-03-31

Classical and path integral Monte Carlo (CMC, PIMC) "on the fly" calculations are carried out to investigate anharmonic quantum effects on the thermal equilibrium structure of the H5(+) cluster. The idea to follow in our computations is based on using a combination of the above-mentioned nuclear classical and quantum statistical methods, and first-principles density functional (DFT) electronic structure calculations. The interaction energies are computed within the DFT framework using the B3(H) hybrid functional, specially designed for hydrogen-only systems. The global minimum of the potential is predicted to be a nonplanar configuration of C(2v) symmetry, while the next three low-lying stationary points on the surface correspond to extremely low-energy barriers for the internal proton transfer and to the rotation of the H2 molecules, around the C2 axis of H5(+), connecting the symmetric C(2v) minima in the planar and nonplanar orientations. On the basis of full-dimensional converged PIMC calculations, results on the quantum vibrational zero-point energy (ZPE) and state of H5(+) are reported at a low temperature of 10 K, and the influence of the above-mentioned topological features of the surface on its probability distributions is clearly demonstrated.

Zero-point energy constraint in quasi-classical trajectory calculations.

PubMed

Xie, Zhen; Bowman, Joel M

2006-04-27

A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.

Quantifying electron transfer reactions in biological systems: what interactions play the major role?

NASA Astrophysics Data System (ADS)

Sjulstok, Emil; Olsen, Jógvan Magnus Haugaard; Solov'Yov, Ilia A.

2015-12-01

Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.

Anisotropic exchange interaction induced by a single photon in semiconductor microcavities

NASA Astrophysics Data System (ADS)

Chiappe, G.; Fernández-Rossier, J.; Louis, E.; Anda, E. V.

2005-12-01

We investigate coupling of localized spins in a semiconductor quantum dot embedded in a microcavity. The lowest cavity mode and the quantum dot exciton are coupled and close in energy, forming a polariton. The fermions forming the exciton interact with localized spins via exchange. Exact diagonalization of a Hamiltonian in which photons, spins, and excitons are treated quantum mechanically shows that a single polariton induces a sizable indirect anisotropic exchange interaction between spins. At sufficiently low temperatures strong ferromagnetic correlations show up without an appreciable increase in exciton population. In the case of a (Cd,Mn)Te quantum dot, Mn-Mn ferromagnetic coupling is still significant at 1 K : spin-spin correlation around 3 for exciton occupation smaller than 0.3. We find that the interaction mediated by photon-polaritons is 10 times stronger than the one induced by a classical field for equal Rabi splitting.

Flying relativistic mirrors for nonlinear QED studies.

NASA Astrophysics Data System (ADS)

Bulanov, Stepan; Schroeder, Carl; Esarey, Eric; Leemans, Wim

2017-10-01

Recent progress in laser technology has led to a dramatic increase of laser power and intensity. As a result, the laser-matter interaction will happen in the radiation dominated regimes. In a strong electromagnetic field, electrons can be accelerated to such high velocities that the radiation reaction starts to play an important role. The radiation effects change drastically the laser-plasma interaction leading to fast energy losses. Moreover, previously unexplored regimes of the interaction will be entered into, in which quantum electrodynamics (QED) can occur. Depending on the laser intensity and wavelength, either classical or quantum mode of radiation reaction prevail. In order to study different regimes of interaction as well as the transition from one into another the utilization of flying relativistic mirrors, which can generate electromagnetic pulses with varying frequency and intensity, is proposed. The scheme is demonstrated for multiphoton Compton scattering. Work supported by U.S. DOE under Contract No. DE-AC02-05CH11231.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

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

DOE PAGES

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

2018-03-12

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

Computational algorithms dealing with the classical and statistical mechanics of celestial scale polymers in space elevator technology

NASA Astrophysics Data System (ADS)

Knudsen, Steven; Golubovic, Leonardo

Prospects to build Space Elevator (SE) systems have become realistic with ultra-strong materials such as carbon nano-tubes and diamond nano-threads. At cosmic length-scales, space elevators can be modeled as polymer like floppy strings of tethered mass beads. A new venue in SE science has emerged with the introduction of the Rotating Space Elevator (RSE) concept supported by novel algorithms discussed in this presentation. An RSE is a loopy string reaching into outer space. Unlike the classical geostationary SE concepts of Tsiolkovsky, Artsutanov, and Pearson, our RSE exhibits an internal rotation. Thanks to this, objects sliding along the RSE loop spontaneously oscillate between two turning points, one of which is close to the Earth whereas the other one is in outer space. The RSE concept thus solves a major problem in SE technology which is how to supply energy to the climbers moving along space elevator strings. The investigation of the classical and statistical mechanics of a floppy string interacting with objects sliding along it required development of subtle computational algorithms described in this presentation

Correlated electron-nuclear dissociation dynamics: classical versus quantum motion

NASA Astrophysics Data System (ADS)

Schaupp, Thomas; Albert, Julian; Engel, Volker

2017-01-01

We investigate the coupled electron-nuclear dynamics in a model system which undergoes dissociation. In choosing different initial conditions, the cases of adiabatic and non-adiabatic dissociation are realized. We treat the coupled electronic and nuclear motion in the complete configuration space so that classically, no surface hopping procedures have to be incorporated in the case that more than a single adiabatic electronic state is populated during the fragmentation. Due to the anharmonic interaction potential, it is expected that classical mechanics substantially deviate from quantum mechanics. However, we provide examples where the densities and fragmentation yields obtained from the two treatments are in astonishingly strong agreement in the case that one starts in the electronic ground state initially. As expected, larger deviations are found if one starts in electronically excited states where trajectories are sampled from the more spatially extended electronic wave function. In that case, higher initial energies are accessed, and the motion proceeds in regions with increasing degree of anharmonicity. Contribution to the Topical Issue "Dynamics of Molecular Systems (MOLEC 2016)", edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.

Solute atmospheres at dislocations

DOE PAGES

Hirth, John P.; Barnett, David M.; Hoagland, Richard G.

2017-06-01

In this study, a two-dimensional plane strain elastic solution is determined for the Cottrell solute atmosphere around an edge dislocation in an infinitely long cylinder of finite radius (the matrix), in which rows of solutes are represented by cylindrical rods with in-plane hydrostatic misfit (axial misfit is also considered). The periphery of the matrix is traction-free, thus introducing an image solute field which generates a solute-solute interaction energy that has not been considered previously. The relevant energy for the field of any distribution of solutes coexistent with a single edge dislocation along the (matrix) cylinder axis is determined, and coherencymore » effects are discussed and studied. Monte Carlo simulations accounting for all pertinent interactions over a range of temperatures are found to yield solute distributions different from classical results, namely, (1) Fermi-Dirac condensations at low temperatures at the free surface, (2) the majority of the atmosphere lying within an unexpectedly large non-linear interaction region near the dislocation core, and (3) temperature-dependent asymmetrical solute arrangements that promote bending. The solute distributions at intermediate temperatures show a 1/r dependence in agreement with previous linearized approximations. With a standard state of solute corresponding to a mean concentration, c 0, the relevant interaction energy expression presented in this work is valid when extended to large concentrations for which Henry's Law and Vegard's Law do not apply.« less

Solute atmospheres at dislocations

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

Hirth, John P.; Barnett, David M.; Hoagland, Richard G.

In this study, a two-dimensional plane strain elastic solution is determined for the Cottrell solute atmosphere around an edge dislocation in an infinitely long cylinder of finite radius (the matrix), in which rows of solutes are represented by cylindrical rods with in-plane hydrostatic misfit (axial misfit is also considered). The periphery of the matrix is traction-free, thus introducing an image solute field which generates a solute-solute interaction energy that has not been considered previously. The relevant energy for the field of any distribution of solutes coexistent with a single edge dislocation along the (matrix) cylinder axis is determined, and coherencymore » effects are discussed and studied. Monte Carlo simulations accounting for all pertinent interactions over a range of temperatures are found to yield solute distributions different from classical results, namely, (1) Fermi-Dirac condensations at low temperatures at the free surface, (2) the majority of the atmosphere lying within an unexpectedly large non-linear interaction region near the dislocation core, and (3) temperature-dependent asymmetrical solute arrangements that promote bending. The solute distributions at intermediate temperatures show a 1/r dependence in agreement with previous linearized approximations. With a standard state of solute corresponding to a mean concentration, c 0, the relevant interaction energy expression presented in this work is valid when extended to large concentrations for which Henry's Law and Vegard's Law do not apply.« less

Application of the N-quantum approximation to the proton radius problem

NASA Astrophysics Data System (ADS)

Cowen, Steven

This thesis is organized into three parts: 1. Introduction and bound state calculations of electronic and muonic hydrogen, 2. Bound states in motion, and 3.Treatment of soft photons. In the first part, we apply the N-Quantum Approximation (NQA) to electronic and muonic hydrogen and search for any new corrections to energy levels that could account for the 0.31 meV discrepancy of the proton radius problem. We derive a bound state equation and compare our numerical solutions and wave functions to those of the Dirac equation. We find NQA Lamb shift diagrams and calculate the associated energy shift contributions. We do not find any new corrections large enough to account for the discrepancy. In part 2, we discuss the effects of motion on bound states using the NQA. We find classical Lorentz contraction of the lowest order NQA wave function. Finally, in part 3, we develop a clothing transformation for interacting fields in order to produce the correct asymptotic limits. We find the clothing eliminates a trilinear interacting Hamiltonian term and produces a quadrilinear soft photon interaction term.

Deconstructing Free Energies in the Law of Matching Water Affinities.

PubMed

Shi, Yu; Beck, Thomas

2017-03-09

The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

Material Science Smart Coatings

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

Rubinstein, A. I.; Sabirianov, R. F.; Namavar, Fereydoon

2014-07-01

The contribution of electrostatic interactions to the free energy of binding between model protein and a ceramic implant surface in the aqueous solvent, considered in the framework of the nonlocal electrostatic model, is calculated as a function of the implant low-frequency dielectric constant. We show that the existence of a dynamically ordered (low-dielectric) interfacial solvent layer at the protein-solvent and ceramic-solvent interface markedly increases charging energy of the protein and ceramic implant, and consequently makes the electrostatic contribution to the protein-ceramic binding energy more favorable (attractive). Our analysis shows that the corresponding electrostatic energy between protein and oxide ceramics dependsmore » nonmonotonically on the dielectric constant of ceramic, ε C. Obtained results indicate that protein can attract electrostatically to the surface if ceramic material has a moderate ε C below or about 35 (in particularly ZrO 2 or Ta 2O 5). This is in contrast to classical (local) consideration of the solvent, which demonstrates an unfavorable electrostatic interaction of protein with typical metal oxide ceramic materials (ε C>10). Thus, a solid implant coated by combining oxide ceramic with a reduced dielectric constant can be beneficial to strengthen the electrostatic binding of the protein-implant complex.« less

[Flexible Guidance of Ultra-Short Laser Pulses in Ophthalmic Therapy Systems].

PubMed

Blum, J; Blum, M; Rill, M S; Haueisen, J

2017-01-01

In the last 20 years, the role of ultrashort pulsed lasers in ophthalmology has become increasingly important. However, it is still impossible to guide ultra-short laser pulses with standard glass fibres. The highly energetic femtosecond pulses would destroy the fibre material, and non-linear dispersion effects would significantly change beam parameters. In contrast, photonic crystal fibres mainly guide the laser pulses in air, so that absorption and dispersive pulse broadening have essentially no effect. This article compares classical beam guidance with mirrors, lenses and prisms with photonic crystal fibres and describes the underlying concepts and the current state of technology. A classical mirror arm possesses more variable optical properties, while the HCF (Hollow-Core Photonic Crystal Fibre) must be matched in terms of the laser energy and the laser spectrum. In contrast, the HCF has more advantages in respect of handling, system integration and costs. For applications based on photodisruptive laser-tissue interaction, the relatively low damage threshold of photonic crystal fibres compared to classic beam guiding systems is unacceptable. If, however, pulsed laser radiation has a sufficiently low peak intensity, e.g. as used for plasma-induced ablation, photonic crystal fibres can definitely be considered as an alternative solution to classic beam guidance. Georg Thieme Verlag KG Stuttgart · New York.

Augmented potential, energy densities, and virial relations in the weak- and strong-interaction limits of DFT

NASA Astrophysics Data System (ADS)

Vuckovic, Stefan; Levy, Mel; Gori-Giorgi, Paola

2017-12-01

The augmented potential introduced by Levy and Zahariev [Phys. Rev. Lett. 113, 113002 (2014)] is shifted with respect to the standard exchange-correlation potential of the Kohn-Sham density functional theory by a density-dependent constant that makes the total energy become equal to the sum of the occupied orbital energies. In this work, we analyze several features of this approach, focusing on the limit of infinite coupling strength and studying the shift and the corresponding energy density at different correlation regimes. We present and discuss coordinate scaling properties of the augmented potential, study its connection to the response potential, and use the shift to analyze the classical jellium and uniform gas models. We also study other definitions of the energy densities in relation to the functional construction by local interpolations along the adiabatic connection. Our findings indicate that the energy density that is defined in terms of the electrostatic potential of the exchange-correlation hole is particularly well suited for this purpose.

Photosynthetic Energy Transfer at the Quantum/Classical Border.

PubMed

Keren, Nir; Paltiel, Yossi

2018-06-01

Quantum mechanics diverges from the classical description of our world when very small scales or very fast processes are involved. Unlike classical mechanics, quantum effects cannot be easily related to our everyday experience and are often counterintuitive to us. Nevertheless, the dimensions and time scales of the photosynthetic energy transfer processes puts them close to the quantum/classical border, bringing them into the range of measurable quantum effects. Here we review recent advances in the field and suggest that photosynthetic processes can take advantage of the sensitivity of quantum effects to the environmental 'noise' as means of tuning exciton energy transfer efficiency. If true, this design principle could be a base for 'nontrivial' coherent wave property nano-devices. Copyright © 2018 Elsevier Ltd. All rights reserved.

The water hexamer: three-body interactions, structures, energetics, and OH-stretch spectroscopy at finite temperature.

PubMed

Tainter, C J; Skinner, J L

2012-09-14

Using a newly developed and recently parameterized classical empirical simulation model for water that involves explicit three-body interactions, we determine the eleven most stable isomers of the water hexamer. We find that the lowest energy isomer is one of the cage structures, in agreement with far-IR and microwave experiments. The energy ordering for the binding energies is cage > glove > book > bag > chair > boat > chaise, and energies relative to the cage are in good agreement with CCSD(T) calculations. The three-body contributions to the cage, book, and chair are also in reasonable agreement with CCSD(T) results. The energy of each isomer results from a delicate balance involving the number of hydrogen bonds, the strain of these hydrogen bonds, and cooperative and anti-cooperative three-body interactions, whose contribution we can understand simply from the form of the three-body interactions in the simulation model. Oxygen-oxygen distances in the cage and book isomers are in good agreement with microwave experiments. Hydrogen-bond distances depend on both donor and acceptor, which can again be understood from the three-body model. Fully anharmonic OH-stretch spectra are calculated for these low-energy structures, and compared with shifted harmonic results from ab initio and density functional theory calculations. Replica-exchange molecular dynamics simulations were performed from 40 to 194 K, which show that the cage isomer has the lowest free energy from 0 to 70 K, and the book isomer has the lowest free energy from 70 to 194 K. OH-stretch spectra were calculated between 40 and 194 K, and results at 40, 63, and 79 K were compared to recent experiments, leading to re-assignment of the peaks in the experimental spectra. We calculate local OH-stretch cumulative spectral densities for different donor-acceptor types and compare to analogous results for liquid water.

Autonomous quantum to classical transitions and the generalized imaging theorem

NASA Astrophysics Data System (ADS)

Briggs, John S.; Feagin, James M.

2016-03-01

The mechanism of the transition of a dynamical system from quantum to classical mechanics is of continuing interest. Practically it is of importance for the interpretation of multi-particle coincidence measurements performed at macroscopic distances from a microscopic reaction zone. Here we prove the generalized imaging theorem which shows that the spatial wave function of any multi-particle quantum system, propagating over distances and times large on an atomic scale but still microscopic, and subject to deterministic external fields and particle interactions, becomes proportional to the initial momentum wave function where the position and momentum coordinates define a classical trajectory. Currently, the quantum to classical transition is considered to occur via decoherence caused by stochastic interaction with an environment. The imaging theorem arises from unitary Schrödinger propagation and so is valid without any environmental interaction. It implies that a simultaneous measurement of both position and momentum will define a unique classical trajectory, whereas a less complete measurement of say position alone can lead to quantum interference effects.

Autonomous quantum to classical transitions and the generalized imaging theorem

DOE PAGES

Briggs, John S.; Feagin, James M.

2016-03-16

The mechanism of the transition of a dynamical system from quantum to classical mechanics is of continuing interest. Practically it is of importance for the interpretation of multi-particle coincidence measurements performed at macroscopic distances from a microscopic reaction zone. We prove the generalized imaging theorem which shows that the spatial wave function of any multi-particle quantum system, propagating over distances and times large on an atomic scale but still microscopic, and subject to deterministic external fields and particle interactions, becomes proportional to the initial momentum wave function where the position and momentum coordinates define a classical trajectory. Now, the quantummore » to classical transition is considered to occur via decoherence caused by stochastic interaction with an environment. The imaging theorem arises from unitary Schrödinger propagation and so is valid without any environmental interaction. It implies that a simultaneous measurement of both position and momentum will define a unique classical trajectory, whereas a less complete measurement of say position alone can lead to quantum interference effects.« less

Multiscale Experimental and Theoretical Investigations of Spin Crossover FeII Complexes: Examples of [Fe(phen)2(NCS)2] and [Fe(PM-BiA)2(NCS)2

PubMed Central

Matar, Samir F.; Guionneau, Philippe; Chastanet, Guillaume

2015-01-01

For spin crossover (SCO) complexes, computation results are reported and confirmed with experiments at multiscale levels of the isolated molecule and extended solid on the one hand and theory on the other hand. The SCO phenomenon which characterizes organometallics based on divalent iron in an octahedral FeN6-like environment with high spin (HS) and low spin (LS) states involves the LS/HS switching at the cost of small energies provided by temperature, pressure or light, the latter connected with Light-Induced Excited Spin-State Trapping (LIESST) process. Characteristic infra red (IR) and Raman vibration frequencies are computed within density functional theory (DFT) framework. In [Fe(phen)2(NCS)2] a connection of selected frequencies is established with an ultra-fast light-induced LS → HS photoswitching mechanism. In the extended solid, density of state DOS and electron localization function (ELF) are established for both LS and HS forms, leading to characterizion of the compound as an insulator in both spin states with larger gaps for LS configuration, while keeping molecular features in the solid. In [Fe(PM-BiA)2(NCS)2], by combining DFT and classical molecular dynamics, the properties and the domains of existence of the different phases are obtained by expressing the potential energy surfaces in a short range potential for Fe–N interactions. Applying such Fe–N potentials inserted in a classical force field and carrying out molecular dynamics (MD) in so-called “semi-classical MD” calculations, lead to the relative energies of HS/LS configurations of the crystal and to the assessment of the experimental (P, T) phase diagram. PMID:25686037

Electric and magnetic dipoles in the Lorentz and Einstein-Laub formulations of classical electrodynamics

NASA Astrophysics Data System (ADS)

Mansuripur, Masud

2015-01-01

The classical theory of electrodynamics cannot explain the existence and structure of electric and magnetic dipoles, yet it incorporates such dipoles into its fundamental equations, simply by postulating their existence and properties, just as it postulates the existence and properties of electric charges and currents. Maxwell's macroscopic equations are mathematically exact and self-consistent differential equations that relate the electromagnetic (EM) field to its sources, namely, electric charge-density 𝜌𝜌free, electric current-density 𝑱𝑱free, polarization 𝑷𝑷, and magnetization 𝑴𝑴. At the level of Maxwell's macroscopic equations, there is no need for models of electric and magnetic dipoles. For example, whether a magnetic dipole is an Amperian current-loop or a Gilbertian pair of north and south magnetic monopoles has no effect on the solution of Maxwell's equations. Electromagnetic fields carry energy as well as linear and angular momenta, which they can exchange with material media—the seat of the sources of the EM field—thereby exerting force and torque on these media. In the Lorentz formulation of classical electrodynamics, the electric and magnetic fields, 𝑬𝑬 and 𝑩𝑩, exert forces and torques on electric charge and current distributions. An electric dipole is then modeled as a pair of electric charges on a stick (or spring), and a magnetic dipole is modeled as an Amperian current loop, so that the Lorentz force law can be applied to the corresponding (bound) charges and (bound) currents of these dipoles. In contrast, the Einstein-Laub formulation circumvents the need for specific models of the dipoles by simply providing a recipe for calculating the force- and torque-densities exerted by the 𝑬𝑬 and 𝑯𝑯 fields on charge, current, polarization and magnetization. The two formulations, while similar in many respects, have significant differences. For example, in the Lorentz approach, the Poynting vector is 𝑺𝑺𝐿𝐿 = 𝜇𝜇0 -1𝑬𝑬 × 𝑩𝑩, and the linear and angular momentum densities of the EM field are 𝓹𝓹𝐿𝐿 = 𝜀𝜀0𝑬𝑬 × 𝑩𝑩 and 𝓛𝓛𝐿𝐿 = 𝒓𝒓 × 𝓹𝓹𝐿𝐿, whereas in the Einstein-Laub formulation the corresponding entities are 𝑺𝑺𝐸𝐸𝐸𝐸= 𝑬𝑬 × 𝑯𝑯, 𝓹𝓹𝐸𝐸𝐸𝐸= 𝑬𝑬 × 𝑯𝑯⁄𝑐𝑐2, and 𝓛𝓛𝐸𝐸𝐸𝐸= 𝒓𝒓 × 𝓹𝓹𝐸𝐸𝐸𝐸. (Here 𝜇𝜇0 and 𝜀𝜀0 are the permeability and permittivity of free space, 𝑐𝑐 is the speed of light in vacuum, 𝑩𝑩 = 𝜇𝜇0𝑯𝑯 + 𝑴𝑴, and 𝒓𝒓 is the position vector.) Such differences can be reconciled by recognizing the need for the so-called hidden energy and hidden momentum associated with Amperian current loops of the Lorentz formalism. (Hidden entities of the sort do not arise in the Einstein-Laub treatment of magnetic dipoles.) Other differences arise from over-simplistic assumptions concerning the equivalence between free charges and currents on the one hand, and their bound counterparts on the other. A more nuanced treatment of EM force and torque densities exerted on polarization and magnetization in the Lorentz approach would help bridge the gap that superficially separates the two formulations. Atoms and molecules may collide with each other and, in general, material constituents can exchange energy, momentum, and angular momentum via direct mechanical interactions. In the case of continuous media, elastic and hydrodynamic stresses, phenomenological forces such as those related to exchange coupling in ferromagnets, etc., subject small volumes of materials to external forces and torques. Such matter-matter interactions, although fundamentally EM in nature, are distinct from field-matter interactions in classical physics. Beyond the classical regime, however, the dichotomy that distinguishes the EM field from EM sources gets blurred. An electron's wavefunction may overlap that of an atomic nucleus, thereby initiating a contact interaction between the magnetic dipole moments of the two particles. Or a neutron passing through a ferromagnetic material may give rise to scattering events involving overlaps between the wave-functions of the neutron and magnetic electrons. Such matter-matter interactions exert equal and opposite forces and/or torques on the colliding particles, and their observable effects often shed light on the nature of the particles involved. It is through such observations that the Amperian model of a magnetic dipole has come to gain prominence over the Gilbertian model. In situations involving overlapping particle wave-functions, it is imperative to take account of the particle-particle interaction energy when computing the scattering amplitudes. As far as total force and total torque on a given volume of material are concerned, such particle-particle interactions do not affect the outcome of calculations, since the mutual actions of the two (overlapping) particles cancel each other out. Both Lorentz and Einstein-Laub formalisms thus yield the same total force and total torque on a given volume—provided that hidden entities are properly removed. The Lorentz formalism, with its roots in the Amperian current-loop model, correctly predicts the interaction energy between two overlapping magnetic dipoles 𝒎𝒎1 and 𝒎𝒎2 as being proportional to -𝒎𝒎1 • 𝒎𝒎2. In contrast, the Einstein-Laub formalism, which is ignorant of such particle-particle interactions, needs to account for them separately.

Canonical partition functions: ideal quantum gases, interacting classical gases, and interacting quantum gases

NASA Astrophysics Data System (ADS)

Zhou, Chi-Chun; Dai, Wu-Sheng

2018-02-01

In statistical mechanics, for a system with a fixed number of particles, e.g. a finite-size system, strictly speaking, the thermodynamic quantity needs to be calculated in the canonical ensemble. Nevertheless, the calculation of the canonical partition function is difficult. In this paper, based on the mathematical theory of the symmetric function, we suggest a method for the calculation of the canonical partition function of ideal quantum gases, including ideal Bose, Fermi, and Gentile gases. Moreover, we express the canonical partition functions of interacting classical and quantum gases given by the classical and quantum cluster expansion methods in terms of the Bell polynomial in mathematics. The virial coefficients of ideal Bose, Fermi, and Gentile gases are calculated from the exact canonical partition function. The virial coefficients of interacting classical and quantum gases are calculated from the canonical partition function by using the expansion of the Bell polynomial, rather than calculated from the grand canonical potential.

When gluons go odd: how classical gluon fields generate odd azimuthal harmonics for the two-gluon correlation function in high-energy collisions

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

Kovchegov, Yuri V.; Skokov, Vladimir V.

We show that, in the saturation/Color Glass Condensate framework, odd azimuthal harmonics of the two-gluon correlation function with a long-range separation in rapidity are generated by the higher-order saturation corrections in the interactions with the projectile and the target. At the very least, the odd harmonics require three scatterings in the projectile and three scatterings in the target. We derive the leading-order expression for the two-gluon production cross section which generates odd harmonics: the expression includes all-order interactions with the target and three interactions with the projectile. Here, we evaluate the obtained expression both analytically and numerically, confirming that themore » odd-harmonics contribution to the two-gluon production in the saturation framework is non-zero.« less

Dimension-dependent stimulated radiative interaction of a single electron quantum wavepacket

NASA Astrophysics Data System (ADS)

Gover, Avraham; Pan, Yiming

2018-06-01

In the foundation of quantum mechanics, the spatial dimensions of electron wavepacket are understood only in terms of an expectation value - the probability distribution of the particle location. One can still inquire how the quantum electron wavepacket size affects a physical process. Here we address the fundamental physics problem of particle-wave duality and the measurability of a free electron quantum wavepacket. Our analysis of stimulated radiative interaction of an electron wavepacket, accompanied by numerical computations, reveals two limits. In the quantum regime of long wavepacket size relative to radiation wavelength, one obtains only quantum-recoil multiphoton sidebands in the electron energy spectrum. In the opposite regime, the wavepacket interaction approaches the limit of classical point-particle acceleration. The wavepacket features can be revealed in experiments carried out in the intermediate regime of wavepacket size commensurate with the radiation wavelength.

When gluons go odd: how classical gluon fields generate odd azimuthal harmonics for the two-gluon correlation function in high-energy collisions

DOE PAGES

Kovchegov, Yuri V.; Skokov, Vladimir V.

2018-04-30

We show that, in the saturation/Color Glass Condensate framework, odd azimuthal harmonics of the two-gluon correlation function with a long-range separation in rapidity are generated by the higher-order saturation corrections in the interactions with the projectile and the target. At the very least, the odd harmonics require three scatterings in the projectile and three scatterings in the target. We derive the leading-order expression for the two-gluon production cross section which generates odd harmonics: the expression includes all-order interactions with the target and three interactions with the projectile. Here, we evaluate the obtained expression both analytically and numerically, confirming that themore » odd-harmonics contribution to the two-gluon production in the saturation framework is non-zero.« less

Effective temperatures and the breakdown of the Stokes-Einstein relation for particle suspensions.

PubMed

Mendoza, Carlos I; Santamaría-Holek, I; Pérez-Madrid, A

2015-09-14

The short- and long-time breakdown of the classical Stokes-Einstein relation for colloidal suspensions at arbitrary volume fractions is explained here by examining the role that confinement and attractive interactions play in the intra- and inter-cage dynamics executed by the colloidal particles. We show that the measured short-time diffusion coefficient is larger than the one predicted by the classical Stokes-Einstein relation due to a non-equilibrated energy transfer between kinetic and configuration degrees of freedom. This transfer can be incorporated in an effective kinetic temperature that is higher than the temperature of the heat bath. We propose a Generalized Stokes-Einstein relation (GSER) in which the effective temperature replaces the temperature of the heat bath. This relation then allows to obtain the diffusion coefficient once the viscosity and the effective temperature are known. On the other hand, the temporary cluster formation induced by confinement and attractive interactions of hydrodynamic nature makes the long-time diffusion coefficient to be smaller than the corresponding one obtained from the classical Stokes-Einstein relation. Then, the use of the GSER allows to obtain an effective temperature that is smaller than the temperature of the heat bath. Additionally, we provide a simple expression based on a differential effective medium theory that allows to calculate the diffusion coefficient at short and long times. Comparison of our results with experiments and simulations for suspensions of hard and porous spheres shows an excellent agreement in all cases.

Solid-solid collapse transition in a two dimensional model molecular system.

PubMed

Singh, Rakesh S; Bagchi, Biman

2013-11-21

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains.

Solid-solid collapse transition in a two dimensional model molecular system

NASA Astrophysics Data System (ADS)

Singh, Rakesh S.; Bagchi, Biman

2013-11-01

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains.

Attraction between Opposing Planar Dipolar Polymer Brushes

DOE PAGES

Mahalik, J. P.; Sumpter, Bobby G.; Kumar, Rajeev

2017-08-01

In this paper, we use a field theory approach to study the effects of permanent dipoles on interpenetration and free energy changes as a function of distance between two identical planar polymer brushes. Melts (i.e., solvent-free) and solvated brushes made up of polymers grafted on nonadsorbing substrates are studied. In particular, the weak coupling limit of the dipolar interactions is considered, which leads to concentration-dependent pairwise interactions, and the effects of orientational order are neglected. It is predicted that a gradual increase in the dipole moment of the polymer segments can lead to attractive interactions between the brushes at intermediatemore » separation distances. Finally, because classical theory of polymer brushes based on the strong stretching limit (SSL) and the standard self-consistent field theory (SCFT) simulations using the Flory’s χ parameter always predicts repulsive interactions at all separations, our work highlights the importance of dipolar interactions in tailoring and accurately predicting forces between polar polymeric interfaces in contact with each other.« less

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

Mahalik, J. P.; Sumpter, Bobby G.; Kumar, Rajeev

In this paper, we use a field theory approach to study the effects of permanent dipoles on interpenetration and free energy changes as a function of distance between two identical planar polymer brushes. Melts (i.e., solvent-free) and solvated brushes made up of polymers grafted on nonadsorbing substrates are studied. In particular, the weak coupling limit of the dipolar interactions is considered, which leads to concentration-dependent pairwise interactions, and the effects of orientational order are neglected. It is predicted that a gradual increase in the dipole moment of the polymer segments can lead to attractive interactions between the brushes at intermediatemore » separation distances. Finally, because classical theory of polymer brushes based on the strong stretching limit (SSL) and the standard self-consistent field theory (SCFT) simulations using the Flory’s χ parameter always predicts repulsive interactions at all separations, our work highlights the importance of dipolar interactions in tailoring and accurately predicting forces between polar polymeric interfaces in contact with each other.« less

Decoherence Effect on Quantum Correlation and Entanglement in a Two-qubit Spin Chain

NASA Astrophysics Data System (ADS)

Pourkarimi, Mohammad Reza; Rahnama, Majid; Rooholamini, Hossein

2015-04-01

Assuming a two-qubit system in Werner state which evolves in Heisenberg XY model with Dzyaloshinskii-Moriya (DM) interaction under the effect of different environments. We evaluate and compare quantum entanglement, quantum and classical correlation measures. It is shown that in the absence of decoherence effects, there is a critical value of DM interaction for which entanglement may vanish while quantum and classical correlations do not. In the presence of environment the behavior of correlations depends on the kind of system-environment interaction. Correlations can be sustained by manipulating Hamiltonian anisotropic-parameter in a dissipative environment. Quantum and classical correlations are more stable than entanglement generally.

Vibrational spectra of halide-water dimers: Insights on ion hydration from full-dimensional quantum calculations on many-body potential energy surfaces

NASA Astrophysics Data System (ADS)

Bajaj, Pushp; Wang, Xiao-Gang; Carrington, Tucker; Paesani, Francesco

2018-03-01

Full-dimensional vibrational spectra are calculated for both X-(H2O) and X-(D2O) dimers (X = F, Cl, Br, I) at the quantum-mechanical level. The calculations are carried out on two sets of recently developed potential energy functions (PEFs), namely, Thole-type model energy (TTM-nrg) and many-body energy (MB-nrg), using the symmetry-adapted Lanczos algorithm with a product basis set including all six vibrational coordinates. Although both TTM-nrg and MB-nrg PEFs are derived from coupled-cluster single double triple-F12 data obtained in the complete basis set limit, they differ in how many-body effects are represented at short range. Specifically, while both models describe long-range interactions through the combination of two-body dispersion and many-body classical electrostatics, the relatively simple Born-Mayer functions employed in the TTM-nrg PEFs to represent short-range interactions are replaced in the MB-nrg PEFs by permutationally invariant polynomials to achieve chemical accuracy. For all dimers, the MB-nrg vibrational spectra are in close agreement with the available experimental data, correctly reproducing anharmonic and nuclear quantum effects. In contrast, the vibrational frequencies calculated with the TTM-nrg PEFs exhibit significant deviations from the experimental values. The comparison between the TTM-nrg and MB-nrg results thus reinforces the notion that an accurate representation of both short-range interactions associated with electron density overlap and long-range many-body electrostatic interactions is necessary for a correct description of hydration phenomena at the molecular level.

SmartHome: a domotic framework based on smart sensing and actuator network to reduce energy wastes

NASA Astrophysics Data System (ADS)

Santamaria, Amilcare Francesco; De Rango, Floriano; Falbo, Domenico; Barletta, Domenico

2014-05-01

Domestic environment and human interaction with services supplied by domotic devices is going to be a very interesting application field. With a domotic system is possible to achieve great interaction between human beings, environments and smart devices. The enhancing of these interactions is the main goal of this work whose intent is to improve the classic concept of domotics. The framework we developed can be used for several application fields such as lighting, heating, conditioning or water management and energy consumption. In particular, the proposed system can optimize energy consumptions by rising awareness to users that have full control of their house and the possibility to save money and reduce the impact of the energetic consumes to the earth, matching the new "green" motto requirements. In this way, the overall system wants to match the central concept of Internet Of Things (IoT) as well. From this point of view a complex automation system with smart devices make possible a more efficient way to produce, follow and manage domotic policies. Following the spread of IoT, for this work we designed and implemented new plug-and-play and ready-to-use smart devices that are part of a complex automation system that offers a user-friendly web application and allows users to control and interact with different plans of their house in order to make life more comfortable and be aware of their energy consumptions. Control and awareness arc the two key points that led us to develop the proposed system.

Quantifying the statistical importance of utilizing regression over classic energy intensity calculations for tracking efficiency improvements in industry

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

Nimbalkar, Sachin U.; Wenning, Thomas J.; Guo, Wei

In the United States, manufacturing facilities account for about 32% of total domestic energy consumption in 2014. Robust energy tracking methodologies are critical to understanding energy performance in manufacturing facilities. Due to its simplicity and intuitiveness, the classic energy intensity method (i.e. the ratio of total energy use over total production) is the most widely adopted. However, the classic energy intensity method does not take into account the variation of other relevant parameters (i.e. product type, feed stock type, weather, etc.). Furthermore, the energy intensity method assumes that the facilities’ base energy consumption (energy use at zero production) is zero,more » which rarely holds true. Therefore, it is commonly recommended to utilize regression models rather than the energy intensity approach for tracking improvements at the facility level. Unfortunately, many energy managers have difficulties understanding why regression models are statistically better than utilizing the classic energy intensity method. While anecdotes and qualitative information may convince some, many have major reservations about the accuracy of regression models and whether it is worth the time and effort to gather data and build quality regression models. This paper will explain why regression models are theoretically and quantitatively more accurate for tracking energy performance improvements. Based on the analysis of data from 114 manufacturing plants over 12 years, this paper will present quantitative results on the importance of utilizing regression models over the energy intensity methodology. This paper will also document scenarios where regression models do not have significant relevance over the energy intensity method.« less

Quantum algorithm for energy matching in hard optimization problems

NASA Astrophysics Data System (ADS)

Baldwin, C. L.; Laumann, C. R.

2018-06-01

We consider the ability of local quantum dynamics to solve the "energy-matching" problem: given an instance of a classical optimization problem and a low-energy state, find another macroscopically distinct low-energy state. Energy matching is difficult in rugged optimization landscapes, as the given state provides little information about the distant topography. Here, we show that the introduction of quantum dynamics can provide a speedup over classical algorithms in a large class of hard optimization problems. Tunneling allows the system to explore the optimization landscape while approximately conserving the classical energy, even in the presence of large barriers. Specifically, we study energy matching in the random p -spin model of spin-glass theory. Using perturbation theory and exact diagonalization, we show that introducing a transverse field leads to three sharp dynamical phases, only one of which solves the matching problem: (1) a small-field "trapped" phase, in which tunneling is too weak for the system to escape the vicinity of the initial state; (2) a large-field "excited" phase, in which the field excites the system into high-energy states, effectively forgetting the initial energy; and (3) the intermediate "tunneling" phase, in which the system succeeds at energy matching. The rate at which distant states are found in the tunneling phase, although exponentially slow in system size, is exponentially faster than classical search algorithms.

A new analytical potential energy surface for the singlet state of He{sub 2}H{sup +}

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

Liang Jingjuan; Zhang Qinggang; Yang Chuanlu

2012-03-07

The analytic potential energy surface (APES) for the exchange reaction of HeH{sup +} (X{sup 1}{Sigma}{sup +}) + He at the lowest singlet state 1{sup 1}A{sup /} has been built. The APES is expressed as Aguado-Paniagua function based on the many-body expansion. Using the adaptive non-linear least-squares algorithm, the APES is fitted from 15 682 ab initio energy points calculated with the multireference configuration interaction calculation with a large d-aug-cc-pV5Z basis set. To testify the new APES, we calculate the integral cross sections for He + H{sup +}He (v= 0, 1, 2, j= 0) {yields} HeH{sup +}+ He by means ofmore » quasi-classical trajectory and compare them with the previous result in literature.« less

Steering attosecond electron wave packets with light.

PubMed

Kienberger, R; Hentschel, M; Uiberacker, M; Spielmann, Ch; Kitzler, M; Scrinzi, A; Wieland, M; Westerwalbesloh, Th; Kleineberg, U; Heinzmann, U; Drescher, M; Krausz, F

2002-08-16

Photoelectrons excited by extreme ultraviolet or x-ray photons in the presence of a strong laser field generally suffer a spread of their energies due to the absorption and emission of laser photons. We demonstrate that if the emitted electron wave packet is temporally confined to a small fraction of the oscillation period of the interacting light wave, its energy spectrum can be up- or downshifted by many times the laser photon energy without substantial broadening. The light wave can accelerate or decelerate the electron's drift velocity, i.e., steer the electron wave packet like a classical particle. This capability strictly relies on a sub-femtosecond duration of the ionizing x-ray pulse and on its timing to the phase of the light wave with a similar accuracy, offering a simple and potentially single-shot diagnostic tool for attosecond pump-probe spectroscopy.

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

Curchod, Basile F. E.; Agostini, Federica, E-mail: agostini@mpi-halle.mpg.de; Gross, E. K. U.

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 contrastmore » 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.« less

Classical and quantum dynamics in an inverse square potential

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

Guillaumín-España, Elisa, E-mail: ege@correo.azc.uam.mx; Núñez-Yépez, H. N., E-mail: nyhn@xanum.uam.mx; Salas-Brito, A. L., E-mail: asb@correo.azc.uam.mx

2014-10-15

The classical motion of a particle in a 3D inverse square potential with negative energy, E, is shown to be geodesic, i.e., equivalent to the particle's free motion on a non-compact phase space manifold irrespective of the sign of the coupling constant. We thus establish that all its classical orbits with E < 0 are unbounded. To analyse the corresponding quantum problem, the Schrödinger equation is solved in momentum space. No discrete energy levels exist in the unrenormalized case and the system shows a complete “fall-to-the-center” with an energy spectrum unbounded by below. Such behavior corresponds to the non-existence ofmore » bound classical orbits. The symmetry of the problem is SO(3) × SO(2, 1) corroborating previously obtained results.« less

Effects of functionalization of carbon nanotubes on their dispersion in an ethylene glycol-water binary mixture--a molecular dynamics and ONIOM investigation.

PubMed

Balamurugan, Kanagasabai; Baskar, Prathab; Kumar, Ravva Mahesh; Das, Sumitesh; Subramanian, Venkatesan

2014-11-28

The present work utilizes classical molecular dynamics simulations to investigate the covalent functionalization of carbon nanotubes (CNTs) and their interaction with ethylene glycol (EG) and water molecules. The MD simulation reveals the dispersion of functionalized carbon nanotubes and the prevention of aggregation in aqueous medium. Further, residue-wise radial distribution function (RRDF) and atomic radial distribution function (ARDF) calculations illustrate the extent of interaction of -OH and -COOH functionalized CNTs with water molecules and the non-functionalized CNT surface with EG. As the presence of the number of functionalized nanotubes increases, enhancement in the propensity for the interaction with water molecules can be observed. However, the same trend decreases for the interaction of EG molecules. In addition, the ONIOM (M06-2X/6-31+G**:AM1) calculations have also been carried out on model systems to quantitatively determine the interaction energy (IE). It is found from these calculations that the relative enhancement in the interaction of water molecules with functionalized CNTs is highly favorable when compared to the interaction of EG.

Quantum weak turbulence with applications to semiconductor lasers

NASA Astrophysics Data System (ADS)

Lvov, Yuri Victorovich

Based on a model Hamiltonian appropriate for the description of fermionic systems such as semiconductor lasers, we describe a natural asymptotic closure of the BBGKY hierarchy in complete analogy with that derived for classical weak turbulence. The main features of the interaction Hamiltonian are the inclusion of full Fermi statistics containing Pauli blocking and a simple, phenomenological, uniformly weak two particle interaction potential equivalent to the static screening approximation. The resulting asymytotic closure and quantum kinetic Boltzmann equation are derived in a self consistent manner without resorting to a priori statistical hypotheses or cumulant discard assumptions. We find a new class of solutions to the quantum kinetic equation which are analogous to the Kolmogorov spectra of hydrodynamics and classical weak turbulence. They involve finite fluxes of particles and energy across momentum space and are particularly relevant for describing the behavior of systems containing sources and sinks. We explore these solutions by using differential approximation to collision integral. We make a prima facie case that these finite flux solutions can be important in the context of semiconductor lasers. We show that semiconductor laser output efficiency can be improved by exciting these finite flux solutions. Numerical simulations of the semiconductor Maxwell Bloch equations support the claim.

Accurate classical short-range forces for the study of collision cascades in Fe–Ni–Cr

DOE PAGES

Béland, Laurent Karim; Tamm, Artur; Mu, Sai; ...

2017-05-10

The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded-atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed.more » The pairwise terms and the embedding terms of the potential are modi ed in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni 50Fe 50, Ni 80Cr 20 and Ni 33Fe 33Cr 33. The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.« less

Behavior of light polarization in photon-scalar interaction

NASA Astrophysics Data System (ADS)

Azizi, Azizollah; Nasirimoghadam, Soudabe

2017-11-01

Quantum theories of gravity help us to improve our insight into the gravitational interactions. Motivated by the interesting effect of gravity on the photon trajectory, we treat a quantum recipe concluding a classical interaction of light and a massive object such as the sun. We use the linear quantum gravity to compute the classical potential of a photon interacting with a massive scalar. The leading terms have a traditional 1/r subordinate and demonstrate a polarization-dependent behavior. This result challenges the equivalence principle; attractive and/or repulsive interactions are admissible.

A classical reactive potential for molecular clusters of sulphuric acid and water

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

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2015-10-12

We present a two state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, itmore » is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent. SMK was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; JLS and IJF were supported by the IMPACT scheme at University College London (UCL). We acknowledge the UCL Legion High Performance Computing Facility, and associated support services together with the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy under Contract No. DE-AC02- 05CH11231. JLS thanks Dr. Gregory Schenter, Dr. Theo Kurtén and Prof. Hanna Vehkamäki for important guidance and discussions.« less

Beam energy considerations for gold nano-particle enhanced radiation treatment.

PubMed

Van den Heuvel, F; Locquet, Jean-Pierre; Nuyts, S

2010-08-21

A novel approach using nano-technology enhanced radiation modalities is investigated. The proposed methodology uses antibodies labeled with organically inert metals with a high atomic number. Irradiation using photons with energies in the kilo-electron volt (keV) range shows an increase in dose due to a combination of an increase in photo-electric interactions and a pronounced generation of Auger and/or Coster-Krönig (A-CK) electrons. The dependence of the dose deposition on various factors is investigated using Monte Carlo simulation models. The factors investigated include agent concentration, spectral dependence looking at mono-energetic sources as well as classical bremsstrahlung sources. The optimization of the energy spectrum is performed in terms of physical dose enhancement as well as the dose deposited by Auger and/or Coster-Krönig electrons and their biological effectiveness. A quasi-linear dependence on concentration and an exponential decrease within the target medium is observed. The maximal dose enhancement is dependent on the position of the target in the beam. Apart from irradiation with low-photon energies (10-20 keV) there is no added benefit from the increase in generation of Auger electrons. Interestingly, a regular 110 kVp bremsstrahlung spectrum shows a comparable enhancement in comparison with the optimized mono-energetic sources. In conclusion we find that the use of enhanced nano-particles shows promise to be implemented quite easily in regular clinics on a physical level due to the advantageous properties in classical beams.

Beam energy considerations for gold nano-particle enhanced radiation treatment

NASA Astrophysics Data System (ADS)

Van den Heuvel, F.; Locquet, Jean-Pierre; Nuyts, S.

2010-08-01

A novel approach using nano-technology enhanced radiation modalities is investigated. The proposed methodology uses antibodies labeled with organically inert metals with a high atomic number. Irradiation using photons with energies in the kilo-electron volt (keV) range shows an increase in dose due to a combination of an increase in photo-electric interactions and a pronounced generation of Auger and/or Coster-Krönig (A-CK) electrons. The dependence of the dose deposition on various factors is investigated using Monte Carlo simulation models. The factors investigated include agent concentration, spectral dependence looking at mono-energetic sources as well as classical bremsstrahlung sources. The optimization of the energy spectrum is performed in terms of physical dose enhancement as well as the dose deposited by Auger and/or Coster-Krönig electrons and their biological effectiveness. A quasi-linear dependence on concentration and an exponential decrease within the target medium is observed. The maximal dose enhancement is dependent on the position of the target in the beam. Apart from irradiation with low-photon energies (10-20 keV) there is no added benefit from the increase in generation of Auger electrons. Interestingly, a regular 110 kVp bremsstrahlung spectrum shows a comparable enhancement in comparison with the optimized mono-energetic sources. In conclusion we find that the use of enhanced nano-particles shows promise to be implemented quite easily in regular clinics on a physical level due to the advantageous properties in classical beams.

Quantum algorithms for quantum field theories.

PubMed

Jordan, Stephen P; Lee, Keith S M; Preskill, John

2012-06-01

Quantum field theory reconciles quantum mechanics and special relativity, and plays a central role in many areas of physics. We developed a quantum algorithm to compute relativistic scattering probabilities in a massive quantum field theory with quartic self-interactions (φ(4) theory) in spacetime of four and fewer dimensions. Its run time is polynomial in the number of particles, their energy, and the desired precision, and applies at both weak and strong coupling. In the strong-coupling and high-precision regimes, our quantum algorithm achieves exponential speedup over the fastest known classical algorithm.

Electron removal from H and He atoms in collisions with C q+ , O q+ ions

NASA Astrophysics Data System (ADS)

Janev, R. K.; McDowell, M. R. C.

1984-06-01

Cross sections for electron capture and ionisation in collision of partially and completely stripped C q+ , N q+ and O q+ ions with hydrogen and helium atoms have been calculated at selected energies. The classical trajectory Monte Carlo method was used with a variable-charge pseudopotential to describe the interaction of the active electron with the projectile ion. A scalling relationship has been derived for the electron removal (capture and ionisation) cross section which allows a unifield representation of the data.

Algebraic classification of Weyl anomalies in arbitrary dimensions.

PubMed

Boulanger, Nicolas

2007-06-29

Conformally invariant systems involving only dimensionless parameters are known to describe particle physics at very high energy. In the presence of an external gravitational field, the conformal symmetry may generalize to the Weyl invariance of classical massless field systems in interaction with gravity. In the quantum theory, the latter symmetry no longer survives: A Weyl anomaly appears. Anomalies are a cornerstone of quantum field theory, and, for the first time, a general, purely algebraic understanding of the universal structure of the Weyl anomalies is obtained, in arbitrary dimensions and independently of any regularization scheme.

Structural interactions in ionic liquids linked to higher-order Poisson-Boltzmann equations

NASA Astrophysics Data System (ADS)

Blossey, R.; Maggs, A. C.; Podgornik, R.

2017-06-01

We present a derivation of generalized Poisson-Boltzmann equations starting from classical theories of binary fluid mixtures, employing an approach based on the Legendre transform as recently applied to the case of local descriptions of the fluid free energy. Under specific symmetry assumptions, and in the linearized regime, the Poisson-Boltzmann equation reduces to a phenomenological equation introduced by Bazant et al. [Phys. Rev. Lett. 106, 046102 (2011)], 10.1103/PhysRevLett.106.046102, whereby the structuring near the surface is determined by bulk coefficients.

Quasistatic elastoplasticity via Peridynamics: existence and localization

NASA Astrophysics Data System (ADS)

Kružík, Martin; Mora-Corral, Carlos; Stefanelli, Ulisse

2018-04-01

Peridynamics is a nonlocal continuum mechanical theory based on minimal regularity on the deformations. Its key trait is that of replacing local constitutive relations featuring spacial differential operators with integrals over differences of displacement fields over a suitable positive interaction range. The advantage of such perspective is that of directly including nonregular situations, in which discontinuities in the displacement field may occur. In the linearized elastic setting, the mechanical foundation of the theory and its mathematical amenability have been thoroughly analyzed in the last years. We present here the extension of Peridynamics to linearized elastoplasticity. This calls for considering the time evolution of elastic and plastic variables, as the effect of a combination of elastic energy storage and plastic energy dissipation mechanisms. The quasistatic evolution problem is variationally reformulated and solved by time discretization. In addition, by a rigorous evolutive Γ -convergence argument we prove that the nonlocal peridynamic model converges to classic local elastoplasticity as the interaction range goes to zero.

Classical density-functional theory of inhomogeneous water including explicit molecular structure and nonlinear dielectric response.

PubMed

Lischner, Johannes; Arias, T A

2010-02-11

We present an accurate free-energy functional for liquid water written in terms of a set of effective potential fields in which fictitious noninteracting water molecules move. The functional contains an exact expression of the entropy of noninteracting molecules and thus provides an ideal starting point for the inclusion of complex intermolecular interactions which depend on the orientation of the interacting molecules. We show how an excess free-energy functional can be constructed to reproduce the following properties of water: the dielectric response; the experimental site-site correlation functions; the surface tension; the bulk modulus of the liquid and the variation of this modulus with pressure; the density of the liquid and the vapor phase; and liquid-vapor coexistence. As a demonstration, we present results for the application of this theory to the behavior of liquid water in a parallel plate capacitor. In particular, we make predictions for the dielectric response of water in the nonlinear regime, finding excellent agreement with known data.

Dissipation of 'dark energy' by cortex in knowledge retrieval.

PubMed

Capolupo, Antonio; Freeman, Walter J; Vitiello, Giuseppe

2013-03-01

We have devised a thermodynamic model of cortical neurodynamics expressed at the classical level by neural networks and at the quantum level by dissipative quantum field theory. Our model is based on features in the spatial images of cortical activity newly revealed by high-density electrode arrays. We have incorporated the mechanism and necessity for so-called dark energy in knowledge retrieval. We have extended the model first using the Carnot cycle to define our measures for energy, entropy and temperature, and then using the Rankine cycle to incorporate criticality and phase transitions. We describe the dynamics of two interactive fields of neural activity that express knowledge, one at high and the other at low energy density, and the two operators that create and annihilate the fields. We postulate that the extremely high density of energy sequestered briefly in cortical activity patterns can account for the vividness, richness of associations, and emotional intensity of memories recalled by stimuli. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantum shielding effects on the Gamow penetration factor for nuclear fusion reaction in quantum plasmas

NASA Astrophysics Data System (ADS)

Lee, Myoung-Jae; Jung, Young-Dae

2017-01-01

The quantum shielding effects on the nuclear fusion reaction process are investigated in quantum plasmas. The closed expression of the classical turning point for the Gamow penetration factor in quantum plasmas is obtained by the Lambert W-function. The closed expressions of the Gamow penetration factor and the cross section for the nuclear fusion reaction in quantum plasmas are obtained as functions of the plasmon energy and the relative kinetic energy by using the effective interaction potential with the WKB analysis. It is shown that the influence of quantum screening suppresses the Sommerfeld reaction factor. It is also shown that the Gamow penetration factor increases with an increase of the plasmon energy. It is also shown that the quantum shielding effect enhances the deuterium formation by the proton-proton reaction in quantum plasmas. In addition, it is found that the energy dependences on the reaction cross section and the Gamow penetration factor are more significant in high plasmon-energy domains.

On a quantum particle in laser channels

NASA Astrophysics Data System (ADS)

Dik, A. V.; Frolov, E. N.; Dabagov, S. B.

2018-02-01

In this paper the effective potential describing interaction of a scalar quantum particle with arbitrary nonuniform laser field is derived for a wide spectrum of the particle energies. The presented method allows to take into account all the features of the effective potential for a scalar particle. The derived expression for effective potential for quantum particle has the same form as the one presented earlier for a classical particle. A special case for channeling of a quantum particle as well as accompanying channeling radiation in a field formed by two crossed plane laser waves is considered. It is shown that relativistic particles moving near the laser channel bottom should be examined as quantum ones at both arbitrarily large longitudinal energies and laser fields of accessible intensities.

A Short Essay on the Uses of Free Energy

ERIC Educational Resources Information Center

Koutandos, Spyridon

2013-01-01

In this article we examine cases of more classical and less classical nature compared to results found by quantum mechanics and attribute a form of Free Energy discontinuity for each case within a boundary layer. The concept of a boundary layer is broadened as to include areas of first or second variations of the Gibbs free energy. It is…

Detecting gravitational decoherence with clocks: Limits on temporal resolution from a classical-channel model of gravity

NASA Astrophysics Data System (ADS)

Khosla, Kiran E.; Altamirano, Natacha

2017-05-01

The notion of time is given a different footing in quantum mechanics and general relativity, treated as a parameter in the former and being an observer-dependent property in the latter. From an operational point of view time is simply the correlation between a system and a clock, where an idealized clock can be modeled as a two-level system. We investigate the dynamics of clocks interacting gravitationally by treating the gravitational interaction as a classical information channel. This model, known as the classical-channel gravity (CCG), postulates that gravity is mediated by a fundamentally classical force carrier and is therefore unable to entangle particles gravitationally. In particular, we focus on the decoherence rates and temporal resolution of arrays of N clocks, showing how the minimum dephasing rate scales with N , and the spatial configuration. Furthermore, we consider the gravitational redshift between a clock and a massive particle and show that a classical-channel model of gravity predicts a finite-dephasing rate from the nonlocal interaction. In our model we obtain a fundamental limitation in time accuracy that is intrinsic to each clock.

Graph-theoretic quantum system modelling for neuronal microtubules as hierarchical clustered quantum Hopfield networks

NASA Astrophysics Data System (ADS)

Srivastava, D. P.; Sahni, V.; Satsangi, P. S.

2014-08-01

Graph-theoretic quantum system modelling (GTQSM) is facilitated by considering the fundamental unit of quantum computation and information, viz. a quantum bit or qubit as a basic building block. Unit directional vectors "ket 0" and "ket 1" constitute two distinct fundamental quantum across variable orthonormal basis vectors, for the Hilbert space, specifying the direction of propagation of information, or computation data, while complementary fundamental quantum through, or flow rate, variables specify probability parameters, or amplitudes, as surrogates for scalar quantum information measure (von Neumann entropy). This paper applies GTQSM in continuum of protein heterodimer tubulin molecules of self-assembling polymers, viz. microtubules in the brain as a holistic system of interacting components representing hierarchical clustered quantum Hopfield network, hQHN, of networks. The quantum input/output ports of the constituent elemental interaction components, or processes, of tunnelling interactions and Coulombic bidirectional interactions are in cascade and parallel interconnections with each other, while the classical output ports of all elemental components are interconnected in parallel to accumulate micro-energy functions generated in the system as Hamiltonian, or Lyapunov, energy function. The paper presents an insight, otherwise difficult to gain, for the complex system of systems represented by clustered quantum Hopfield network, hQHN, through the application of GTQSM construct.

Canonical-ensemble state-averaged complete active space self-consistent field (SA-CASSCF) strategy for problems with more diabatic than adiabatic states: Charge-bond resonance in monomethine cyanines

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

Olsen, Seth, E-mail: seth.olsen@uq.edu.au

2015-01-28

This paper reviews basic results from a theory of the a priori classical probabilities (weights) in state-averaged complete active space self-consistent field (SA-CASSCF) models. It addresses how the classical probabilities limit the invariance of the self-consistency condition to transformations of the complete active space configuration interaction (CAS-CI) problem. Such transformations are of interest for choosing representations of the SA-CASSCF solution that are diabatic with respect to some interaction. I achieve the known result that a SA-CASSCF can be self-consistently transformed only within degenerate subspaces of the CAS-CI ensemble density matrix. For uniformly distributed (“microcanonical”) SA-CASSCF ensembles, self-consistency is invariant tomore » any unitary CAS-CI transformation that acts locally on the ensemble support. Most SA-CASSCF applications in current literature are microcanonical. A problem with microcanonical SA-CASSCF models for problems with “more diabatic than adiabatic” states is described. The problem is that not all diabatic energies and couplings are self-consistently resolvable. A canonical-ensemble SA-CASSCF strategy is proposed to solve the problem. For canonical-ensemble SA-CASSCF, the equilibrated ensemble is a Boltzmann density matrix parametrized by its own CAS-CI Hamiltonian and a Lagrange multiplier acting as an inverse “temperature,” unrelated to the physical temperature. Like the convergence criterion for microcanonical-ensemble SA-CASSCF, the equilibration condition for canonical-ensemble SA-CASSCF is invariant to transformations that act locally on the ensemble CAS-CI density matrix. The advantage of a canonical-ensemble description is that more adiabatic states can be included in the support of the ensemble without running into convergence problems. The constraint on the dimensionality of the problem is relieved by the introduction of an energy constraint. The method is illustrated with a complete active space valence-bond (CASVB) analysis of the charge/bond resonance electronic structure of a monomethine cyanine: Michler’s hydrol blue. The diabatic CASVB representation is shown to vary weakly for “temperatures” corresponding to visible photon energies. Canonical-ensemble SA-CASSCF enables the resolution of energies and couplings for all covalent and ionic CASVB structures contributing to the SA-CASSCF ensemble. The CASVB solution describes resonance of charge- and bond-localized electronic structures interacting via bridge resonance superexchange. The resonance couplings can be separated into channels associated with either covalent charge delocalization or chemical bonding interactions, with the latter significantly stronger than the former.« less

Canonical-ensemble state-averaged complete active space self-consistent field (SA-CASSCF) strategy for problems with more diabatic than adiabatic states: charge-bond resonance in monomethine cyanines.

PubMed

Olsen, Seth

2015-01-28

This paper reviews basic results from a theory of the a priori classical probabilities (weights) in state-averaged complete active space self-consistent field (SA-CASSCF) models. It addresses how the classical probabilities limit the invariance of the self-consistency condition to transformations of the complete active space configuration interaction (CAS-CI) problem. Such transformations are of interest for choosing representations of the SA-CASSCF solution that are diabatic with respect to some interaction. I achieve the known result that a SA-CASSCF can be self-consistently transformed only within degenerate subspaces of the CAS-CI ensemble density matrix. For uniformly distributed ("microcanonical") SA-CASSCF ensembles, self-consistency is invariant to any unitary CAS-CI transformation that acts locally on the ensemble support. Most SA-CASSCF applications in current literature are microcanonical. A problem with microcanonical SA-CASSCF models for problems with "more diabatic than adiabatic" states is described. The problem is that not all diabatic energies and couplings are self-consistently resolvable. A canonical-ensemble SA-CASSCF strategy is proposed to solve the problem. For canonical-ensemble SA-CASSCF, the equilibrated ensemble is a Boltzmann density matrix parametrized by its own CAS-CI Hamiltonian and a Lagrange multiplier acting as an inverse "temperature," unrelated to the physical temperature. Like the convergence criterion for microcanonical-ensemble SA-CASSCF, the equilibration condition for canonical-ensemble SA-CASSCF is invariant to transformations that act locally on the ensemble CAS-CI density matrix. The advantage of a canonical-ensemble description is that more adiabatic states can be included in the support of the ensemble without running into convergence problems. The constraint on the dimensionality of the problem is relieved by the introduction of an energy constraint. The method is illustrated with a complete active space valence-bond (CASVB) analysis of the charge/bond resonance electronic structure of a monomethine cyanine: Michler's hydrol blue. The diabatic CASVB representation is shown to vary weakly for "temperatures" corresponding to visible photon energies. Canonical-ensemble SA-CASSCF enables the resolution of energies and couplings for all covalent and ionic CASVB structures contributing to the SA-CASSCF ensemble. The CASVB solution describes resonance of charge- and bond-localized electronic structures interacting via bridge resonance superexchange. The resonance couplings can be separated into channels associated with either covalent charge delocalization or chemical bonding interactions, with the latter significantly stronger than the former.

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

Zhang, Ying-Jie, E-mail: yingjiezhang@qfnu.edu.cn; Han, Wei; Xia, Yun-Jie, E-mail: yjxia@qfnu.edu.cn

We propose a scheme of controlling entanglement dynamics of a quantum system by applying the external classical driving field for two atoms separately located in a single-mode photon cavity. It is shown that, with a judicious choice of the classical-driving strength and the atom–photon detuning, the effective atom–photon interaction Hamiltonian can be switched from Jaynes–Cummings model to anti-Jaynes–Cummings model. By tuning the controllable atom–photon interaction induced by the classical field, we illustrate that the evolution trajectory of the Bell-like entanglement states can be manipulated from entanglement-sudden-death to no-entanglement-sudden-death, from no-entanglement-invariant to entanglement-invariant. Furthermore, the robustness of the initial Bell-like entanglementmore » can be improved by the classical driving field in the leaky cavities. This classical-driving-assisted architecture can be easily extensible to multi-atom quantum system for scalability.« less

Classical Trajectories and Quantum Spectra

NASA Technical Reports Server (NTRS)

Mielnik, Bogdan; Reyes, Marco A.

1996-01-01

A classical model of the Schrodinger's wave packet is considered. The problem of finding the energy levels corresponds to a classical manipulation game. It leads to an approximate but non-perturbative method of finding the eigenvalues, exploring the bifurcations of classical trajectories. The role of squeezing turns out decisive in the generation of the discrete spectra.

Model lipid bilayers mimic non-specific interactions of gold nanoparticles with macrophage plasma membranes.

PubMed

Montis, Costanza; Generini, Viola; Boccalini, Giulia; Bergese, Paolo; Bani, Daniele; Berti, Debora

2018-04-15

Understanding the interaction between nanomaterials and biological interfaces is a key unmet goal that still hampers clinical translation of nanomedicine. Here we investigate and compare non-specific interaction of gold nanoparticles (AuNPs) with synthetic lipid and wild type macrophage membranes. A comprehensive data set was generated by systematically varying the structural and physicochemical properties of the AuNPs (size, shape, charge, surface functionalization) and of the synthetic membranes (composition, fluidity, bending properties and surface charge), which allowed to unveil the matching conditions for the interaction of the AuNPs with macrophage plasma membranes in vitro. This effort directly proved for the first time that synthetic bilayers can be set to mimic and predict with high fidelity key aspects of nanoparticle interaction with macrophage eukaryotic plasma membranes. It then allowed to model the experimental observations according to classical interface thermodynamics and in turn determine the paramount role played by non-specific contributions, primarily electrostatic, Van der Waals and bending energy, in driving nanoparticle-plasma membrane interactions. Copyright © 2018 Elsevier Inc. All rights reserved.

Medium-induced change of the optical response of metal clusters in rare-gas matrices

NASA Astrophysics Data System (ADS)

Xuan, Fengyuan; Guet, Claude

2017-10-01

Interaction with the surrounding medium modifies the optical response of embedded metal clusters. For clusters from about ten to a few hundreds of silver atoms, embedded in rare-gas matrices, we study the environment effect within the matrix random phase approximation with exact exchange (RPAE) quantum approach, which has proved successful for free silver clusters. The polarizable surrounding medium screens the residual two-body RPAE interaction, adds a polarization term to the one-body potential, and shifts the vacuum energy of the active delocalized valence electrons. Within this model, we calculate the dipole oscillator strength distribution for Ag clusters embedded in helium droplets, neon, argon, krypton, and xenon matrices. The main contribution to the dipole surface plasmon red shift originates from the rare-gas polarization screening of the two-body interaction. The large size limit of the dipole surface plasmon agrees well with the classical prediction.

Homogeneous quantum electrodynamic turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.

1992-01-01

The electromagnetic field equations and Dirac equations for oppositely charged wave functions are numerically time-integrated using a spatial Fourier method. The numerical approach used, a spectral transform technique, is based on a continuum representation of physical space. The coupled classical field equations contain a dimensionless parameter which sets the strength of the nonlinear interaction (as the parameter increases, interaction volume decreases). For a parameter value of unity, highly nonlinear behavior in the time-evolution of an individual wave function, analogous to ideal fluid turbulence, is observed. In the truncated Fourier representation which is numerically implemented here, the quantum turbulence is homogeneous but anisotropic and manifests itself in the nonlinear evolution of equilibrium modal spatial spectra for the probability density of each particle and also for the electromagnetic energy density. The results show that nonlinearly interacting fermionic wave functions quickly approach a multi-mode, dynamic equilibrium state, and that this state can be determined by numerical means.

Investigating Student Understanding for a Statistical Analysis of Two Thermally Interacting Solids

NASA Astrophysics Data System (ADS)

Loverude, Michael E.

2010-10-01

As part of an ongoing research and curriculum development project for upper-division courses in thermal physics, we have developed a sequence of tutorials in which students apply statistical methods to examine the behavior of two interacting Einstein solids. In the sequence, students begin with simple results from probability and develop a means for counting the states in a single Einstein solid. The students then consider the thermal interaction of two solids, and observe that the classical equilibrium state corresponds to the most probable distribution of energy between the two solids. As part of the development of the tutorial sequence, we have developed several assessment questions to probe student understanding of various aspects of this system. In this paper, we describe the strengths and weaknesses of student reasoning, both qualitative and quantitative, to assess the readiness of students for one tutorial in the sequence.

Motion of isolated open vortex filaments evolving under the truncated local induction approximation

NASA Astrophysics Data System (ADS)

Van Gorder, Robert A.

2017-11-01

The study of nonlinear waves along open vortex filaments continues to be an area of active research. While the local induction approximation (LIA) is attractive due to locality compared with the non-local Biot-Savart formulation, it has been argued that LIA appears too simple to model some relevant features of Kelvin wave dynamics, such as Kelvin wave energy transfer. Such transfer of energy is not feasible under the LIA due to integrability, so in order to obtain a non-integrable model, a truncated LIA, which breaks the integrability of the classical LIA, has been proposed as a candidate model with which to study such dynamics. Recently Laurie et al. ["Interaction of Kelvin waves and nonlocality of energy transfer in superfluids," Phys. Rev. B 81, 104526 (2010)] derived truncated LIA systematically from Biot-Savart dynamics. The focus of the present paper is to study the dynamics of a section of common open vortex filaments under the truncated LIA dynamics. We obtain the analog of helical, planar, and more general filaments which rotate without a change in form in the classical LIA, demonstrating that while quantitative differences do exist, qualitatively such solutions still exist under the truncated LIA. Conversely, solitons and breather solutions found under the LIA should not be expected under the truncated LIA, as the existence of such solutions relies on the existence of an infinite number of conservation laws which is violated due to loss of integrability. On the other hand, similarity solutions under the truncated LIA can be quite different to their counterparts found for the classical LIA, as they must obey a t1/3 type scaling rather than the t1/2 type scaling commonly found in the LIA and Biot-Savart dynamics. This change in similarity scaling means that Kelvin waves are radiated at a slower rate from vortex kinks formed after reconnection events. The loss of soliton solutions and the difference in similarity scaling indicate that dynamics emergent under the truncated LIA can indeed differ a great deal from those previously studied under the classical LIA.

Catenanes: A molecular mechanics analysis of the (C13H26)2 Structure 13-13 D2.

PubMed

Lii, Jenn-Huei; Allinger, Norman L; Hu, Ching-Han; Schaefer, Henry F

2016-01-05

Molecular mechanics (MM4) studies have been carried out on the catenane (C13H26)2, specifically 13-13D2. The structure obtained is in general agreement with second-order perturbation theory. More importantly, the MM4 structure allows a breakdown of the energy of the molecule into its component classical parts. This allows an understanding of why the structure is so distorted, in terms of C-C bonding and nonbonding interactions, van der Waals repulsion, C-C-C and C-C-H angle bending, torsional energies, stretch-bend, torsion-stretch, and bend-torsion-bend interactions. Clearly, the hole in 113-membered ring is too small for the other ring to fit through comfortably. There are too many atoms trying to fit into the limited space at the same time, leading to large van der Waals repulsions. The rings distort in such a way as to enlarge this available space, and lower the total energy of the molecule. While the distortions are spread around the rings, one of the nominally tetrahedral C-C-C bond angles in each ring is opened to 147.9° by MM4 (146.8° by MP2). The stability of the compound is discussed in terms of the strain energy. © 2015 Wiley Periodicals, Inc.

Coherent Structures in Magnetic Confinement Systems

NASA Astrophysics Data System (ADS)

Horton, W.

2006-04-01

Coherent structures are long-lived, nonlinear localized solutions of the selfconsistient plasma-electromagnetic field equations. They contain appreciable energy density and control various transport and magnetic reconnection processes in plasmas. These structures are self-binding from the nonlinearity balancing, or overcoming, the wave dispersion of energy in smaller amplitude structures. The structures evolve out of the nonlinear interactions in various instabilities or external driving fields. The theoretical basis for these structures are reviewed giving examples from various plasma instabilities and their reduced descriptions from the appropriate partial differential equations. A classic example from drift waves is the formation of monopole, dipole and tripolar vortex structures which have been created in both laboratory and simulation experiments. For vortices, the long life-time and nonlinear interactions of the structures can be understood with conservation laws of angular momentum given by the vorticity field associated with dynamics. Other morphologies include mushrooms, Kelvin-Helmholtz vorticity roll-up, streamers and blobs. We show simulation movies of various examples drawn from ETG modes in NSTX, H-mode like shear flow layers in LAPD and the vortices measured with soft x-ray tomography in the GAMMA 10 tandem mirror. Coherent current-sheet structures form in driven magnetic reconnection layers and control the rate of transformation of magnetic energy to flow and thermal energy.

Features of primary damage by high energy displacement cascades in concentrated Ni-based alloys

DOE PAGES

Béland, Laurent Karim; Lu, Chenyang; Osetskiy, Yuri N.; ...

2016-02-25

Alloying of Ni with Fe or Co reduces primary damage production under ion irradiation. Similar results have been obtained from classical molecular dynamics simulations of 1, 10, 20, and 40 keV collision cascades in Ni, NiFe, and NiCo. In all cases, a mix of imperfect stacking fault tetrahedra, faulted loops with a 1/3 {111} Burgers vector, and glissile interstitial loops with a 1/2 {110} Burgers vector were formed, along with small sessile point defect complexes and clusters. Primary damage reduction occurs by three mechanisms. First, Ni-Co, Ni-Fe, Co-Co, and Fe-Fe short-distance repulsive interactions are stiffer than Ni-Ni interactions, which leadmore » to a decrease in damage formation during the transition from the supersonic ballistic regime to the sonic regime. This largely controls final defect production. Second, alloying decreases thermal conductivity, leading to a longer thermal spike lifetime. The associated annealing reduces final damage production. These two mechanisms are especially important at cascades energies less than 40 keV. Third, at the higher energies, the production of large defect clusters by subcascades is inhibited in the alloys. A number of challenges and limitations pertaining to predictive atomistic modeling of alloys under high-energy particle irradiation are discussed.« less

A semi-classical approach to the calculation of highly excited rotational energies for asymmetric-top molecules

PubMed Central

Schmiedt, Hanno; Schlemmer, Stephan; Yurchenko, Sergey N.; Yachmenev, Andrey

2017-01-01

We report a new semi-classical method to compute highly excited rotational energy levels of an asymmetric-top molecule. The method forgoes the idea of a full quantum mechanical treatment of the ro-vibrational motion of the molecule. Instead, it employs a semi-classical Green's function approach to describe the rotational motion, while retaining a quantum mechanical description of the vibrations. Similar approaches have existed for some time, but the method proposed here has two novel features. First, inspired by the path integral method, periodic orbits in the phase space and tunneling paths are naturally obtained by means of molecular symmetry analysis. Second, the rigorous variational method is employed for the first time to describe the molecular vibrations. In addition, we present a new robust approach to generating rotational energy surfaces for vibrationally excited states; this is done in a fully quantum-mechanical, variational manner. The semi-classical approach of the present work is applied to calculating the energies of very highly excited rotational states and it reduces dramatically the computing time as well as the storage and memory requirements when compared to the fullly quantum-mechanical variational approach. Test calculations for excited states of SO2 yield semi-classical energies in very good agreement with the available experimental data and the results of fully quantum-mechanical calculations. PMID:28000807

Mixed quantum/classical investigation of the photodissociation of NH3(Ã) and a practical method for maintaining zero-point energy in classical trajectories

NASA Astrophysics Data System (ADS)

Bonhommeau, David; Truhlar, Donald G.

2008-07-01

The photodissociation dynamics of ammonia upon excitation of the out-of-plane bending mode (mode ν2 with n2=0,…,6 quanta of vibration) in the à electronic state is investigated by means of several mixed quantum/classical methods, and the calculated final-state properties are compared to experiments. Five mixed quantum/classical methods are tested: one mean-field approach (the coherent switching with decay of mixing method), two surface-hopping methods [the fewest switches with time uncertainty (FSTU) and FSTU with stochastic decay (FSTU/SD) methods], and two surface-hopping methods with zero-point energy (ZPE) maintenance [the FSTU /SD+trajectory projection onto ZPE orbit (TRAPZ) and FSTU /SD+minimal TRAPZ (mTRAPZ) methods]. We found a qualitative difference between final NH2 internal energy distributions obtained for n2=0 and n2>1, as observed in experiments. Distributions obtained for n2=1 present an intermediate behavior between distributions obtained for smaller and larger n2 values. The dynamics is found to be highly electronically nonadiabatic with all these methods. NH2 internal energy distributions may have a negative energy tail when the ZPE is not maintained throughout the dynamics. The original TRAPZ method was designed to maintain ZPE in classical trajectories, but we find that it leads to unphysically high internal vibrational energies. The mTRAPZ method, which is new in this work and provides a general method for maintaining ZPE in either single-surface or multisurface trajectories, does not lead to unphysical results and is much less time consuming. The effect of maintaining ZPE in mixed quantum/classical dynamics is discussed in terms of agreement with experimental findings. The dynamics for n2=0 and n2=6 are also analyzed to reveal details not available from experiment, in particular, the time required for quenching of electronic excitation and the adiabatic energy gap and geometry at the time of quenching.

Mixed quantum/classical investigation of the photodissociation of NH3(A) and a practical method for maintaining zero-point energy in classical trajectories.

PubMed

Bonhommeau, David; Truhlar, Donald G

2008-07-07

The photodissociation dynamics of ammonia upon excitation of the out-of-plane bending mode (mode nu(2) with n(2)=0,[ellipsis (horizontal)],6 quanta of vibration) in the A electronic state is investigated by means of several mixed quantum/classical methods, and the calculated final-state properties are compared to experiments. Five mixed quantum/classical methods are tested: one mean-field approach (the coherent switching with decay of mixing method), two surface-hopping methods [the fewest switches with time uncertainty (FSTU) and FSTU with stochastic decay (FSTU/SD) methods], and two surface-hopping methods with zero-point energy (ZPE) maintenance [the FSTUSD+trajectory projection onto ZPE orbit (TRAPZ) and FSTUSD+minimal TRAPZ (mTRAPZ) methods]. We found a qualitative difference between final NH(2) internal energy distributions obtained for n(2)=0 and n(2)>1, as observed in experiments. Distributions obtained for n(2)=1 present an intermediate behavior between distributions obtained for smaller and larger n(2) values. The dynamics is found to be highly electronically nonadiabatic with all these methods. NH(2) internal energy distributions may have a negative energy tail when the ZPE is not maintained throughout the dynamics. The original TRAPZ method was designed to maintain ZPE in classical trajectories, but we find that it leads to unphysically high internal vibrational energies. The mTRAPZ method, which is new in this work and provides a general method for maintaining ZPE in either single-surface or multisurface trajectories, does not lead to unphysical results and is much less time consuming. The effect of maintaining ZPE in mixed quantum/classical dynamics is discussed in terms of agreement with experimental findings. The dynamics for n(2)=0 and n(2)=6 are also analyzed to reveal details not available from experiment, in particular, the time required for quenching of electronic excitation and the adiabatic energy gap and geometry at the time of quenching.

Cache and energy efficient algorithms for Nussinov's RNA Folding.

PubMed

Zhao, Chunchun; Sahni, Sartaj

2017-12-06

An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.

Shapes, spectra and new methods in nonlinear spatial optics

NASA Astrophysics Data System (ADS)

Sun, Can

For a myriad of optical applications, the quality of the light source is poor and the beam is inherently spatially partially-coherent. For this broad class of systems, wave dynamics depends not only on the wave intensity, but also on its distribution of spatial frequencies. Unfortunately, this entire spectrum of problems has often been overlooked - for reasons of theoretical ease or experimental difficulties. Here, we remedy this by demonstrating a novel experimental setup which, for the first time, allows arbitrarily modulation of the spatial spectra of light to obtain any distribution of interest. Using modulation instability as an example, we isolate the effect of different spectral shapes and observe distinct beam dynamics. Next, we turn to a thermodynamic description of the long-term evolution of statistical fields. For quantum systems, a major consequence is Bose-Einstein Condensation. However, recent theoretical studies have suggested that quantum mechanics is not necessary for the condensation process: classical waves with random phases can also self-organize into a coherent state. Starting from a random ensemble, nonlinear interactions can lead to a turbulent energy cascade towards longer spatial scales. In complete analogy with the kinetics of a gas system, there is a statistical dynamics of waves in which particle velocities map to wavepacket k-vectors while collisions are mimicked by four-wave mixing. As with collisions, each wave interaction is formally reversible, yet entropy principles mandate that the ensemble evolves towards an equilibrium state of maximum disorder. The result is an equipartition of energy, in the form of a Rayleigh-Jeans spectrum, with information about the condensation process recorded in small-scale fluctuations. Here, we give the first experimental observation of the condensation of classical waves in any media. Using classical light in a self-defocusing photorefractive, we observe all aspects of the condensation process, including the population of a coherent state, spectral redistribution towards the Rayleigh-Jeans spectrum, and formal reversibility of the interactions. The latter is proved experimentally by introducing a digital "Maxwell's Demon" to reverse (phase-conjugate) the momentum of each wavepacket and recover the original "thermal cloud". The results integrate digital and physical methods of nonlinear processing, confirm fundamental ideas in wave turbulence, and greatly extend the range of Bose-Einstein theory.

Quasi-classical approaches to vibronic spectra revisited

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Frustration by competing interactions in the highly-distorted double perovskites La2NaRuO6 and La2NaOsO6

NASA Astrophysics Data System (ADS)

Aczel, A. A.; Bugaris, D. E.; Li, L.; Yan, J.-Q.; de La Cruz, C.; Zur Loye, H.-C.; Nagler, S. E.

2013-03-01

The usual classical behavior of S = 3/2, B-site ordered double perovskites results in simple, commensurate magnetic ground states. In contrast, heat capacity and neutron powder diffraction measurements for the S = 3/2 systems La2NaB'O6 (B' = Ru, Os) reveal an incommensurate magnetic ground state for La2NaRuO6 and a drastically suppressed ordered moment for La2NaOsO6. This behavior is attributed to the large monoclinic structural distortions of these double perovskites. The distortions have the effect of weakening the nearest neighbor superexchange interactions, presumably to an energy scale that is comparable to the next nearest neighbor superexchange. The exotic ground states in these materials can then arise from a competition between these two types of antiferromagnetic interactions, providing a novel mechanism for achieving frustration in the double perovskite family. Work at ORNL is supported by the Division of Scientific User Facilities and the Materials Science and Engineering Division, DOE Basic Energy Sciences. Work at the University of South Carolina is supported by the Heterogeneous Functional Materials Research Center, funded by DOE under award number de-sc0001061.

Electrifying model catalysts for understanding electrocatalytic reactions in liquid electrolytes.

PubMed

Faisal, Firas; Stumm, Corinna; Bertram, Manon; Waidhas, Fabian; Lykhach, Yaroslava; Cherevko, Serhiy; Xiang, Feifei; Ammon, Maximilian; Vorokhta, Mykhailo; Šmíd, Břetislav; Skála, Tomáš; Tsud, Nataliya; Neitzel, Armin; Beranová, Klára; Prince, Kevin C; Geiger, Simon; Kasian, Olga; Wähler, Tobias; Schuster, Ralf; Schneider, M Alexander; Matolín, Vladimír; Mayrhofer, Karl J J; Brummel, Olaf; Libuda, Jörg

2018-07-01

Electrocatalysis is at the heart of our future transition to a renewable energy system. Most energy storage and conversion technologies for renewables rely on electrocatalytic processes and, with increasing availability of cheap electrical energy from renewables, chemical production will witness electrification in the near future 1-3 . However, our fundamental understanding of electrocatalysis lags behind the field of classical heterogeneous catalysis that has been the dominating chemical technology for a long time. Here, we describe a new strategy to advance fundamental studies on electrocatalytic materials. We propose to 'electrify' complex oxide-based model catalysts made by surface science methods to explore electrocatalytic reactions in liquid electrolytes. We demonstrate the feasibility of this concept by transferring an atomically defined platinum/cobalt oxide model catalyst into the electrochemical environment while preserving its atomic surface structure. Using this approach, we explore particle size effects and identify hitherto unknown metal-support interactions that stabilize oxidized platinum at the nanoparticle interface. The metal-support interactions open a new synergistic reaction pathway that involves both metallic and oxidized platinum. Our results illustrate the potential of the concept, which makes available a systematic approach to build atomically defined model electrodes for fundamental electrocatalytic studies.

Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD

NASA Astrophysics Data System (ADS)

Blanco-Díaz, Edgar G.; Vázquez-Montelongo, Erik A.; Cisneros, G. Andrés; Castrejón-González, Edgar Omar

2018-02-01

Non-covalent interactions (NCIs) play a crucial role in the behavior and properties of ionic liquids (ILs). These interactions are particularly important for non-equilibrium properties such as the change in viscosity due to shearing forces (shear viscosity). Therefore, a detailed understanding of these interactions can improve our understanding of these important classes of liquids. Here, we have employed quantum mechanical energy decomposition analysis (EDA) and NCI analysis to investigate a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. EDA based on symmetry-adapted perturbation theory (SAPT) for the complete monomers, as well as fragment SAPT (FSAPT), for the functional fragments has been carried out. In general, the electrostatic component comprises ≈80% of the intermolecular interaction, and significant contributions from other components (induction and dispersion) are also observed, especially for interactions involving bifurcated hydrogen bonds. The FSAPT analysis suggests that caution is warranted when employing simplified assumptions for non-bonded interactions, e.g., focusing only on hydrogen bonds between functional fragments, since this view may not provide a complete picture of the complicated interactions between the ions. In non-equilibrium molecular dynamics, the total interaction energies of some fragments have a significant qualitative change as the shear rate increases. Our results indicate that the inter-fragment interactions play a fundamental role in the viscous behavior of ILs, suggesting that the exclusive use of geometric criteria to analyze inter-molecular interactions in these systems is not sufficient to investigate shear-thinning effects.

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

PubMed

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

2018-01-01

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

Nonlinear Schrödinger equation and classical-field description of thermal radiation

NASA Astrophysics Data System (ADS)

Rashkovskiy, Sergey A.

2018-03-01

It is shown that the thermal radiation can be described without quantization of energy in the framework of classical field theory using the nonlinear Schrödinger equation which is considered as a classical field equation. Planck's law for the spectral energy density of thermal radiation and the Einstein A-coefficient for spontaneous emission are derived without using the concept of the energy quanta. It is shown that the spectral energy density of thermal radiation is apparently not a universal function of frequency, as follows from the Planck's law, but depends weakly on the nature of atoms, while Planck's law is valid only as an approximation in the limit of weak excitation of atoms. Spin and relativistic effects are not considered in this paper.

Testing the QGSJET01 and QGSJETII-04 models with the help of atmospheric muons

NASA Astrophysics Data System (ADS)

Dedenko, Leonid G.; Lukyashin, Anton V.; Roganova, Tatiana M.; Fedorova, Galina F.

2017-06-01

More accurate original calculations of the atmospheric vertical muon energy spectra at energies 102 - 105 GeV have been carried out in terms of the QGSJET01 and QGSJETII-04 models. The Gaisser-Honda approximations of the measured energy spectra of primary protons, helium and nitrogen nuclei have been used. The CORSIKA package has been used to simulate cascades in the standard atmosphere induced by different primary particles with various fixed energies E. Statistics of simulated cascades for secondary particles with energies (0.01 - 1) · E was increased up to 106. It has been shown that predictions of the QGSJET01 and QGSJETII-04 models for these muon fluxes are below the data of the classical experiments L3 + Cosmic, MACRO and LVD by factors of ˜ 1.7-2 at energies above 102 GeV. It has been concluded that these tested models underestimate the production of the most energetic secondary particles, namely, π-mesons and K-mesons, in interactions of primary protons and other primary nuclei with nuclei in the atmosphere by the same factors.

A tungsten-rhenium interatomic potential for point defect studies

DOE PAGES

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-28

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

A tungsten-rhenium interatomic potential for point defect studies

NASA Astrophysics Data System (ADS)

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-01

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).

A tungsten-rhenium interatomic potential for point defect studies

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

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

First-principles binary diffusion coefficients for H, H 2 and four normal alkanes + N 2

DOE PAGES

Jasper, Ahren W.; Kamarchik, Eugene; Miller, James A.; ...

2014-09-30

Collision integrals related to binary (dilute gas) diffusion are calculated classically for six species colliding with N 2. The most detailed calculations make no assumptions regarding the complexity of the potential energy surface, and the resulting classical collision integrals are in excellent agreement with previous semiclassical results for H + N 2 and H 2 + N 2 and with recent experimental results for C n H 2n+2 + N 2, n = 2–4. The detailed classical results are used to test the accuracy of three simplifying assumptions typically made when calculating collision integrals: (1) approximating the intermolecular potential asmore » isotropic, (2) neglecting the internal structure of the colliders (i.e., neglecting inelasticity), and (3) employing unphysical R –12 repulsive interactions. The effect of anisotropy is found to be negligible for H + N 2 and H 2 + N 2 (in agreement with previous quantum mechanical and semiclassical results for systems involving atomic and diatomic species) but is more significant for larger species at low temperatures. For example, the neglect of anisotropy decreases the diffusion coefficient for butane + N 2 by 15% at 300 K. The neglect of inelasticity, in contrast, introduces only very small errors. Approximating the repulsive wall as an unphysical R –12 interaction is a significant source of error at all temperatures for the weakly interacting systems H + N 2 and H 2 + N 2, with errors as large as 40%. For the normal alkanes in N 2, which feature stronger interactions, the 12/6 Lennard–Jones approximation is found to be accurate, particularly at temperatures above –700 K where it predicts the full-dimensional result to within 5% (although with somewhat different temperature dependence). Overall, the typical practical approach of assuming isotropic 12/6 Lennard–Jones interactions is confirmed to be suitable for combustion applications except for weakly interacting systems, such as H + N 2. For these systems, anisotropy and inelasticity can safely be neglected but a more detailed description of the repulsive wall is required for quantitative predictions. Moreover, a straightforward approach for calculating effective isotropic potentials with realistic repulsive walls is described. An analytic expression for the calculated diffusion coefficient for H + N 2 is presented and is estimated to have a 2-sigma error bar of only 0.7%.« less

3D-QSAR based on quantum-chemical molecular fields: toward an improved description of halogen interactions.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Müller, Marco; Schmidt, Friedemann; Clark, Timothy

2012-09-24

Current 3D-QSAR methods such as CoMFA or CoMSIA make use of classical force-field approaches for calculating molecular fields. Thus, they can not adequately account for noncovalent interactions involving halogen atoms like halogen bonds or halogen-π interactions. These deficiencies in the underlying force fields result from the lack of treatment of the anisotropy of the electron density distribution of those atoms, known as the "σ-hole", although recent developments have begun to take specific interactions such as halogen bonding into account. We have now replaced classical force field derived molecular fields by local properties such as the local ionization energy, local electron affinity, or local polarizability, calculated using quantum-mechanical (QM) techniques that do not suffer from the above limitation for 3D-QSAR. We first investigate the characteristics of QM-based local property fields to show that they are suitable for statistical analyses after suitable pretreatment. We then analyze these property fields with partial least-squares (PLS) regression to predict biological affinities of two data sets comprising factor Xa and GABA-A/benzodiazepine receptor ligands. While the resulting models perform equally well or even slightly better in terms of consistency and predictivity than the classical CoMFA fields, the most important aspect of these augmented field-types is that the chemical interpretation of resulting QM-based property field models reveals unique SAR trends driven by electrostatic and polarizability effects, which cannot be extracted directly from CoMFA electrostatic maps. Within the factor Xa set, the interaction of chlorine and bromine atoms with a tyrosine side chain in the protease S1 pocket are correctly predicted. Within the GABA-A/benzodiazepine ligand data set, PLS models of high predictivity resulted for our QM-based property fields, providing novel insights into key features of the SAR for two receptor subtypes and cross-receptor selectivity of the ligands. The detailed interpretation of regression models derived using improved QM-derived property fields thus provides a significant advantage by revealing chemically meaningful correlations with biological activity and helps in understanding novel structure-activity relationship features. This will allow such knowledge to be used to design novel molecules on the basis of interactions additional to steric and hydrogen-bonding features.

Interaction of structural core protein of Classical Swine Fever Virus with endoplasmic reticulum-associated degradation pathway protein OS9

USDA-ARS?s Scientific Manuscript database

Classical Swine Fever Virus (CSFV) Core protein is involved in virus RNA protection, transcription regulation and virus virulence. To discover additional Core protein functions a yeast two-hybrid system was used to identify host proteins that interact with Core. Among the identified host proteins, t...

Interaction between core protein of classical swine fever virus with cellular IQGAP1 proetin appears essential for virulence in swine

USDA-ARS?s Scientific Manuscript database

Here we show that IQGAP1, a cellular protein that plays a pivotal role as a regulator of the cytoskeleton affecting cell adhesion, polarization and migration, interacts with Classical Swine Fever Virus (CSFV) Core protein. Sequence analyses identified a defined set of residues within CSFV Core prote...

The Effectiveness of Using Cloud-Based Cross-Device IRS to Support Classical Chinese Learning

ERIC Educational Resources Information Center

Wang, Yi-Hsuan

2017-01-01

The purpose of the present study was to examine the effects of integrating a cloud-based cross-device interactive response system (CCIRS) on enhancing students' classical Chinese learning. The system is a cloud-based IRS system which provides instructors and learners with an environment in which to achieve immediate interactive learning and…

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Mixed Quantum/Classical Theory for Molecule-Molecule Inelastic Scattering: Derivations of Equations and Application to N2 + H2 System.

PubMed

Semenov, Alexander; Babikov, Dmitri

2015-12-17

The mixed quantum classical theory, MQCT, for inelastic scattering of two molecules is developed, in which the internal (rotational, vibrational) motion of both collision partners is treated with quantum mechanics, and the molecule-molecule scattering (translational motion) is described by classical trajectories. The resultant MQCT formalism includes a system of coupled differential equations for quantum probability amplitudes, and the classical equations of motion in the mean-field potential. Numerical tests of this theory are carried out for several most important rotational state-to-state transitions in the N2 + H2 system, in a broad range of collision energies. Besides scattering resonances (at low collision energies) excellent agreement with full-quantum results is obtained, including the excitation thresholds, the maxima of cross sections, and even some smaller features, such as slight oscillations of energy dependencies. Most importantly, at higher energies the results of MQCT are nearly identical to the full quantum results, which makes this approach a good alternative to the full-quantum calculations that become computationally expensive at higher collision energies and for heavier collision partners. Extensions of this theory to include vibrational transitions or general asymmetric-top rotor (polyatomic) molecules are relatively straightforward.

Gravitational self-interactions of a degenerate quantum scalar field

NASA Astrophysics Data System (ADS)

Chakrabarty, Sankha S.; Enomoto, Seishi; Han, Yaqi; Sikivie, Pierre; Todarello, Elisa M.

2018-02-01

We develop a formalism to help calculate in quantum field theory the departures from the description of a system by classical field equations. We apply the formalism to a homogeneous condensate with attractive contact interactions and to a homogeneous self-gravitating condensate in critical expansion. In their classical descriptions, such condensates persist forever. We show that in their quantum description, parametric resonance causes quanta to jump in pairs out of the condensate into all modes with wave vector less than some critical value. We calculate, in each case, the time scale over which the homogeneous condensate is depleted and after which a classical description is invalid. We argue that the duration of classicality of inhomogeneous condensates is shorter than that of homogeneous condensates.

Fine-tuned broad binding capability of human lipocalin-type prostaglandin D synthase for various small lipophilic ligands.

PubMed

Kume, Satoshi; Lee, Young-Ho; Nakatsuji, Masatoshi; Teraoka, Yoshiaki; Yamaguchi, Keisuke; Goto, Yuji; Inui, Takashi

2014-03-18

The hydrophobic cavity of lipocalin-type prostaglandin D synthase (L-PGDS) has been suggested to accommodate various lipophilic ligands through hydrophobic effects, but its energetic origin remains unknown. We characterized 18 buffer-independent binding systems between human L-PGDS and lipophilic ligands using isothermal titration calorimetry. Although the classical hydrophobic effect was mostly detected, all complex formations were driven by favorable enthalpic gains. Gibbs energy changes strongly correlated with the number of hydrogen bond acceptors of ligand. Thus, the broad binding capability of L-PGDS for ligands should be viewed as hydrophilic interactions delicately tuned by enthalpy-entropy compensation using combined effects of hydrophilic and hydrophobic interactions. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Dissipation of ‘dark energy’ by cortex in knowledge retrieval

NASA Astrophysics Data System (ADS)

Capolupo, Antonio; Freeman, Walter J.; Vitiello, Giuseppe

2013-03-01

We have devised a thermodynamic model of cortical neurodynamics expressed at the classical level by neural networks and at the quantum level by dissipative quantum field theory. Our model is based on features in the spatial images of cortical activity newly revealed by high-density electrode arrays. We have incorporated the mechanism and necessity for so-called dark energy in knowledge retrieval. We have extended the model first using the Carnot cycle to define our measures for energy, entropy and temperature, and then using the Rankine cycle to incorporate criticality and phase transitions. We describe the dynamics of two interactive fields of neural activity that express knowledge, one at high and the other at low energy density, and the two operators that create and annihilate the fields. We postulate that the extremely high density of energy sequestered briefly in cortical activity patterns can account for the vividness, richness of associations, and emotional intensity of memories recalled by stimuli.

Charge transfer and ionization in collisions of Si3+ with H from low to high energy

NASA Astrophysics Data System (ADS)

Wang, J. G.; He, B.; Ning, Y.; Liu, C. L.; Yan, J.; Stancil, P. C.; Schultz, D. R.

2006-11-01

Charge transfer processes due to collisions of ground state Si3+(3sS1) ions with atomic hydrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) and classical-trajectory Monte Carlo (CTMC) methods. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial coupling matrix elements obtained from Herrero [J. Phys. B 29, 5583 (1996)] which were calculated with a full configuration-interaction method. Total and state-selective single-electron capture cross sections are obtained for collision energies from 0.01eV/u to 1MeV/u . Total and state-selective rate coefficients are also presented for temperatures from 2×103K to 107K . Comparison with existing data reveals that the total CTMC cross sections are in good agreement with the experimental measurements at the higher considered energies and that previous Landau-Zener calculations underestimate the total rate coefficients by a factor of up to two. The CTMC calculations of target ionization are presented for high energies.

Monte Carlo calculations of diatomic molecule gas flows including rotational mode excitation

NASA Technical Reports Server (NTRS)

Yoshikawa, K. K.; Itikawa, Y.

1976-01-01

The direct simulation Monte Carlo method was used to solve the Boltzmann equation for flows of an internally excited nonequilibrium gas, namely, of rotationally excited homonuclear diatomic nitrogen. The semi-classical transition probability model of Itikawa was investigated for its ability to simulate flow fields far from equilibrium. The behavior of diatomic nitrogen was examined for several different nonequilibrium initial states that are subjected to uniform mean flow without boundary interactions. A sample of 1000 model molecules was observed as the gas relaxed to a steady state starting from three specified initial states. The initial states considered are: (1) complete equilibrium, (2) nonequilibrium, equipartition (all rotational energy states are assigned the mean energy level obtained at equilibrium with a Boltzmann distribution at the translational temperature), and (3) nonequipartition (the mean rotational energy is different from the equilibrium mean value with respect to the translational energy states). In all cases investigated the present model satisfactorily simulated the principal features of the relaxation effects in nonequilibrium flow of diatomic molecules.

Holography as a highly efficient renormalization group flow. I. Rephrasing gravity

NASA Astrophysics Data System (ADS)

Behr, Nicolas; Kuperstein, Stanislav; Mukhopadhyay, Ayan

2016-07-01

We investigate how the holographic correspondence can be reformulated as a generalization of Wilsonian renormalization group (RG) flow in a strongly interacting large-N quantum field theory. We first define a highly efficient RG flow as one in which the Ward identities related to local conservation of energy, momentum and charges preserve the same form at each scale. To achieve this, it is necessary to redefine the background metric and external sources at each scale as functionals of the effective single-trace operators. These redefinitions also absorb the contributions of the multitrace operators to these effective Ward identities. Thus, the background metric and external sources become effectively dynamical, reproducing the dual classical gravity equations in one higher dimension. Here, we focus on reconstructing the pure gravity sector as a highly efficient RG flow of the energy-momentum tensor operator, leaving the explicit constructive field theory approach for generating such RG flows to the second part of the work. We show that special symmetries of the highly efficient RG flows carry information through which we can decode the gauge fixing of bulk diffeomorphisms in the corresponding gravity equations. We also show that the highly efficient RG flow which reproduces a given classical gravity theory in a given gauge is unique provided the endpoint can be transformed to a nonrelativistic fixed point with a finite number of parameters under a universal rescaling. The results obtained here are used in the second part of this work, where we do an explicit field-theoretic construction of the RG flow and obtain the dual classical gravity theory.

Effects of Extrinsic Mortality on the Evolution of Aging: A Stochastic Modeling Approach

PubMed Central

Shokhirev, Maxim Nikolaievich; Johnson, Adiv Adam

2014-01-01

The evolutionary theories of aging are useful for gaining insights into the complex mechanisms underlying senescence. Classical theories argue that high levels of extrinsic mortality should select for the evolution of shorter lifespans and earlier peak fertility. Non-classical theories, in contrast, posit that an increase in extrinsic mortality could select for the evolution of longer lifespans. Although numerous studies support the classical paradigm, recent data challenge classical predictions, finding that high extrinsic mortality can select for the evolution of longer lifespans. To further elucidate the role of extrinsic mortality in the evolution of aging, we implemented a stochastic, agent-based, computational model. We used a simulated annealing optimization approach to predict which model parameters predispose populations to evolve longer or shorter lifespans in response to increased levels of predation. We report that longer lifespans evolved in the presence of rising predation if the cost of mating is relatively high and if energy is available in excess. Conversely, we found that dramatically shorter lifespans evolved when mating costs were relatively low and food was relatively scarce. We also analyzed the effects of increased predation on various parameters related to density dependence and energy allocation. Longer and shorter lifespans were accompanied by increased and decreased investments of energy into somatic maintenance, respectively. Similarly, earlier and later maturation ages were accompanied by increased and decreased energetic investments into early fecundity, respectively. Higher predation significantly decreased the total population size, enlarged the shared resource pool, and redistributed energy reserves for mature individuals. These results both corroborate and refine classical predictions, demonstrating a population-level trade-off between longevity and fecundity and identifying conditions that produce both classical and non-classical lifespan effects. PMID:24466165

One-electron pseudo-potential investigation of NO(X2Π)-Arn clusters (n = 1,2,3,4)

NASA Astrophysics Data System (ADS)

Hammami, H.; Ben Mohamed, F. E.; Mohamed, D.; Ben El Hadj Rhouma, M.; Al Mogren, M. M.; Hochlaf, M.

2017-10-01

In this work, we investigate the minimal energy and low-lying isomers of the ground state of NOArn clusters using a hybrid pseudo-potential model, where a single electron quantum description is combined with the classical argon-argon pair potential and an expansion in terms of the Legendre polynomials. In such model, we use two centres of polarisation for NO+, where we considered for each nuclear configuration an analytic dipole polarisation for N+ and O+. The reliability of our model is checked by comparison of the NO(X2Π)-Ar potential energy surface with that deduced using the multireference configuration interaction (MRCI+Q) approach. The results of this formalism agree quite well with the MRCI ones over a wide range of nuclear arrangements.

Generalization of the Activated Complex Theory of Reaction Rates. II. Classical Mechanical Treatment

DOE R&D Accomplishments Database

Marcus, R. A.

1964-01-01

In its usual classical form activated complex theory assumes a particular expression for the kinetic energy of the reacting system -- one associated with a rectilinear motion along the reaction coordinate. The derivation of the rate expression given in the present paper is based on the general kinetic energy expression.

Astrocyte - neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions - in silico study supported by in vitro expression data

PubMed Central

2011-01-01

Background Neuro-glial interactions are important for normal functioning of the brain as well as brain energy metabolism. There are two major working models - in the classical view, both neurons and astrocytes can utilize glucose as the energy source through oxidative metabolism, whereas in the astrocyte-neuron lactate shuttle hypothesis (ANLSH) it is the astrocyte which can consume glucose through anaerobic glycolysis to pyruvate and then to lactate, and this lactate is secreted to the extracellular space to be taken up by the neuron for further oxidative degradation. Results In this computational study, we have included hypoxia-induced genetic regulation of these enzymes and transporters, and analyzed whether the ANLSH model can provide an advantage to either cell type in terms of supplying the energy demand. We have based this module on our own experimental analysis of hypoxia-dependent regulation of transcription of key metabolic enzymes. Using this experimentation-supported in silico modeling, we show that under both normoxic and hypoxic conditions in a given time period ANLSH model does indeed provide the neuron with more ATP than in the classical view. Conclusions Although the ANLSH is energetically more favorable for the neuron, it is not the case for the astrocyte in the long term. Considering the fact that astrocytes are more resilient to hypoxia, we would propose that there is likely a switch between the two models, based on the energy demand of the neuron, so as to maintain the survival of the neuron under hypoxic or glucose-and-oxygen-deprived conditions. PMID:21995951

Astrocyte-neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions--in silico study supported by in vitro expression data.

PubMed

Genc, Seda; Kurnaz, Isil A; Ozilgen, Mustafa

2011-10-13

Neuro-glial interactions are important for normal functioning of the brain as well as brain energy metabolism. There are two major working models--in the classical view, both neurons and astrocytes can utilize glucose as the energy source through oxidative metabolism, whereas in the astrocyte-neuron lactate shuttle hypothesis (ANLSH) it is the astrocyte which can consume glucose through anaerobic glycolysis to pyruvate and then to lactate, and this lactate is secreted to the extracellular space to be taken up by the neuron for further oxidative degradation. In this computational study, we have included hypoxia-induced genetic regulation of these enzymes and transporters, and analyzed whether the ANLSH model can provide an advantage to either cell type in terms of supplying the energy demand. We have based this module on our own experimental analysis of hypoxia-dependent regulation of transcription of key metabolic enzymes. Using this experimentation-supported in silico modeling, we show that under both normoxic and hypoxic conditions in a given time period ANLSH model does indeed provide the neuron with more ATP than in the classical view. Although the ANLSH is energetically more favorable for the neuron, it is not the case for the astrocyte in the long term. Considering the fact that astrocytes are more resilient to hypoxia, we would propose that there is likely a switch between the two models, based on the energy demand of the neuron, so as to maintain the survival of the neuron under hypoxic or glucose-and-oxygen-deprived conditions.

Higher derivative extensions of 3 d Chern-Simons models: conservation laws and stability

NASA Astrophysics Data System (ADS)

Kaparulin, D. S.; Karataeva, I. Yu.; Lyakhovich, S. L.

2015-11-01

We consider the class of higher derivative 3 d vector field models with the field equation operator being a polynomial of the Chern-Simons operator. For the nth-order theory of this type, we provide a general recipe for constructing n-parameter family of conserved second rank tensors. The family includes the canonical energy-momentum tensor, which is unbounded, while there are bounded conserved tensors that provide classical stability of the system for certain combinations of the parameters in the Lagrangian. We also demonstrate the examples of consistent interactions which are compatible with the requirement of stability.

Entanglement enhances cooling in microscopic quantum refrigerators.

PubMed

Brunner, Nicolas; Huber, Marcus; Linden, Noah; Popescu, Sandu; Silva, Ralph; Skrzypczyk, Paul

2014-03-01

Small self-contained quantum thermal machines function without external source of work or control but using only incoherent interactions with thermal baths. Here we investigate the role of entanglement in a small self-contained quantum refrigerator. We first show that entanglement is detrimental as far as efficiency is concerned-fridges operating at efficiencies close to the Carnot limit do not feature any entanglement. Moving away from the Carnot regime, we show that entanglement can enhance cooling and energy transport. Hence, a truly quantum refrigerator can outperform a classical one. Furthermore, the amount of entanglement alone quantifies the enhancement in cooling.

Strong coupling between surface plasmon polariton and laser dye rhodamine 800

NASA Astrophysics Data System (ADS)

Valmorra, Federico; Bröll, Markus; Schwaiger, Stephan; Welzel, Nadine; Heitmann, Detlef; Mendach, Stefan

2011-08-01

We report on strong coupling between surface plasmon polaritons on a thin silver film and laser dye Rhodamine 800. Attenuated total reflection measurements reveal that the pure surface plasmon polaritons interact with the Rhodamine 800 absorption lines exhibiting pronounced anticrossings in the dispersion relation. We show that the corresponding energy gap can be tailored by the concentration of dye molecules in the dielectric matrix between 50 meV and 70 meV. We can well model our data by a classical transfer matrix approach as well as by a quantum mechanical coupled oscillator ansatz.

Teaching thermal physics in the paradigms project

NASA Astrophysics Data System (ADS)

Roundy, David

2011-10-01

Thermal physics is probably the most disliked course in the physics major curriculum, with students feeling that they are being led through a mathematical maze, leading to an unsatisfactory conclusion. Classical thermodynamics involves scary derivatives, while statistical mechanics leads to lengthy summations and is difficult to apply to interacting systems. It is unsurprising that students find themselves failing to see the physics for the math. In this talk, I will discuss my experiences teaching the Energy and Entropy paradigm, and will introduce materials we have developed to aide student understanding of partial derivatives and their relationship to experimental observables.

Duration of classicality in highly degenerate interacting Bosonic systems

DOE PAGES

Sikivie, Pierre; Todarello, Elisa M.

2017-04-28

We study sets of oscillators that have high quantum occupancy and that interact by exchanging quanta. It is shown by analytical arguments and numerical simulation that such systems obey classical equations of motion only on time scales of order their relaxation time τ and not longer than that. The results are relevant to the cosmology of axions and axion-like particles.

DBI potential, DBI inflation action and general Lagrangian relative to phantom, K-essence and quintessence

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

Zhang, Qing; Huang, Yong-Chang, E-mail: ychuang@bjut.edu.cn

We derive a Dirac-Born-Infeld (DBI) potential and DBI inflation action by rescaling the metric. The determinant of the induced metric naturally includes the kinetic energy and the potential energy. In particular, the potential energy and kinetic energy can convert into each other in any order, which is in agreement with the limit of classical physics. This is quite different from the usual DBI action. We show that the Taylor expansion of the DBI action can be reduced into the form in the non-linear classical physics. These investigations are the support for the statement that the results of string theory aremore » consistent with quantum mechanics and classical physics. We deduce the Phantom, K-essence, Quintessence and Generalized Klein-Gordon Equation from the DBI model.« less

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach.

PubMed

Rubinstein, Alexander I; Sabirianov, Renat F; Namavar, Fereydoon

2016-10-14

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander I.; Sabirianov, Renat F.; Namavar, Fereydoon

2016-10-01

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ˜80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Perturbative thermodynamic geometry of nonextensive ideal classical, Bose, and Fermi gases.

PubMed

Mohammadzadeh, Hosein; Adli, Fereshteh; Nouri, Sahereh

2016-12-01

We investigate perturbative thermodynamic geometry of nonextensive ideal classical, Bose, and Fermi gases. We show that the intrinsic statistical interaction of nonextensive Bose (Fermi) gas is attractive (repulsive) similar to the extensive case but the value of thermodynamic curvature is changed by a nonextensive parameter. In contrary to the extensive ideal classical gas, the nonextensive one may be divided to two different regimes. According to the deviation parameter of the system to the nonextensive case, one can find a special value of fugacity, z^{*}, where the sign of thermodynamic curvature is changed. Therefore, we argue that the nonextensive parameter induces an attractive (repulsive) statistical interaction for zz^{*}) for an ideal classical gas. Also, according to the singular point of thermodynamic curvature, we consider the condensation of nonextensive Boson gas.

The energy-momentum tensor(s) in classical gauge theories

DOE PAGES

Blaschke, Daniel N.; Gieres, François; Reboud, Méril; ...

2016-07-12

We give an introduction to, and review of, the energy-momentum tensors in classical gauge field theories in Minkowski space, and to some extent also in curved space-time. For the canonical energy-momentum tensor of non-Abelian gauge fields and of matter fields coupled to such fields, we present a new and simple improvement procedure based on gauge invariance for constructing a gauge invariant, symmetric energy-momentum tensor. In conclusion, the relationship with the Einstein-Hilbert tensor following from the coupling to a gravitational field is also discussed.

Many-Body Quantum Chaos: Analytic Connection to Random Matrix Theory

NASA Astrophysics Data System (ADS)

Kos, Pavel; Ljubotina, Marko; Prosen, Tomaž

2018-04-01

A key goal of quantum chaos is to establish a relationship between widely observed universal spectral fluctuations of clean quantum systems and random matrix theory (RMT). Most prominent features of such RMT behavior with respect to a random spectrum, both encompassed in the spectral pair correlation function, are statistical suppression of small level spacings (correlation hole) and enhanced stiffness of the spectrum at large spectral ranges. For single-particle systems with fully chaotic classical counterparts, the problem has been partly solved by Berry [Proc. R. Soc. A 400, 229 (1985), 10.1098/rspa.1985.0078] within the so-called diagonal approximation of semiclassical periodic-orbit sums, while the derivation of the full RMT spectral form factor K (t ) (Fourier transform of the spectral pair correlation function) from semiclassics has been completed by Müller et al. [Phys. Rev. Lett. 93, 014103 (2004), 10.1103/PhysRevLett.93.014103]. In recent years, the questions of long-time dynamics at high energies, for which the full many-body energy spectrum becomes relevant, are coming to the forefront even for simple many-body quantum systems, such as locally interacting spin chains. Such systems display two universal types of behaviour which are termed the "many-body localized phase" and "ergodic phase." In the ergodic phase, the spectral fluctuations are excellently described by RMT, even for very simple interactions and in the absence of any external source of disorder. Here we provide a clear theoretical explanation for these observations. We compute K (t ) in the leading two orders in t and show its agreement with RMT for nonintegrable, time-reversal invariant many-body systems without classical counterparts, a generic example of which are Ising spin-1 /2 models in a periodically kicking transverse field. In particular, we relate K (t ) to partition functions of a class of twisted classical Ising models on a ring of size t ; hence, the leading-order RMT behavior K (t )≃2 t is a consequence of translation and reflection symmetry of the Ising partition function.

Shear modulus of neutron star crust

NASA Astrophysics Data System (ADS)

Baiko, D. A.

2011-09-01

The shear modulus of solid neutron star crust is calculated by the thermodynamic perturbation theory, taking into account ion motion. At a given density, the crust is modelled as a body-centred cubic Coulomb crystal of fully ionized atomic nuclei of one type with a uniform charge-compensating electron background. Classic and quantum regimes of ion motion are considered. The calculations in the classic temperature range agree well with previous Monte Carlo simulations. At these temperatures, the shear modulus is given by the sum of a positive contribution due to the static lattice and a negative ∝ T contribution due to the ion motion. The quantum calculations are performed for the first time. The main result is that at low temperatures the contribution to the shear modulus due to the ion motion saturates at a constant value, associated with zero-point ion vibrations. Such behaviour is qualitatively similar to the zero-point ion motion contribution to the crystal energy. The quantum effects may be important for lighter elements at higher densities, where the ion plasma temperature is not entirely negligible compared to the typical Coulomb ion interaction energy. The results of numerical calculations are approximated by convenient fitting formulae. They should be used for precise neutron star oscillation modelling, a rapidly developing branch of stellar seismology.

Selectivity and self-diffusion of CO2 and H2 in a mixture on a graphite surface

PubMed Central

Trinh, Thuat T.; Vlugt, Thijs J. H.; Hägg, May-Britt; Bedeaux, Dick; Kjelstrup, Signe

2013-01-01

We performed classical molecular dynamics (MD) simulations to understand the mechanism of adsorption from a gas mixture of CO2 and H2 (mole fraction of CO2 = 0.30) and diffusion along a graphite surface, with the aim to help enrich industrial off-gases in CO2, separating out H2. The temperature of the system in the simulation covered typical industrial conditions for off-gas treatment (250–550 K). The interaction energy of single molecules CO2 or H2 on graphite surface was calculated with classical force fields (FFs) and with Density Functional Theory (DFT). The results were in good agreement. The binding energy of CO2 on graphite surface is three times larger than that of H2. At lower temperatures, the selectivity of CO2 over H2 is five times larger than at higher temperatures. The position of the dividing surface was used to explain how the adsorption varies with pore size. In the temperature range studied, the self-diffusion coefficient of CO2 is always smaller than of H2. The temperature variation of the selectivities and the self-diffusion coefficient imply that the carbon molecular sieve membrane can be used for gas enrichment of CO2. PMID:24790965

Quantum close coupling calculation of transport and relaxation properties for Hg-H2 system

NASA Astrophysics Data System (ADS)

Nemati-Kande, Ebrahim; Maghari, Ali

2016-11-01

Quantum mechanical close coupling calculation of the state-to-state transport and relaxation cross sections have been done for Hg-H2 molecular system using a high-level ab initio potential energy surface. Rotationally averaged cross sections were also calculated to obtain the energy dependent Senftleben-Beenakker cross sections at the energy range of 0.005-25,000 cm-1. Boltzmann averaging of the energy dependent Senftleben-Beenakker cross sections showed the temperature dependency over a wide temperature range of 50-2500 K. Interaction viscosity and diffusion coefficients were also calculated using close coupling cross sections and full classical Mason-Monchick approximation. The results were compared with each other and with the available experimental data. It was found that Mason-Monchick approximation for viscosity is more reliable than diffusion coefficient. Furthermore, from the comparison of the experimental diffusion coefficients with the result of the close coupling and Mason-Monchick approximation, it was found that the Hg-H2 potential energy surface used in this work can reliably predict diffusion coefficient data.

Decoherence can relax cosmic acceleration

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

Markkanen, Tommi

In this work we investigate the semi-classical backreaction for a quantised conformal scalar field and classical vacuum energy. In contrast to the usual approximation of a closed system, our analysis includes an environmental sector such that a quantum-to-classical transition can take place. We show that when the system decoheres into a mixed state with particle number as the classical observable de Sitter space is destabilized, which is observable as a gradually decreasing Hubble rate. In particular we show that at late times this mechanism can drive the curvature of the Universe to zero and has an interpretation as the decaymore » of the vacuum energy demonstrating that quantum effects can be relevant for the fate of the Universe.« less

An investigation of student understanding of classical ideas related to quantum mechanics: Potential energy diagrams and spatial probability density

NASA Astrophysics Data System (ADS)

Stephanik, Brian Michael

This dissertation describes the results of two related investigations into introductory student understanding of ideas from classical physics that are key elements of quantum mechanics. One investigation probes the extent to which students are able to interpret and apply potential energy diagrams (i.e., graphs of potential energy versus position). The other probes the extent to which students are able to reason classically about probability and spatial probability density. The results of these investigations revealed significant conceptual and reasoning difficulties that students encounter with these topics. The findings guided the design of instructional materials to address the major problems. Results from post-instructional assessments are presented that illustrate the impact of the curricula on student learning.

Classical and quantum dynamics of a kicked relativistic particle in a box

NASA Astrophysics Data System (ADS)

Yusupov, J. R.; Otajanov, D. M.; Eshniyazov, V. E.; Matrasulov, D. U.

2018-03-01

We study classical and quantum dynamics of a kicked relativistic particle confined in a one dimensional box. It is found that in classical case for chaotic motion the average kinetic energy grows in time, while for mixed regime the growth is suppressed. However, in case of regular motion energy fluctuates around certain value. Quantum dynamics is treated by solving the time-dependent Dirac equation with delta-kicking potential, whose exact solution is obtained for single kicking period. In quantum case, depending on the values of the kicking parameters, the average kinetic energy can be quasi periodic, or fluctuating around some value. Particle transport is studied by considering spatio-temporal evolution of the Gaussian wave packet and by analyzing the trembling motion.

Quantum heat engine with coupled superconducting resonators

NASA Astrophysics Data System (ADS)

Hardal, Ali Ü. C.; Aslan, Nur; Wilson, C. M.; Müstecaplıoǧlu, Özgür E.

2017-12-01

We propose a quantum heat engine composed of two superconducting transmission line resonators interacting with each other via an optomechanical-like coupling. One resonator is periodically excited by a thermal pump. The incoherently driven resonator induces coherent oscillations in the other one due to the coupling. A limit cycle, indicating finite power output, emerges in the thermodynamical phase space. The system implements an all-electrical analog of a photonic piston. Instead of mechanical motion, the power output is obtained as a coherent electrical charging in our case. We explore the differences between the quantum and classical descriptions of our system by solving the quantum master equation and classical Langevin equations. Specifically, we calculate the mean number of excitations, second-order coherence, as well as the entropy, temperature, power, and mean energy to reveal the signatures of quantum behavior in the statistical and thermodynamic properties of the system. We find evidence of a quantum enhancement in the power output of the engine at low temperatures.

Quantum heat engine with coupled superconducting resonators.

PubMed

Hardal, Ali Ü C; Aslan, Nur; Wilson, C M; Müstecaplıoğlu, Özgür E

2017-12-01

We propose a quantum heat engine composed of two superconducting transmission line resonators interacting with each other via an optomechanical-like coupling. One resonator is periodically excited by a thermal pump. The incoherently driven resonator induces coherent oscillations in the other one due to the coupling. A limit cycle, indicating finite power output, emerges in the thermodynamical phase space. The system implements an all-electrical analog of a photonic piston. Instead of mechanical motion, the power output is obtained as a coherent electrical charging in our case. We explore the differences between the quantum and classical descriptions of our system by solving the quantum master equation and classical Langevin equations. Specifically, we calculate the mean number of excitations, second-order coherence, as well as the entropy, temperature, power, and mean energy to reveal the signatures of quantum behavior in the statistical and thermodynamic properties of the system. We find evidence of a quantum enhancement in the power output of the engine at low temperatures.

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

Classical trajectories in polar-asymmetric laser fields: Synchronous THz and XUV emission

NASA Astrophysics Data System (ADS)

Gragossian, Aram; Seletskiy, Denis V.; Sheik-Bahae, Mansoor

2016-10-01

The interaction of intense near- and mid-infrared laser pulses with rare gases has produced bursts of radiation with spectral content extending into the extreme ultraviolet and soft x-ray region of electromagnetic spectrum. On the other end of the spectrum, laser-driven gas plasmas has been shown to produce coherent sub-harmonic optical waveforms, covering from terahertz (THz) to mid- and near-infrared frequency spectral band. Both processes can be enhanced via a combination of a driving field and its second harmonic. Despite this striking similarity, only limited experimental and theoretical attempts have been made to address these two regimes simultaneously. Here we present systematic experiments and a unifying picture of these processes, based on our extension of the semi-classical three-step model. Further understanding of the generation and coherent control of time-synchronized transients with photon energies from meV to 1 keV can lead to numerous technological advances and to an intriguing possibilities of ultra-broadband investigations into complex condensed matter systems.

Quantum and classical dynamics of water dissociation on Ni(111): A test of the site-averaging model in dissociative chemisorption of polyatomic molecules

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

Jiang, Bin; Department of Chemical Physics, University of Science and Technology of China, Hefei 230026; Guo, Hua, E-mail: hguo@unm.edu

Recently, we reported the first highly accurate nine-dimensional global potential energy surface (PES) for water interacting with a rigid Ni(111) surface, built on a large number of density functional theory points [B. Jiang and H. Guo, Phys. Rev. Lett. 114, 166101 (2015)]. Here, we investigate site-specific reaction probabilities on this PES using a quasi-seven-dimensional quantum dynamical model. It is shown that the site-specific reactivity is largely controlled by the topography of the PES instead of the barrier height alone, underscoring the importance of multidimensional dynamics. In addition, the full-dimensional dissociation probability is estimated by averaging fixed-site reaction probabilities with appropriatemore » weights. To validate this model and gain insights into the dynamics, additional quasi-classical trajectory calculations in both full and reduced dimensions have also been performed and important dynamical factors such as the steering effect are discussed.« less

Nonequilibrium Transport and the Bernoulli Effect of Electrons in a Two-Dimensional Electron Gas

NASA Astrophysics Data System (ADS)

Kaya, Ismet I.

2013-02-01

Nonequilibrium transport of charged carriers in a two-dimensional electron gas is summarized from an experimental point of view. The transport regime in which the electron-electron interactions are enhanced at high bias leads to a range of striking effects in a two-dimensional electron gas. This regime of transport is quite different than the ballistic transport in which particles propagate coherently with no intercarrier energy transfer and the diffusive transport in which the momentum of the electron system is lost with the involvement of the phonons. Quite a few hydrodynamic phenomena observed in classical gasses have the electrical analogs in the current flow. When intercarrier scattering events dominate the transport, the momentum sharing via narrow angle scattering among the hot and cold electrons lead to negative resistance and electron pumping which can be viewed as the analog of the Bernoulli-Venturi effect observed classical gasses. The recent experimental findings and the background work in the field are reviewed.

Modeling micelle formation and interfacial properties with iSAFT classical density functional theory

NASA Astrophysics Data System (ADS)

Wang, Le; Haghmoradi, Amin; Liu, Jinlu; Xi, Shun; Hirasaki, George J.; Miller, Clarence A.; Chapman, Walter G.

2017-03-01

Surfactants reduce the interfacial tension between phases, making them an important additive in a number of industrial and commercial applications from enhanced oil recovery to personal care products (e.g., shampoo and detergents). To help obtain a better understanding of the dependence of surfactant properties on molecular structure, a classical density functional theory, also known as interfacial statistical associating fluid theory, has been applied to study the effects of surfactant architecture on micelle formation and interfacial properties for model nonionic surfactant/water/oil systems. In this approach, hydrogen bonding is explicitly included. To minimize the free energy, the system minimizes interactions between hydrophobic components and hydrophilic components with water molecules hydrating the surfactant head group. The theory predicts micellar structure, effects of surfactant architecture on critical micelle concentration, aggregation number, and interfacial tension isotherm of surfactant/water systems in qualitative agreement with experimental data. Furthermore, this model is applied to study swollen micelles and reverse swollen micelles that are necessary to understand the formation of a middle-phase microemulsion.

Thermally Driven One-Fluid Electron-Proton Solar Wind: Eight-Moment Approximation

NASA Astrophysics Data System (ADS)

Olsen, Espen Lyngdal; Leer, Egil

1996-05-01

In an effort to improve the "classical" solar wind model, we study an eight-moment approximation hydrodynamic solar wind model, in which the full conservation equation for the heat conductive flux is solved together with the conservation equations for mass, momentum, and energy. We consider two different cases: In one model the energy flux needed to drive the solar wind is supplied as heat flux from a hot coronal base, where both the density and temperature are specified. In the other model, the corona is heated. In that model, the coronal base density and temperature are also specified, but the temperature increases outward from the coronal base due to a specified energy flux that is dissipated in the corona. The eight-moment approximation solutions are compared with the results from a "classical" solar wind model in which the collision-dominated gas expression for the heat conductive flux is used. It is shown that the "classical" expression for the heat conductive flux is generally not valid in the solar wind. In collisionless regions of the flow, the eight-moment approximation gives a larger thermalization of the heat conductive flux than the models using the collision-dominated gas approximation for the heat flux, but the heat flux is still larger than the "saturation heat flux." This leads to a breakdown of the electron distribution function, which turns negative in the collisionless region of the flow. By increasing the interaction between the electrons, the heat flux is reduced, and a reasonable shape is obtained on the distribution function. By solving the full set of equations consistent with the eight-moment distribution function for the electrons, we are thus able to draw inferences about the validity of the eight-moment description of the solar wind as well as the validity of the very commonly used collision-dominated gas approximation for the heat conductive flux in the solar wind.

Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2009-12-31

To systematically construct a low-dimensional free-energy landscape of RNA systems from a classical molecular dynamics simulation, various versions of the principal component analysis (PCA) are compared: the cPCA using the Cartesian coordinates of all atoms, the dPCA using the sine/cosine-transformed six backbone dihedral angles as well as the glycosidic torsional angle chi and the pseudorotational angle P, the aPCA which ignores the circularity of the 6 + 2 dihedral angles of the RNA, and the dPCA(etatheta), which approximates the 6 backbone dihedral angles by 2 pseudotorsional angles eta and theta. As representative examples, a 10-nucleotide UUCG hairpin and the 36-nucleotide segment SL1 of the Psi site of HIV-1 are studied by classical molecular dynamics simulation, using the Amber all-atom force field and explicit solvent. It is shown that the conformational heterogeneity of the RNA hairpins can only be resolved by an angular PCA such as the dPCA but not by the cPCA using Cartesian coordinates. Apart from possible artifacts due to the coupling of overall and internal motion, this is because the details of hydrogen bonding and stacking interactions but also of global structural rearrangements of the RNA are better discriminated by dihedral angles. In line with recent experiments, it is found that the free energy landscape of RNA hairpins is quite rugged and contains various metastable conformational states which may serve as an intermediate for unfolding.

A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water ice: Defining Adsorption in Classical Molecular Dynamics

NASA Astrophysics Data System (ADS)

Dupuy, John L.; Lewis, Steven P.; Stancil, P. C.

2016-11-01

Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H2) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5-400 K] across seven different temperatures of dust grains [10-70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99-0.22.

A non-classical Mindlin plate model incorporating microstructure, surface energy and foundation effects.

PubMed

Gao, X-L; Zhang, G Y

2016-07-01

A non-classical model for a Mindlin plate resting on an elastic foundation is developed in a general form using a modified couple stress theory, a surface elasticity theory and a two-parameter Winkler-Pasternak foundation model. It includes all five kinematic variables possible for a Mindlin plate. The equations of motion and the complete boundary conditions are obtained simultaneously through a variational formulation based on Hamilton's principle, and the microstructure, surface energy and foundation effects are treated in a unified manner. The newly developed model contains one material length-scale parameter to describe the microstructure effect, three surface elastic constants to account for the surface energy effect, and two foundation parameters to capture the foundation effect. The current non-classical plate model reduces to its classical elasticity-based counterpart when the microstructure, surface energy and foundation effects are all suppressed. In addition, the new model includes the Mindlin plate models considering the microstructure dependence or the surface energy effect or the foundation influence alone as special cases, recovers the Kirchhoff plate model incorporating the microstructure, surface energy and foundation effects, and degenerates to the Timoshenko beam model including the microstructure effect. To illustrate the new Mindlin plate model, the static bending and free vibration problems of a simply supported rectangular plate are analytically solved by directly applying the general formulae derived.

A non-classical Mindlin plate model incorporating microstructure, surface energy and foundation effects

PubMed Central

Zhang, G. Y.

2016-01-01

A non-classical model for a Mindlin plate resting on an elastic foundation is developed in a general form using a modified couple stress theory, a surface elasticity theory and a two-parameter Winkler–Pasternak foundation model. It includes all five kinematic variables possible for a Mindlin plate. The equations of motion and the complete boundary conditions are obtained simultaneously through a variational formulation based on Hamilton's principle, and the microstructure, surface energy and foundation effects are treated in a unified manner. The newly developed model contains one material length-scale parameter to describe the microstructure effect, three surface elastic constants to account for the surface energy effect, and two foundation parameters to capture the foundation effect. The current non-classical plate model reduces to its classical elasticity-based counterpart when the microstructure, surface energy and foundation effects are all suppressed. In addition, the new model includes the Mindlin plate models considering the microstructure dependence or the surface energy effect or the foundation influence alone as special cases, recovers the Kirchhoff plate model incorporating the microstructure, surface energy and foundation effects, and degenerates to the Timoshenko beam model including the microstructure effect. To illustrate the new Mindlin plate model, the static bending and free vibration problems of a simply supported rectangular plate are analytically solved by directly applying the general formulae derived. PMID:27493578

Dynamic Network-Based Epistasis Analysis: Boolean Examples

PubMed Central

Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.

2011-01-01

In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and single-path assumption, but also by demonstrating the importance of considering temporal dynamics, and specifically introducing the usefulness of Boolean network models and also reviewing some key properties of network approaches. PMID:22645556

Linear solvation energy relationship (LSER) characterization of the normal phase retention mechanism on hypercrosslinked polystyrenes.

PubMed

Wu, Di; Jiang, Ping; Lucy, Charles A

2018-03-30

Linear solvation energy relationships (LSERs) were applied to retention on hypercrosslinked polystyrene on silica (HC-Tol) to elucidate the type and relative importance of molecular interactions between model solutes and the HC-Tol stationary phase. Classical amino phase and another hypercrosslinked phase (5-HGN) were used as reference columns. On both the HC-Tol and amino, polar interactions predominate and contribute to retention. Solute volume V has no impact on retention on the amino column, while V has a slightly negative influence on retention for the HC-Tol column. The differences in coefficient v between the amino and the HC-Tol columns might explain why the HC-Tol is capable of group-type separations. 5-HGN phase has smaller a and b values compared to HC-Tol, which means that 5-HGN is not as basic or acidic in terms of hydrogen bonds as is HC-Tol. This suggests that the hydrogen bonding character of the HC-Tol phase arises from its silica substrate. Copyright © 2018 Elsevier B.V. All rights reserved.

Electron beam cooling in intense focussed laser pulses

NASA Astrophysics Data System (ADS)

Yoffe, Samuel R.; Noble, Adam; Macleod, Alexander J.; Jaroszynski, Dino A.

2017-05-01

In the coming years, a new generation of high-power laser facilities (such as the Extreme Light Infrastructure) will become operational, for which it is important to understand how the interaction with intense laser pulses affects the bulk properties of relativistic electron bunches. At such high field intensities, we expect both radiation reaction and quantum effects to have a dominant role to play in determining the dynamics. The reduction in relative energy spread (beam cooling) at the expense of mean beam energy predicted by classical theories of radiation reaction has been shown to occur equally in the longitudinal and transverse directions, whereas this symmetry is broken when the theory is extended to approximate certain quantum effects. The reduction in longitudinal cooling suggests that the effects of radiation reaction could be better observed in measurements of the transverse distribution, which for real-world laser pulses motivates the investigation of the angular dependence of the interaction. Using a stochastic single-photon emission model with a (Gaussian beam) focussed pulse, we find strong angular dependence of the stochastic heating.

Calogero-Sutherland system with two types interacting spins

NASA Astrophysics Data System (ADS)

Kharchev, S.; Levin, A.; Olshanetsky, M.; Zotov, A.

2017-08-01

We consider the classical Calogero-Sutherland system with two types of interacting spin variables. It can be reduced to the standard Calogero-Sutherland system, when one of the spin variables vanishes. We describe the model in the Hitchin approach and prove complete integrability of the system by constructing the Lax pair and the classical r-matrix with the spectral parameter on a singular curve.

Spinomotive force induced by a transverse displacement current in a thin metal or doped-semiconductor sheet: Classical and quantum views.

NASA Astrophysics Data System (ADS)

Hu, Chia-Ren

2004-03-01

We present classical macroscopic, microscopic, and quantum mechanical arguments to show that in a metallic or electron/hole-doped semiconducting sheet thinner than the screening length, a displacement current applied normal to it can induce a spinomotive force along it. The magnitude is weak but clearly detectable. The classical arguments are purely electromagnetic. The quantum argument, based on the Dirac equation, shows that the predicted effect originates from the spin-orbit interaction, but not of the usual kind. That is, it relies on an external electric field, whereas the usual S-O interaction involves the electric field generated by the ions. Because the Dirac equation incorporatesThomas precession, which is due to relativistic kinematics, the quantum prediction is a factor of two smaller than the classical prediction. Replacing the displacement current by a charge current, and one obtains a new source for the spin-Hall effect. Classical macroscopic argument also predicts its existence, but the other two views are controversial.

Fluctuating local field method probed for a description of small classical correlated lattices

NASA Astrophysics Data System (ADS)

Rubtsov, Alexey N.

2018-05-01

Thermal-equilibrated finite classical lattices are considered as a minimal model of the systems showing an interplay between low-energy collective fluctuations and single-site degrees of freedom. Standard local field approach, as well as classical limit of the bosonic DMFT method, do not provide a satisfactory description of Ising and Heisenberg small lattices subjected to an external polarizing field. We show that a dramatic improvement can be achieved within a simple approach, in which the local field appears to be a fluctuating quantity related to the low-energy degree(s) of freedom.

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

PubMed

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

2018-05-14

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

A device-oriented optimizer for solving ground state problems on an approximate quantum computer, Part II: Experiments for interacting spin and molecular systems

NASA Astrophysics Data System (ADS)

Kandala, Abhinav; Mezzacapo, Antonio; Temme, Kristan; Bravyi, Sergey; Takita, Maika; Chavez-Garcia, Jose; Córcoles, Antonio; Smolin, John; Chow, Jerry; Gambetta, Jay

Hybrid quantum-classical algorithms can be used to find variational solutions to generic quantum problems. Here, we present an experimental implementation of a device-oriented optimizer that uses superconducting quantum hardware. The experiment relies on feedback between the quantum device and classical optimization software which is robust to measurement noise. Our device-oriented approach uses naturally available interactions for the preparation of trial states. We demonstrate the application of this technique for solving interacting spin and molecular structure problems.

Complex Virus-Host Interactions Involved in the Regulation of Classical Swine Fever Virus Replication: A Minireview.

PubMed

Li, Su; Wang, Jinghan; Yang, Qian; Naveed Anwar, Muhammad; Yu, Shaoxiong; Qiu, Hua-Ji

2017-07-05

Classical swine fever (CSF), caused by classical swine fever virus (CSFV), is one of the most devastating epizootic diseases of pigs in many countries. Viruses are small intracellular parasites and thus rely on the cellular factors for replication. Fundamental aspects of CSFV-host interactions have been well described, such as factors contributing to viral attachment, modulation of genomic replication and translation, antagonism of innate immunity, and inhibition of cell apoptosis. However, those host factors that participate in the viral entry, assembly, and release largely remain to be elucidated. In this review, we summarize recent progress in the virus-host interactions involved in the life cycle of CSFV and analyze the potential mechanisms of viral entry, assembly, and release. We conclude with future perspectives and highlight areas that require further understanding.

Complex Virus–Host Interactions Involved in the Regulation of Classical Swine Fever Virus Replication: A Minireview

PubMed Central

Li, Su; Wang, Jinghan; Yang, Qian; Naveed Anwar, Muhammad; Yu, Shaoxiong; Qiu, Hua-Ji

2017-01-01

Classical swine fever (CSF), caused by classical swine fever virus (CSFV), is one of the most devastating epizootic diseases of pigs in many countries. Viruses are small intracellular parasites and thus rely on the cellular factors for replication. Fundamental aspects of CSFV–host interactions have been well described, such as factors contributing to viral attachment, modulation of genomic replication and translation, antagonism of innate immunity, and inhibition of cell apoptosis. However, those host factors that participate in the viral entry, assembly, and release largely remain to be elucidated. In this review, we summarize recent progress in the virus–host interactions involved in the life cycle of CSFV and analyze the potential mechanisms of viral entry, assembly, and release. We conclude with future perspectives and highlight areas that require further understanding. PMID:28678154

Generalized Rainich conditions, generalized stress-energy conditions, and the Hawking-Ellis classification

NASA Astrophysics Data System (ADS)

Martín–Moruno, Prado; Visser, Matt

2017-11-01

The (generalized) Rainich conditions are algebraic conditions which are polynomial in the (mixed-component) stress-energy tensor. As such they are logically distinct from the usual classical energy conditions (NEC, WEC, SEC, DEC), and logically distinct from the usual Hawking-Ellis (Segré-Plebański) classification of stress-energy tensors (type I, type II, type III, type IV). There will of course be significant inter-connections between these classification schemes, which we explore in the current article. Overall, we shall argue that it is best to view the (generalized) Rainich conditions as a refinement of the classical energy conditions and the usual Hawking-Ellis classification.

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

PubMed Central

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

2017-01-01

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

Binary Orbits as the Driver of Gamma-Ray Emission and Mass Ejection in Classical Novae

NASA Technical Reports Server (NTRS)

Chomiuk, Laura; Linford, Justin D.; Yang, Jun; O'Brien, T. J.; Paragi, Zsolt; Mioduszewski, Amy J.; Beswick, R. J.; Cheung, C. C.; Mukai, Koji; Nelson, Thomas

2014-01-01

Classical novae are the most common astrophysical thermonuclear explosions, occurring on the surfaces of white dwarf stars accreting gas from companions in binary star systems. Novae typically expel about 10 (sup -4) solar masses of material at velocities exceeding 1,000 kilometers per second.However, the mechanism of mass ejection in novae is poorly understood, and could be dominated by the impulsive flash of thermonuclear energy, prolonged optically thick winds or binary interaction with the nova envelope. Classical novae are now routinely detected at giga-electronvolt gamma-ray wavelengths, suggesting that relativistic particles are accelerated by strong shocks in the ejecta. Here we report high-resolution radio imaging of the gamma-ray-emitting nova V959 Mon. We find that its ejecta were shaped by the motion of the binary system: some gas was expelled rapidly along the poles as a wind from the white dwarf, while denser material drifted out along the equatorial plane, propelled by orbital motion..At the interface between the equatorial and polar regions, we observe synchrotron emission indicative of shocks and relativistic particle acceleration, thereby pinpointing the location of gamma-ray production. Binary shaping of the nova ejecta and associated internal shocks are expected to be widespread among novae, explaining why many novae are gamma-ray emitters.

Critical point of gas-liquid type phase transition and phase equilibrium functions in developed two-component plasma model.

PubMed

Butlitsky, M A; Zelener, B B; Zelener, B V

2014-07-14

A two-component plasma model, which we called a "shelf Coulomb" model has been developed in this work. A Monte Carlo study has been undertaken to calculate equations of state, pair distribution functions, internal energies, and other thermodynamics properties. A canonical NVT ensemble with periodic boundary conditions was used. The motivation behind the model is also discussed in this work. The "shelf Coulomb" model can be compared to classical two-component (electron-proton) model where charges with zero size interact via a classical Coulomb law. With important difference for interaction of opposite charges: electrons and protons interact via the Coulomb law for large distances between particles, while interaction potential is cut off on small distances. The cut off distance is defined by an arbitrary ɛ parameter, which depends on system temperature. All the thermodynamics properties of the model depend on dimensionless parameters ɛ and γ = βe(2)n(1/3) (where β = 1/kBT, n is the particle's density, kB is the Boltzmann constant, and T is the temperature) only. In addition, it has been shown that the virial theorem works in this model. All the calculations were carried over a wide range of dimensionless ɛ and γ parameters in order to find the phase transition region, critical point, spinodal, and binodal lines of a model system. The system is observed to undergo a first order gas-liquid type phase transition with the critical point being in the vicinity of ɛ(crit) ≈ 13(T(*)(crit) ≈ 0.076), γ(crit) ≈ 1.8(v(*)(crit) ≈ 0.17), P(*)(crit) ≈ 0.39, where specific volume v* = 1/γ(3) and reduced temperature T(*) = ɛ(-1).

Ionic Structure at Dielectric Interfaces

NASA Astrophysics Data System (ADS)

Jing, Yufei

The behavior of ions in liquids confined between macromolecules determines the outcome of many nanoscale assembly processes in synthetic and biological materials such as colloidal dispersions, emulsions, hydrogels, DNA, cell membranes, and proteins. Theoretically, the macromolecule-liquid boundary is often modeled as a dielectric interface and an important quantity of interest is the ionic structure in a liquid confined between two such interfaces. The knowledge gleaned from the study of ionic structure in such models can be useful in several industrial applications, such as biosensors, lithium-ion batteries double-layer supercapacitors for energy storage and seawater desalination. Electrostatics plays a critical role in the development of such functional materials. Many of the functions of these materials, result from charge and composition heterogeneities. There are great challenges in solving electrostatics problems in heterogeneous media with arbitrary shapes because electrostatic interactions remains unknown but depend on the particular density of charge distributions. Charged molecules in heterogeneous media affect the media's dielectric response and hence the interaction between the charges is unknown since it depends on the media and on the geometrical properties of the interfaces. To determine the properties of heterogeneous systems including crucial effects neglected in classical mean field models such as the hard core of the ions, the dielectric mismatch and interfaces with arbitrary shapes. The effect of hard core interactions accounts properly for short range interactions and the effect of local dielectric heterogeneities in the presence of ions and/or charged molecules for long-range interactions are both analyzed via an energy variational principle that enables to update charges and the medium's response in the same simulation time step. In particular, we compute the ionic structure in a model system of electrolyte confined by two planar dielectric interfaces using molecular dynamics(MD) simulations and compared it with liquid state theory result. We explore the effects of high electrolyte concentrations, multivalent ions, and dielectric contrasts on the ionic distributions. We observe the presence of non-monotonous ionic density profiles leading to structure deformation in the fluid which is attributed to the competition between electrostatic and steric (entropic) interactions. We find that thermal forces that arise from symmetry breaking at the interfaces can have a profound effect on the ionic structure and can oftentimes overwhelm the influence of dielectric discontinuity. The combined effect of ionic correlations and inhomogeneous dielectric permittivity significantly changes the character of effective interaction between two interfaces. We show that, in concentrated electrolytes with confinement, it is imperative to take into account the finite-size of the ions as well as proper description of electrostatic interactions in heterogeneous media, which is not fully fulfilled by Poisson-Boltzmann based approaches. The effect of electric field at interface between two immiscible electrolyte solutions is studied as well. The classical Poisson-Boltzmann theory has been widely used to describe the corresponding ionic distribution, even though it neglects the polarization and ion correlations typical of these charged systems. Using Monte Carlo simulations, we provide an enhanced description of an oil-water interface in the presence of an electric field without needing any adjustable parameter, including realistic ionic sizes, ion correlations, and image charges. Our data agree with experimental measurements of excess surface tension for a wide range of electrolyte concentrations of LiCl and TBATPB (tetrabutylammonium-tetraphenylborate), contrasting with the result of the classical non-linear Poisson-Boltzmann theory. More importantly, we show that the size-asymmetry between small Li+ and large Cl- ions can significantly increase the electric field near the liquid interface, or can even reverse it locally, at high salt concentrations in the aqueous phase. These observations suggest a novel trapping/release mechanism of charged nanoparticles at oil-water interfaces in the vicinity of the point of zero charge. In addition, we study the effects of size asymmetry and charge asymmetry on ion distribution at a dielectric interface using coarse-grained MD based on an energy variational principle. The goal is to explore charge amplification with exact consideration of surface polarization. We find that both size asymmetry and charge asymmetry lead to charge separation at the interfaces. In addition, charge separation is enhanced by interface polarization. We are currently extending the research to charged interfaces that has broad applications such as batteries and supercapacitors for energy storage.

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

PubMed

Kashefolgheta, Sadra; Vila Verde, Ana

2017-08-09

We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

Numerical investigation of a vortex ring impinging on a coaxial aperture

NASA Astrophysics Data System (ADS)

Hu, Jiacheng; Peterson, Sean D.

2017-11-01

Recent advancements in smart materials have sparked an interest in the development of small scale fluidic energy harvesters for powering distributed applications in aquatic environments, where coherent vortex structures are prevalent. Thus, it is crucial to investigate the interaction of viscous vortices in the proximity of a thin plate (a common harvester configuration). Hence, the present study systematically examines the interaction of a vortex ring impinging on an infinitesimally thin wall with a coaxially aligned annular aperture. The rigid aperture serves as an axisymmetric counterpart of the thin plate, and the vortex ring represents a typical coherent vortex structure. The results indicate that the vortex dynamics can be categorized into two regimes based on the aperture to ring radius ratio (Rr). The rebound regime (Rr < 0.9) exhibits the classical unsteady boundary layer interaction in a vortex ring-wall collision. The vortex ring is able to slip past the aperture when Rr >= 0.9 , and an increase in the vortex ring impulse is observed for 1.0 <= Rr <= 1.3 due to fluid entrainment. Furthermore, pressure loadings are also compared to elucidate an optimal energy harvesting strategy in vortex impact configurations. This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant (RGPIN-05778) and Alexander Graham Bell Canada Graduate Scholarship (CGS-D).

Quantitative characterization of non-classic polarization of cations on clay aggregate stability.

PubMed

Hu, Feinan; Li, Hang; Liu, Xinmin; Li, Song; Ding, Wuquan; Xu, Chenyang; Li, Yue; Zhu, Longhui

2015-01-01

Soil particle interactions are strongly influenced by the concentration, valence and ion species and the pH of the bulk solution, which will also affect aggregate stability and particle transport. In this study, we investigated clay aggregate stability in the presence of different alkali ions (Li+, Na+, K+, and Cs+) at concentrations from10-5 to 10-1 mol L-1. Strong specific ion effects on clay aggregate stability were observed, and showed the order Cs+>K+>Na+>Li+. We found that it was not the effects of ion size, hydration, and dispersion forces in the cation-surface interactions but strong non-classic polarization of adsorbed cations that resulted in these specific effects. In this study, the non-classic dipole moments of each cation species resulting from the non-classic polarization were estimated. By comparing non-classic dipole moments with classic values, the observed dipole moments of adsorbed cations were up to 104 times larger than the classic values for the same cation. The observed non-classic dipole moments sharply increased with decreasing electrolyte concentration. We conclude that strong non-classic polarization could significantly suppress the thickness of the diffuse layer, thereby weakening the electric field near the clay surface and resulting in improved clay aggregate stability. Even though we only demonstrated specific ion effects on aggregate stability with several alkali ions, our results indicate that these effects could be universally important in soil aggregate stability.

Quantitative Characterization of Non-Classic Polarization of Cations on Clay Aggregate Stability

PubMed Central

Hu, Feinan; Li, Hang; Liu, Xinmin; Li, Song; Ding, Wuquan; Xu, Chenyang; Li, Yue; Zhu, Longhui

2015-01-01

Soil particle interactions are strongly influenced by the concentration, valence and ion species and the pH of the bulk solution, which will also affect aggregate stability and particle transport. In this study, we investigated clay aggregate stability in the presence of different alkali ions (Li+, Na+, K+, and Cs+) at concentrations from10−5 to 10−1 mol L−1. Strong specific ion effects on clay aggregate stability were observed, and showed the order Cs+>K+>Na+>Li+. We found that it was not the effects of ion size, hydration, and dispersion forces in the cation–surface interactions but strong non-classic polarization of adsorbed cations that resulted in these specific effects. In this study, the non-classic dipole moments of each cation species resulting from the non-classic polarization were estimated. By comparing non-classic dipole moments with classic values, the observed dipole moments of adsorbed cations were up to 104 times larger than the classic values for the same cation. The observed non-classic dipole moments sharply increased with decreasing electrolyte concentration. We conclude that strong non-classic polarization could significantly suppress the thickness of the diffuse layer, thereby weakening the electric field near the clay surface and resulting in improved clay aggregate stability. Even though we only demonstrated specific ion effects on aggregate stability with several alkali ions, our results indicate that these effects could be universally important in soil aggregate stability. PMID:25874864

Extremely efficient internal exciton dissociation through edge states in layered 2D perovskites

NASA Astrophysics Data System (ADS)

Blancon, J.-C.; Tsai, H.; Nie, W.; Stoumpos, C. C.; Pedesseau, L.; Katan, C.; Kepenekian, M.; Soe, C. M. M.; Appavoo, K.; Sfeir, M. Y.; Tretiak, S.; Ajayan, P. M.; Kanatzidis, M. G.; Even, J.; Crochet, J. J.; Mohite, A. D.

2017-03-01

Understanding and controlling charge and energy flow in state-of-the-art semiconductor quantum wells has enabled high-efficiency optoelectronic devices. Two-dimensional (2D) Ruddlesden-Popper perovskites are solution-processed quantum wells wherein the band gap can be tuned by varying the perovskite-layer thickness, which modulates the effective electron-hole confinement. We report that, counterintuitive to classical quantum-confined systems where photogenerated electrons and holes are strongly bound by Coulomb interactions or excitons, the photophysics of thin films made of Ruddlesden-Popper perovskites with a thickness exceeding two perovskite-crystal units (>1.3 nanometers) is dominated by lower-energy states associated with the local intrinsic electronic structure of the edges of the perovskite layers. These states provide a direct pathway for dissociating excitons into longer-lived free carriers that substantially improve the performance of optoelectronic devices.

Quantum Theory of Wormholes

NASA Astrophysics Data System (ADS)

González-Díaz, Pedro F.

We re-explore the effects of multiply-connected wormholes on ordinary matter at low energies. It is obtained that the path integral that describes these effects is given in terms of a Planckian probability distribution for the Coleman α-parameters, rather than a classical Gaussian distribution law. This implies that the path integral over all low-energy fields with the wormhole effective interactions can no longer vary continuously, and that the quantities α2 are interpretable as the momenta of a quantum field. Using the new result that, rather than being given in terms of the Coleman-Hawking probability, the Euclidean action must equal negative entropy, the model predicts a very small but still nonzero cosmological constant and quite reasonable values for the pion and neutrino masses. The divergence problems of Euclidean quantum gravity are also discussed in the light of the above results.

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

Blancon, Jean -Christophe Robert; Tsai, Hsinhan; Nie, Wanyi

Understanding and controlling charge and energy flow in state-of-the-art semiconductor quantum wells has enabled high-efficiency optoelectronic devices. Two-dimensional (2D) Ruddlesden-Popper perovskites are solution-processed quantum wells wherein the band gap can be tuned by varying the perovskite-layer thickness, which modulates the effective electron-hole confinement. We report that, counterintuitive to classical quantum-confined systems where photogenerated electrons and holes are strongly bound by Coulomb interactions or excitons, the photophysics of thin films made of Ruddlesden-Popper perovskites with a thickness exceeding two perovskite-crystal units (>1.3 nanometers) is dominated by lower-energy states associated with the local intrinsic electronic structure of the edges of the perovskitemore » layers. Furthermore, these states provide a direct pathway for dissociating excitons into longer-lived free carriers that substantially improve the performance of optoelectronic devices.« less

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer

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

Daily, Michael D.; Baer, Marcel D.; Mundy, Christopher J.

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids usingmore » a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical forcefield (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through sidechain-sidechain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described. MDD was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. Research was funded by the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. MDB acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Material & Engineering. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Energy loss of ions by electric-field fluctuations in a magnetized plasma.

PubMed

Nersisyan, Hrachya B; Deutsch, Claude

2011-06-01

The results of a theoretical investigation of the energy loss of charged particles in a magnetized classical plasma due to the electric-field fluctuations are reported. The energy loss for a test particle is calculated through the linear-response theory. At vanishing magnetic field, the electric-field fluctuations lead to an energy gain of the charged particle for all velocities. It has been shown that in the presence of strong magnetic field, this effect occurs only at low velocities. In the case of high velocities, the test particle systematically loses its energy due to the interaction with a stochastic electric field. The net effect of the fluctuations is the systematic reduction of the total energy loss (i.e., the sum of the polarization and stochastic energy losses) at vanishing magnetic field and reduction or enhancement at strong field, depending on the velocity of the particle. It is found that the energy loss of the slow heavy ion contains an anomalous term that depends logarithmically on the projectile mass. The physical origin of this anomalous term is the coupling between the cyclotron motion of the plasma electrons and the long-wavelength, low-frequency fluctuations produced by the projectile ion. This effect may strongly enhance the stochastic energy gain of the particle.

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study.

PubMed

Mudedla, Sathish Kumar; Azhagiya Singam, Ettayapuram Ramaprasad; Balamurugan, Kanagasabai; Subramanian, Venkatesan

2015-11-11

The complexation of small interfering RNA (siRNA) with positively charged gold nanoclusters has been studied in the present investigation with the help of classical molecular dynamics and steered molecular dynamics simulations accompanied by free energy calculations. The results show that gold nanoclusters form a stable complex with siRNA. The wrapping of siRNA around the gold nanocluster depends on the size and charge on the surface of the gold cluster. The binding pattern of the gold nanocluster with siRNA is also influenced by the presence of another cluster. The interaction between the positively charged amines in the gold nanocluster and the negatively charged phosphate group in the siRNA is responsible for the formation of complexes. The binding free energy value increases with the size of the gold cluster and the number of positive charges present on the surface of the gold nanocluster. The results reveal that the binding energy of small gold nanoclusters increases in the presence of another gold nanocluster while the binding of large gold nanoclusters decreases due to the introduction of another gold nanocluster. Overall, the findings have clearly demonstrated the effect of size and charge of gold nanoclusters on their interaction pattern with siRNA.

Rotational quenching of H2O by He: mixed quantum/classical theory and comparison with quantum results.

PubMed

Ivanov, Mikhail; Dubernet, Marie-Lise; Babikov, Dmitri

2014-04-07

The mixed quantum/classical theory (MQCT) formulated in the space-fixed reference frame is used to compute quenching cross sections of several rotationally excited states of water molecule by impact of He atom in a broad range of collision energies, and is tested against the full-quantum calculations on the same potential energy surface. In current implementation of MQCT method, there are two major sources of errors: one affects results at energies below 10 cm(-1), while the other shows up at energies above 500 cm(-1). Namely, when the collision energy E is below the state-to-state transition energy ΔE the MQCT method becomes less accurate due to its intrinsic classical approximation, although employment of the average-velocity principle (scaling of collision energy in order to satisfy microscopic reversibility) helps dramatically. At higher energies, MQCT is expected to be accurate but in current implementation, in order to make calculations computationally affordable, we had to cut off the basis set size. This can be avoided by using a more efficient body-fixed formulation of MQCT. Overall, the errors of MQCT method are within 20% of the full-quantum results almost everywhere through four-orders-of-magnitude range of collision energies, except near resonances, where the errors are somewhat larger.

The Initial Flow of Classical Gluon Fields in Heavy Ion Collisions

NASA Astrophysics Data System (ADS)

Fries, Rainer J.; Chen, Guangyao

2015-03-01

Using analytic solutions of the Yang-Mills equations we calculate the initial flow of energy of the classical gluon field created in collisions of large nuclei at high energies. We find radial and elliptic flow which follows gradients in the initial energy density, similar to a simple hydrodynamic behavior. In addition we find a rapidity-odd transverse flow field which implies the presence of angular momentum and should lead to directed flow in final particle spectra. We trace those energy flow terms to transverse fields from the non-abelian generalization of Gauss' Law and Ampere's and Faraday's Laws.

Yield Stress of Concentrated Zirconia Suspensions: Correlation with Particle Interactions.

PubMed

Megías-Alguacil; Durán; Delgado

2000-11-01

The presence of a sufficient concentration of solid particles in a solution gives rise to a large increase in its viscosity and, more importantly, to significant deviations with respect to its original Newtonian behavior. Different rheological techniques are available to characterize such deviations, but the simplest one, obtention of steady-state rheograms, is already extremely useful with that purpose. In this work, this technique is applied to suspensions of zirconia particles, both synthesized with spherical geometry and commercial. The sigma(shear stress)-gamma;(shear rate) curves show that the suspensions are nonideal plastic, thus exhibiting a finite yield stress, sigma(0), and a shear-thinning flow. It is through sigma(0) that a connection can be established between steady-state rheological behavior and interaction energy between particles, since sigma(0) can be estimated as the maximum attractive force between particles multiplied by the number of bonds per unit area between a given particle and its neighbors. Having an experimental determination of sigma(0), the verification of its relation with the attractive forces requires estimation of the potential energy of interaction between any pair of particles. Two approaches will be considered: one is the classical DLVO model, in which the potential energy, V, is the sum of the van der Waals (V(LW)) and electrostatic (V(EL)) contributions. The second approach is the so-called extended DLVO theory, in which the acid-base interaction V(AB) (related to the hydrophilic repulsion or hydrophobic attraction between the particles) is considered in addition to V(LW) and V(EL). The three contributions can be calculated as a function of the interparticle distance if the particle-solution interface is characterized from both the electric and the thermodynamic points of view. The former is carried out by means of electrophoretic mobility measurements and the latter by contact angle determinations for three probe liquids on zirconia powder layers. Comparison between measured and calculated sigma(0) values was carried out for suspensions of spherical, monodisperse ZrO(2) particles, with volume fraction of solids, straight phi, ranging between 4.6 and 21.7%, in 10(-3) M NaCl solutions. In the case of commercial particles, the effects of both NaCl concentration (10(-5) to 10(-1) M) and volume fraction (3.5 to 21%) were investigated. It is found that the classical DLVO theory cannot be used to predict the yield stress when [NaCl]=10(-5) M, since the high zeta potentials and thick double layers never yield partial differential V/ partial differential R>0 (the interaction is repulsive for all distances) in such a case. A similar problem was encountered in 10(-1) M solutions, but now because V is always attractive, and no maximum force can be found. On the contrary, the extended DLVO model always yield physically reasonable sigma(0) values (coincident with those deduced from the classical approach when calculation is possible in the latter case). The comparison with experimental data shows that theory clearly underestimates sigma(0) by one order of magnitude or even more. The possible role of particle aggregation in this underestimation is discussed in terms of the scaling behavior of sigma(0) as a function of straight phi. Copyright 2000 Academic Press.

Demonstration and implications when 50% beam combiners can behave as 0% or 100% reflector/transmitter inside some interferometers

NASA Astrophysics Data System (ADS)

Roychoudhuri, ChandraSekhar

2017-08-01

The purpose of this paper is to embolden students to raise basic questions regarding the feasibility of "indivisible single photon interference". We do this by presenting experimental results of well-known classical Mach-Zehnder interferometer (MZI) under two different conditions of beam alignment. We routinely do such experiments in our laboratories. In the first case, we align the light beams on the beam combiner (BC) with their Poynting vectors as perfectly collinear. The 50% dielectric boundary can now transmit 100% of the energy of both the beams into either one of the two MZI output ports, depending upon the relative phase between the two beams combined on the BC from the opposite directions. The dielectric boundary layer actively re-directs the energy from one beam to the other. This is pure classical superposition effect. In the second case, we combine the two beams on the BC with a small intersecting angle. Now the BC functions as a 50% beam splitter to both the beams. One can see spatial fringes as the relative phase varies with spatial distance by placing a photo detector array after the BC. At very low intensity, the quantum properties of the photo detector will become apparent because the photo electrons are discrete and are always bound quantum mechanically to its host molecular assembly; and not because light is definitely quantized. Students can learn to distinguish the pedagogical difference between the Superposition Principle (linear sum of wave amplitudes) and the Superposition Effect (square modulus of the sum of all the wave-induced stimulations) as observable intensity variations due to interaction with materials, classical or quantum.

Observable signatures of a classical transition

NASA Astrophysics Data System (ADS)

Johnson, Matthew C.; Lin, Wei

2016-03-01

Eternal inflation arising from a potential landscape predicts that our universe is one realization of many possible cosmological histories. One way to access different cosmological histories is via the nucleation of bubble universes from a metastable false vacuum. Another way to sample different cosmological histories is via classical transitions, the creation of pocket universes through the collision between bubbles. Using relativistic numerical simulations, we examine the possibility of observationally determining if our observable universe resulted from a classical transition. We find that classical transitions produce spatially infinite, approximately open Friedman-Robertson-Walker universes. The leading set of observables in the aftermath of a classical transition are negative spatial curvature and a contribution to the Cosmic Microwave Background temperature quadrupole. The level of curvature and magnitude of the quadrupole are dependent on the position of the observer, and we determine the possible range of observables for two classes of single-scalar field models. For the first class, where the inflationary phase has a lower energy than the vacuum preceding the classical transition, the magnitude of the observed quadrupole generally falls to zero with distance from the collision while the spatial curvature grows to a constant. For the second class, where the inflationary phase has a higher energy than the vacuum preceding the classical transition, the magnitude of the observed quadrupole generically falls to zero with distance from the collision while the spatial curvature grows without bound. We find that the magnitude of the quadrupole and curvature grow with increasing centre of mass energy of the collision, and explore variations of the parameters in the scalar field lagrangian.

Observable signatures of a classical transition

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

Johnson, Matthew C.; Lin, Wei, E-mail: mjohnson@perimeterinstitute.ca, E-mail: lewisweilin@gmail.com

2016-03-01

Eternal inflation arising from a potential landscape predicts that our universe is one realization of many possible cosmological histories. One way to access different cosmological histories is via the nucleation of bubble universes from a metastable false vacuum. Another way to sample different cosmological histories is via classical transitions, the creation of pocket universes through the collision between bubbles. Using relativistic numerical simulations, we examine the possibility of observationally determining if our observable universe resulted from a classical transition. We find that classical transitions produce spatially infinite, approximately open Friedman-Robertson-Walker universes. The leading set of observables in the aftermath ofmore » a classical transition are negative spatial curvature and a contribution to the Cosmic Microwave Background temperature quadrupole. The level of curvature and magnitude of the quadrupole are dependent on the position of the observer, and we determine the possible range of observables for two classes of single-scalar field models. For the first class, where the inflationary phase has a lower energy than the vacuum preceding the classical transition, the magnitude of the observed quadrupole generally falls to zero with distance from the collision while the spatial curvature grows to a constant. For the second class, where the inflationary phase has a higher energy than the vacuum preceding the classical transition, the magnitude of the observed quadrupole generically falls to zero with distance from the collision while the spatial curvature grows without bound. We find that the magnitude of the quadrupole and curvature grow with increasing centre of mass energy of the collision, and explore variations of the parameters in the scalar field lagrangian.« less

Scaling and self-organized criticality in proteins: Lysozyme c

NASA Astrophysics Data System (ADS)

Phillips, J. C.

2009-11-01

Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is often dominated by long-range hydro(phobic/philic) interactions, which both drive protein compaction and mediate protein-protein interactions. In contrast to previous reductionist short-range hydrophobicity scales, the holistic Moret-Zebende hydrophobicity scale [Phys. Rev. E 75, 011920 (2007)] represents a hydroanalytic tool that bioinformatically quantifies SOC in a way fully compatible with evolution. Hydroprofiling identifies chemical trends in the activities and substrate binding abilities of model enzymes and antibiotic animal lysozymes c , as well as defensins, which have been the subject of tens of thousands of experimental studies. The analysis is simple and easily performed and immediately yields insights not obtainable by traditional methods based on short-range real-space interactions, as described either by classical force fields used in molecular-dynamics simulations, or hydrophobicity scales based on transference energies from water to organic solvents or solvent-accessible areas.

Magnetic interactions and magnetic anisotropy in exchange coupled 4f-3d systems: a case study of a heterodinuclear Ce3+-Fe3+ cyanide-bridged complex.

PubMed

Sorace, Lorenzo; Sangregorio, Claudio; Figuerola, Albert; Benelli, Cristiano; Gatteschi, Dante

2009-01-01

We report here a detailed single-crystal EPR and magnetic study of a homologous series of complexes of the type Ln-M (Ln = La(III), Ce(III); M = Fe(III), Co(III)). We were able to obtain a detailed picture of the low-lying levels of Ce(III) and Fe(III) centres through the combined use of single-crystal EPR and magnetic susceptibility data. We show that classical ligand field theory can be of great help in rationalising the energies of the low-lying levels of both the transition-metal and rare-earth ions. The combined analysis of single-crystal EPR and magnetic data of the coupled system Ce-Fe confirmed the great complexity of the interactions involving rare-earth elements. With little uncertainty, it turned out clearly that the description of the interaction involving the lowest lying spin levels requires the introduction of the isotropic, anisotropic and antisymmetric terms.

Comparative analysis of ArnCl2 (2 ? n ? 30) clusters taking into account molecular relaxation effects

NASA Astrophysics Data System (ADS)

Ferreira, G. G.; Borges, E.; Braga, J. P.; Belchior, J. C.

Cluster structures are discussed in a nonrigid analysis, using a modified minima search method based on stochastic processes and classical dynamics simulations. The relaxation process is taken into account considering the internal motion of the Cl2 molecule. Cluster structures are compared with previous works in which the Cl2 molecule is assumed to be rigid. The interactions are modeled using pair potentials: the Aziz and Lennard-Jones potentials for the Ar==Ar interaction, a Morse potential for the Cl==Cl interaction, and a fully spherical/anisotropic Morse-Spline-van der Waals (MSV) potential for the Ar==Cl interaction. As expected, all calculated energies are lower than those obtained in a rigid approximation; one reason may be attributed to the nonrigid contributions of the internal motion of the Cl2 molecule. Finally, the growing processes in molecular clusters are discussed, and it is pointed out that the growing mechanism can be affected due to the nonrigid initial conditions of smaller clusters such as ArnCl2 (n ? 4 or 5), which are seeds for higher-order clusters.

Halogen bonding (X-bonding): A biological perspective

PubMed Central

Scholfield, Matthew R; Zanden, Crystal M Vander; Carter, Megan; Ho, P Shing

2013-01-01

The concept of the halogen bond (or X-bond) has become recognized as contributing significantly to the specificity in recognition of a large class of halogenated compounds. The interaction is most easily understood as primarily an electrostatically driven molecular interaction, where an electropositive crown, or σ-hole, serves as a Lewis acid to attract a variety of electron-rich Lewis bases, in analogous fashion to a classic hydrogen bonding (H-bond) interaction. We present here a broad overview of X-bonds from the perspective of a biologist who may not be familiar with this recently rediscovered class of interactions and, consequently, may be interested in how they can be applied as a highly directional and specific component of the molecular toolbox. This overview includes a discussion for where X-bonds are found in biomolecular structures, and how their structure–energy relationships are studied experimentally and modeled computationally. In total, our understanding of these basic concepts will allow X-bonds to be incorporated into strategies for the rational design of new halogenated inhibitors against biomolecular targets or toward molecular engineering of new biological-based materials. PMID:23225628

Innate immune humoral factors, C1q and factor H, with differential pattern recognition properties, alter macrophage response to carbon nanotubes.

PubMed

Pondman, Kirsten M; Pednekar, Lina; Paudyal, Basudev; Tsolaki, Anthony G; Kouser, Lubna; Khan, Haseeb A; Shamji, Mohamed H; Ten Haken, Bennie; Stenbeck, Gudrun; Sim, Robert B; Kishore, Uday

2015-11-01

Interaction between the complement system and carbon nanotubes (CNTs) can modify their intended biomedical applications. Pristine and derivatised CNTs can activate complement primarily via the classical pathway which enhances uptake of CNTs and suppresses pro-inflammatory response by immune cells. Here, we report that the interaction of C1q, the classical pathway recognition molecule, with CNTs involves charge pattern and classical pathway activation that is partly inhibited by factor H, a complement regulator. C1q and its globular modules, but not factor H, enhanced uptake of CNTs by macrophages and modulated the pro-inflammatory immune response. Thus, soluble complement factors can interact differentially with CNTs and alter the immune response even without complement activation. Coating CNTs with recombinant C1q globular heads offers a novel way of controlling classical pathway activation in nanotherapeutics. Surprisingly, the globular heads also enhance clearance by phagocytes and down-regulate inflammation, suggesting unexpected complexity in receptor interaction. Carbon nanotubes (CNTs) maybe useful in the clinical setting as targeting drug carriers. However, it is also well known that they can interact and activate the complement system, which may have a negative impact on the applicability of CNTs. In this study, the authors functionalized multi-walled CNT (MWNT), and investigated the interaction with the complement pathway. These studies are important so as to gain further understanding of the underlying mechanism in preparation for future use of CNTs in the clinical setting. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Wavelet-based multiscale window transform and energy and vorticity analysis

NASA Astrophysics Data System (ADS)

Liang, Xiang San

A new methodology, Multiscale Energy and Vorticity Analysis (MS-EVA), is developed to investigate sub-mesoscale, meso-scale, and large-scale dynamical interactions in geophysical fluid flows which are intermittent in space and time. The development begins with the construction of a wavelet-based functional analysis tool, the multiscale window transform (MWT), which is local, orthonormal, self-similar, and windowed on scale. The MWT is first built over the real line then modified onto a finite domain. Properties are explored, the most important one being the property of marginalization which brings together a quadratic quantity in physical space with its phase space representation. Based on MWT the MS-EVA is developed. Energy and enstrophy equations for the large-, meso-, and sub-meso-scale windows are derived and their terms interpreted. The processes thus represented are classified into four categories: transport; transfer, conversion, and dissipation/diffusion. The separation of transport from transfer is made possible with the introduction of the concept of perfect transfer. By the property of marginalization, the classical energetic analysis proves to be a particular case of the MS-EVA. The MS-EVA developed is validated with classical instability problems. The validation is carried out through two steps. First, it is established that the barotropic and baroclinic instabilities are indicated by the spatial averages of certain transfer term interaction analyses. Then calculations of these indicators are made with an Eady model and a Kuo model. The results agree precisely with what is expected from their analytical solutions, and the energetics reproduced reveal a consistent and important aspect of the unknown dynamic structures of instability processes. As an application, the MS-EVA is used to investigate the Iceland-Faeroe frontal (IFF) variability. A MS-EVA-ready dataset is first generated, through a forecasting study with the Harvard Ocean Prediction System using the data gathered during the 1993 NRV Alliance cruise. The application starts with a determination of the scale window bounds, which characterize a double-peak structure in either the time wavelet spectrum or the space wavelet spectrum. The resulting energetics, when locally averaged, reveal that there is a clear baroclinic instability happening around the cold tongue intrusion observed in the forecast. Moreover, an interaction analysis shows that the energy released by the instability indeed goes to the meso-scale window and fuel the growth of the intrusion. The sensitivity study shows that, in this case, the key to a successful application is a correct decomposition of the large-scale window from the meso-scale window.

[The theory of mechanical activity of lungs--a creation history, the present and development prospects].

PubMed

Tetenev, F F; Tetenev, K F

2014-01-01

In article the history of creation of the doctrine about respiratory movements of lungs, history of classical mechanics of breathing is stated. Supervision of the paradoxical facts which became a basis for hypothesis creation, then the theory of mechanical activity of lungs are presented. The facts proving mechanical activity of lungs on an inspiration and an expiration are given. Options of interaction of intra pulmonary and extra pulmonary sources of mechanical energy are considered. Theoretical justification for development of the new direction of studying of physiology of mechanical movements of the internal which does not have own skeleton is stated.

Nonexponential Decoherence and Subdiffusion in Atom-Optics Kicked Rotor.

PubMed

Sarkar, Sumit; Paul, Sanku; Vishwakarma, Chetan; Kumar, Sunil; Verma, Gunjan; Sainath, M; Rapol, Umakant D; Santhanam, M S

2017-04-28

Quantum systems lose coherence upon interaction with the environment and tend towards classical states. Quantum coherence is known to exponentially decay in time so that macroscopic quantum superpositions are generally unsustainable. In this work, slower than exponential decay of coherences is experimentally realized in an atom-optics kicked rotor system subjected to nonstationary Lévy noise in the applied kick sequence. The slower coherence decay manifests in the form of quantum subdiffusion that can be controlled through the Lévy exponent. The experimental results are in good agreement with the analytical estimates and numerical simulations for the mean energy growth and momentum profiles of an atom-optics kicked rotor.

Phasing operator for two oscillators in classical field

NASA Technical Reports Server (NTRS)

Kim, Jong-Jean; Koo, Je-Hwan; Bae, Dong-Jae

1993-01-01

The origin of Dicke cooperative states was studied by considering two harmonic oscillators driven by a common field of radiation. The origin is assumed for superradiance in a system of molecules where no mutual interactions exist, but all of the molecules encounter the same field of radiation. A phasing operator as Phi(sub Nu) equals D(alpha) + P(sub Nu)D(alpha), where D(alpha) is the displacing operator and P(sub Nu) the projection operator for constant energy Nu for two oscillators, was derived. The eigenstates of the phasing operator Phi are found to show a finite correlation as in the Dicke cooperative states.

Quantum effects in the capture of charged particles by dipolar polarizable symmetric top molecules. I. General axially nonadiabatic channel treatment.

PubMed

Auzinsh, M; Dashevskaya, E I; Litvin, I; Nikitin, E E; Troe, J

2013-08-28

The rate coefficients for capture of charged particles by dipolar polarizable symmetric top molecules in the quantum collision regime are calculated within an axially nonadiabatic channel approach. It uses the adiabatic approximation with respect to rotational transitions of the target within first-order charge-dipole interaction and takes into account the gyroscopic effect that decouples the intrinsic angular momentum from the collision axis. The results are valid for a wide range of collision energies (from single-wave capture to the classical limit) and dipole moments (from the Vogt-Wannier and fly-wheel to the adiabatic channel limit).

A quantum-classical theory with nonlinear and stochastic dynamics

NASA Astrophysics Data System (ADS)

Burić, N.; Popović, D. B.; Radonjić, M.; Prvanović, S.

2014-12-01

The method of constrained dynamical systems on the quantum-classical phase space is utilized to develop a theory of quantum-classical hybrid systems. Effects of the classical degrees of freedom on the quantum part are modeled using an appropriate constraint, and the interaction also includes the effects of neglected degrees of freedom. Dynamical law of the theory is given in terms of nonlinear stochastic differential equations with Hamiltonian and gradient terms. The theory provides a successful dynamical description of the collapse during quantum measurement.

Bosonization of nonrelativistic fermions on a circle: Tomonaga's problem revisited

NASA Astrophysics Data System (ADS)

Dhar, Avinash; Mandal, Gautam

2006-11-01

We use the recently developed tools for an exact bosonization of a finite number N of nonrelativistic fermions to discuss the classic Tomonaga problem. In the case of noninteracting fermions, the bosonized Hamiltonian naturally splits into an O(N) piece and an O(1) piece. We show that in the large-N and low-energy limit, the O(N) piece in the Hamiltonian describes a massless relativistic boson, while the O(1) piece gives rise to cubic self-interactions of the boson. At finite N and high energies, the low-energy effective description breaks down and the exact bosonized Hamiltonian must be used. We also comment on the connection between the Tomonaga problem and pure Yang-Mills theory on a cylinder. In the dual context of baby universes and multiple black holes in string theory, we point out that the O(N) piece in our bosonized Hamiltonian provides a simple understanding of the origin of two different kinds of nonperturbative O(e-N) corrections to the black hole partition function.

One-Particle Representation of Heat Conduction Described within the Scope of the Second Law.

PubMed

Jesudason, Christopher Gunaseelan

2016-01-01

The Carnot cycle and its deduction of maximum conversion efficiency of heat inputted and outputted isothermally at different temperatures necessitated the construction of isothermal and adiabatic pathways within the cycle that were mechanically "reversible", leading eventually to the Kelvin-Clausius development of the entropy function S with differential dS = dq/T such that [symbol: see text]C dS = 0 where the heat absorption occurs at the isothermal paths of the elementary Carnot cycle. Another required condition is that the heat transfer processes take place infinitely slowly and "reversibly", implying that rates of transfer are not explicitly featured in the theory. The definition of 'heat' as that form of energy that is transferred as a result of a temperature difference suggests that the local mode of transfer of "heat" in the isothermal segments of the pathway implies a Fourier-like heat conduction mechanism which is apparently irreversible, leading to an increase in entropy of the combined reservoirs at either end of the conducting material, and which is deemed reversible mechanically. These paradoxes are circumvented here by first clarifying the terms used before modeling heat transfer as a thermodynamically reversible but mechanically irreversible process and applied to a one dimensional atomic lattice chain of interacting particles subjected to a temperature difference exemplifying Fourier heat conduction. The basis of a "recoverable trajectory" i.e. that which follows a zero entropy trajectory is identified. The Second Law is strictly maintained in this development. A corollary to this zero entropy trajectory is the generalization of the Zeroth law for steady state non-equilibrium systems with varying temperature, and thus to a statement about "equilibrium" in steady state non-thermostatic conditions. An energy transfer rate term is explicitly identified for each particle and agrees quantitatively (and independently) with the rate of heat absorbed at the reservoirs held at different temperatures and located at the two ends of the lattice chain in MD simulations, where all energy terms in the simulation refer to a single particle interacting with its neighbors. These results validate the theoretical model and provides the necessary boundary conditions (for instance with regard to temperature differentials and force fields) that thermodynamical variables must comply with to satisfy the conditions for a recoverable trajectory, and thus determines the solution of the differential and integral equations that are used to model these processes. These developments and results, if fully pursued would imply that not only can the Carnot cycle be viewed as describing a local process of energy-work conversion by a single interacting particle which feature rates of energy transfer and conversion not possible in the classical Carnot development, but that even irreversible local processes might be brought within the scope of this cycle, implying a unified treatment of thermodynamically (i) irreversible (ii) reversible (iii) isothermal and (iv) adiabatic processes by conflating the classically distinct concept of work and heat energy into a single particle interactional process. A resolution to the fundamental and long-standing conjecture of Benofy and Quay concerning the Fourier principle is one consequence of the analysis.

One-Particle Representation of Heat Conduction Described within the Scope of the Second Law

PubMed Central

Jesudason, Christopher Gunaseelan

2016-01-01

The Carnot cycle and its deduction of maximum conversion efficiency of heat inputted and outputted isothermally at different temperatures necessitated the construction of isothermal and adiabatic pathways within the cycle that were mechanically “reversible”, leading eventually to the Kelvin-Clausius development of the entropy function S with differential dS=dq/T such that ∮CdS=0 where the heat absorption occurs at the isothermal paths of the elementary Carnot cycle. Another required condition is that the heat transfer processes take place infinitely slowly and “reversibly”, implying that rates of transfer are not explicitly featured in the theory. The definition of ‘heat’ as that form of energy that is transferred as a result of a temperature difference suggests that the local mode of transfer of “heat” in the isothermal segments of the pathway implies a Fourier-like heat conduction mechanism which is apparently irreversible, leading to an increase in entropy of the combined reservoirs at either end of the conducting material, and which is deemed reversible mechanically. These paradoxes are circumvented here by first clarifying the terms used before modeling heat transfer as a thermodynamically reversible but mechanically irreversible process and applied to a one dimensional atomic lattice chain of interacting particles subjected to a temperature difference exemplifying Fourier heat conduction. The basis of a “recoverable trajectory” i.e. that which follows a zero entropy trajectory is identified. The Second Law is strictly maintained in this development. A corollary to this zero entropy trajectory is the generalization of the Zeroth law for steady state non-equilibrium systems with varying temperature, and thus to a statement about “equilibrium” in steady state non-thermostatic conditions. An energy transfer rate term is explicitly identified for each particle and agrees quantitatively (and independently) with the rate of heat absorbed at the reservoirs held at different temperatures and located at the two ends of the lattice chain in MD simulations, where all energy terms in the simulation refer to a single particle interacting with its neighbors. These results validate the theoretical model and provides the necessary boundary conditions (for instance with regard to temperature differentials and force fields) that thermodynamical variables must comply with to satisfy the conditions for a recoverable trajectory, and thus determines the solution of the differential and integral equations that are used to model these processes. These developments and results, if fully pursued would imply that not only can the Carnot cycle be viewed as describing a local process of energy-work conversion by a single interacting particle which feature rates of energy transfer and conversion not possible in the classical Carnot development, but that even irreversible local processes might be brought within the scope of this cycle, implying a unified treatment of thermodynamically (i) irreversible (ii) reversible (iii) isothermal and (iv) adiabatic processes by conflating the classically distinct concept of work and heat energy into a single particle interactional process. A resolution to the fundamental and long-standing conjecture of Benofy and Quay concerning the Fourier principle is one consequence of the analysis. PMID:26760507

Quantum-classical analogies in waveguide arrays: From Fourier transforms to ion-laser interactions

NASA Astrophysics Data System (ADS)

Moya-Cessa, Héctor M.

2018-04-01

By using the fact that infinite and semi-infinite systems of differential equations may be casted as Schrödinger-like equations we show how quantum-classical analogies may be achieved. In particular we show how the analogies of ion-laser, functions of a phase operator and quantised-field-two-level-atom interactions may be emulated. We also show a realization of the fractional discrete Fourier transform.

Probing low-energy hyperbolic polaritons in van der Waals crystals with an electron microscope.

PubMed

Govyadinov, Alexander A; Konečná, Andrea; Chuvilin, Andrey; Vélez, Saül; Dolado, Irene; Nikitin, Alexey Y; Lopatin, Sergei; Casanova, Fèlix; Hueso, Luis E; Aizpurua, Javier; Hillenbrand, Rainer

2017-07-21

Van der Waals materials exhibit intriguing structural, electronic, and photonic properties. Electron energy loss spectroscopy within scanning transmission electron microscopy allows for nanoscale mapping of such properties. However, its detection is typically limited to energy losses in the eV range-too large for probing low-energy excitations such as phonons or mid-infrared plasmons. Here, we adapt a conventional instrument to probe energy loss down to 100 meV, and map phononic states in hexagonal boron nitride, a representative van der Waals material. The boron nitride spectra depend on the flake thickness and on the distance of the electron beam to the flake edges. To explain these observations, we developed a classical response theory that describes the interaction of fast electrons with (anisotropic) van der Waals slabs, revealing that the electron energy loss is dominated by excitation of hyperbolic phonon polaritons, and not of bulk phonons as often reported. Thus, our work is of fundamental importance for interpreting future low-energy loss spectra of van der Waals materials.Here the authors adapt a STEM-EELS system to probe energy loss down to 100 meV, and apply it to map phononic states in hexagonal boron nitride, revealing that the electron loss is dominated by hyperbolic phonon polaritons.

Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

PubMed Central

Chakravorty, Dhruva K.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

2009-01-01

Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of ~8, and dynamical barrier recrossings decrease the rates by a factor of 3–4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme. PMID:19799395

General integrable n-level, many-mode Janes-Cummings-Dicke models and classical r-matrices with spectral parameters

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

Skrypnyk, T., E-mail: taras.skrypnyk@unimib.it, E-mail: tskrypnyk@imath.kiev.ua

Using the technique of classical r-matrices and quantum Lax operators, we construct the most general form of the quantum integrable “n-level, many-mode” spin-boson Jaynes-Cummings-Dicke-type hamiltonians describing an interaction of a molecule of N n-level atoms with many modes of electromagnetic field and containing, in general, additional non-linear interaction terms. We explicitly obtain the corresponding quantum Lax operators and spin-boson analogs of the generalized Gaudin hamiltonians and prove their quantum commutativity. We investigate symmetries of the obtained models that are associated with the geometric symmetries of the classical r-matrices and construct the corresponding algebra of quantum integrals. We consider in detailmore » three classes of non-skew-symmetric classical r-matrices with spectral parameters and explicitly obtain the corresponding quantum Lax operators and Jaynes-Cummings-Dicke-type hamiltonians depending on the considered r-matrix.« less

Hybrid annealing: Coupling a quantum simulator to a classical computer

NASA Astrophysics Data System (ADS)

Graß, Tobias; Lewenstein, Maciej

2017-05-01

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

Low-energy laser in the treatment of alopecia of the scalp

NASA Astrophysics Data System (ADS)

Ciuchita, Tavi; Usurelu, Mircea; Antipa, Ciprian

1997-12-01

The authors tried to verify the efficacy of low energy laser (LEL) in scalp alopecia. Sixty patients were divided in two groups: A) laser group, 33 patients treated with both LEL and classical therapy; B) control group, 27 patients treated only with classical therapy, Before, during and after treatment, historical samples were done. For the group A the results were rather superior but in a twice shorter time shorter time than group B. The maintenance of the good results needed classical therapy for a long period. We conclude that LEL therapy could have a useful complementary method for the treatment of scalp alopecia.

Thermodynamic integration from classical to quantum mechanics.

PubMed

Habershon, Scott; Manolopoulos, David E

2011-12-14

We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable. © 2011 American Institute of Physics

Heterogeneous Nucleation of Colloidal Crystals on a Glass Substrate with Depletion Attraction.

PubMed

Guo, Suxia; Nozawa, Jun; Hu, Sumeng; Koizumi, Haruhiko; Okada, Junpei; Uda, Satoshi

2017-10-10

The heterogeneous nucleation of colloidal crystals with attractive interactions has been investigated via in situ observations. We have found two types of nucleation processes: a cluster that overcomes the critical size for nucleation with a monolayer, and a method that occurs with two layers. The Gibbs free energy changes (ΔG) for these two types of nucleation processes are evaluated by taking into account the effect of various interfacial energies. In contrast to homogeneous nucleation, the change in interfacial free energy, Δσ, is generated for colloidal nucleation on a foreign substrate such as a cover glass in the present study. The Δσ and step free energy of the first layer, γ 1 , are obtained experimentally based on the equation deduced from classical nucleation theory (CNT). It is concluded that the ΔG of q-2D nuclei is smaller than of monolayer nuclei, provided that the same number of particles are used, which explains the experimental result that the critical size in q-2D nuclei is smaller than that in monolayer nuclei.

The role of radiation reaction in Lienard-Wiechert description of FEL interaction

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

Kimel, I.; Elias, L.R.

1995-12-31

The most common theoretical analysis of the FEL interaction is based on the set of equations consisting of Lorentz and wave equations. This approach explains most of FEL features and, in particular, works well to describe operation in the amplifier mode. In that approach however, there are some difficulties in describing operation in oscillator mode, as well as self amplified spontaneous emission. In particular, it is not possible to describe the start up stage since there is no wave to start with. It is clear that a different approach is required in such situations. That is why we have pursuedmore » the study of the FEL interaction in the framework of Lorentz plus Lienard-Wiechert equations. The Lienard-Wiechert Lorentz equation approach however, presents its own set of problems. Variation in energy of the electrons is given exclusively by the Lorentz equation. Thus, the energy lost due to the radiation process is not properly taken into account. This, of course, is a long standing problem in classical electrodynamics. In order to restore energy conservation radiation reaction has to be incorporated into the framework. The first question in that regard has to do with which form of the radiation reaction equations is the most convenient for computations in the FEL process. This has to do with the fact that historically, radiation reaction has been added in an ad hoc manner instead of being derived from the fundamental equations. Another problem discussed is how to take into account the radiation reaction in a collective manner in the interaction among electrons. Also discussed is the radiation reaction vis a vi the coherence properties of the FEL process.« less

Quantum Monte Carlo Studies of Interaction-Induced Localization in Quantum Dots and Wires

NASA Astrophysics Data System (ADS)

Devrim Güçlü, A.

2009-03-01

We investigate interaction-induced localization of electrons in both quantum dots and inhomogeneous quantum wires using variational and diffusion quantum Monte Carlo methods. Quantum dots and wires are highly tunable systems that enable the study of the physics of strongly correlated electrons. With decreasing electronic density, interactions become stronger and electrons are expected to localize at their classical positions, as in Wigner crystallization in an infinite 2D system. (1) Dots: We show that the addition energy shows a clear progression from features associated with shell structure to those caused by commensurability of a Wigner crystal. This cross-over is, then, a signature of localization; it occurs near rs˜20. For higher values of rs, the configuration symmetry of the quantum dot becomes fully consistent with the classical ground state. (2) Wires: We study an inhomogeneous quasi-one-dimensional system -- a wire with two regions, one at low density and the other high. We find that strong localization occurs in the low density quantum point contact region as the gate potential is increased. The nature of the transition from high to low density depends on the density gradient -- if it is steep, a barrier develops between the two regions, causing Coulomb blockade effects. We find no evidence for ferromagnetic spin polarization for the range of parameters studied. The picture emerging here is in good agreement with the experimental measurements of tunneling between two wires. Collaborators: C. J. Umrigar (Cornell), Hong Jiang (Fritz Haber Institut), Amit Ghosal (IISER Calcutta), and H. U. Baranger (Duke).

Quantum-Classical Correspondence Principle for Work Distributions

NASA Astrophysics Data System (ADS)

Jarzynski, Christopher; Quan, H. T.; Rahav, Saar

2015-07-01

For closed quantum systems driven away from equilibrium, work is often defined in terms of projective measurements of initial and final energies. This definition leads to statistical distributions of work that satisfy nonequilibrium work and fluctuation relations. While this two-point measurement definition of quantum work can be justified heuristically by appeal to the first law of thermodynamics, its relationship to the classical definition of work has not been carefully examined. In this paper, we employ semiclassical methods, combined with numerical simulations of a driven quartic oscillator, to study the correspondence between classical and quantal definitions of work in systems with 1 degree of freedom. We find that a semiclassical work distribution, built from classical trajectories that connect the initial and final energies, provides an excellent approximation to the quantum work distribution when the trajectories are assigned suitable phases and are allowed to interfere. Neglecting the interferences between trajectories reduces the distribution to that of the corresponding classical process. Hence, in the semiclassical limit, the quantum work distribution converges to the classical distribution, decorated by a quantum interference pattern. We also derive the form of the quantum work distribution at the boundary between classically allowed and forbidden regions, where this distribution tunnels into the forbidden region. Our results clarify how the correspondence principle applies in the context of quantum and classical work distributions and contribute to the understanding of work and nonequilibrium work relations in the quantum regime.

Local mass and energy transports in evaporation processes from a vapor-liquid interface in a slit pore based on molecular dynamics

NASA Astrophysics Data System (ADS)

Fujiwara, K.; Shibahara, M.

2018-02-01

Molecular evaporation processes from a vapor-liquid interface formed in a slit-like pore were examined based on the classical molecular dynamics method, in order to elucidate a molecular mechanism of local mass and energy transports in a slit. The calculation system consisted of monatomic molecules and atoms which interact through the 12-6 Lennard-Jones potential. At first, a liquid was situated in a slit with a vapor-liquid interface, and instantaneous amounts of the mass and energy fluxes defined locally in the slit were obtained in two dimensions to reveal local fluctuation properties of the fluid in equilibrium states. Then, imposing a temperature gradient in the calculation system, non-equilibrium evaporation processes in the slit were investigated in details based on the local mass and energy fluxes. In this study, we focused on the fluid which is in the vicinity of the solid surface and in contact with the vapor phase. In the non-equilibrium evaporation processes, the results revealed that the local energy transport mechanism in the vicinity of the solid surface is different from that of the vapor phase, especially in the case of the relatively strong fluid-solid interaction. The results also revealed that the local mass transport in the vicinity of the solid surface can be interpreted based on the mechanism of the local energy transport, and the mechanism provides valuable information about pictures of the evaporation phenomena especially in the vicinity of the hydrophilic surfaces. It suggests that evaluating and changing this mechanism of the local energy transport are necessary to control the local mass flux more precisely in the vicinity of the solid surface.

Molecular dynamics simulations of classical sound absorption in a monatomic gas

NASA Astrophysics Data System (ADS)

Ayub, M.; Zander, A. C.; Huang, D. M.; Cazzolato, B. S.; Howard, C. Q.

2018-05-01

Sound wave propagation in argon gas is simulated using molecular dynamics (MD) in order to determine the attenuation of acoustic energy due to classical (viscous and thermal) losses at high frequencies. In addition, a method is described to estimate attenuation of acoustic energy using the thermodynamic concept of exergy. The results are compared against standing wave theory and the predictions of the theory of continuum mechanics. Acoustic energy losses are studied by evaluating various attenuation parameters and by comparing the changes in behavior at three different frequencies. This study demonstrates acoustic absorption effects in a gas simulated in a thermostatted molecular simulation and quantifies the classical losses in terms of the sound attenuation constant. The approach can be extended to further understanding of acoustic loss mechanisms in the presence of nanoscale porous materials in the simulation domain.

Adhesion of protein residues to substituted (111) diamond surfaces: an insight from density functional theory and classical molecular dynamics simulations.

PubMed

Borisenko, Konstantin B; Reavy, Helen J; Zhao, Qi; Abel, Eric W

2008-09-15

Protein-repellent diamond coatings have great potential value for surface coatings on implants and surgical instruments. The design of these coatings relies on a fundamental understanding of the intermolecular interactions involved in the adhesion of proteins to surfaces. To get insight into these interactions, adhesion energies of glycine to pure and Si and N-doped (111) diamond surfaces represented as clusters were calculated in the gas phase, using density functional theory (DFT) at the B3LYP/6-31G* level. The computed adhesion energies indicated that adhesion of glycine to diamond surface may be modified by introducing additional elements into the surface. The adhesion was also found to induce considerable change in the conformation of glycine when compared with the lowest-energy conformer of the free molecule. In the Si and N-substituted diamond clusters, notable changes in the structures involving the substituents atoms when compared with smaller parent molecules, such as 1-methyl-1-silaadamantane and 1-azaadamantane, were detected. Adhesion free energy differences were estimated for a series of representative peptides (hydrophobic Phe-Gly-Phe, amphiphilic Arg-Gly-Phe, and hydrophilic Arg-Gly-Arg) to a (111) diamond surface substituted with different amounts of N, Si, or F, using molecular dynamics simulations in an explicit water environment employing a Dreiding force field. The calculations were in agreement with the DFT results in that adsorption of the studied peptides to diamond surface is influenced by introducing additional elements to the surface. It has been shown that, in general, substitution will enhance electrostatic interactions between a surface and surrounding water, leading to a weaker adhesion of the studied peptides.

The dissociative chemisorption of methane on Ni(100) and Ni(111): Classical and quantum studies based on the reaction path Hamiltonian

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

Mastromatteo, Michael; Jackson, Bret, E-mail: jackson@chem.umass.edu

Electronic structure methods based on density functional theory are used to construct a reaction path Hamiltonian for CH{sub 4} dissociation on the Ni(100) and Ni(111) surfaces. Both quantum and quasi-classical trajectory approaches are used to compute dissociative sticking probabilities, including all molecular degrees of freedom and the effects of lattice motion. Both approaches show a large enhancement in sticking when the incident molecule is vibrationally excited, and both can reproduce the mode specificity observed in experiments. However, the quasi-classical calculations significantly overestimate the ground state dissociative sticking at all energies, and the magnitude of the enhancement in sticking with vibrationalmore » excitation is much smaller than that computed using the quantum approach or observed in the experiments. The origin of this behavior is an unphysical flow of zero point energy from the nine normal vibrational modes into the reaction coordinate, giving large values for reaction at energies below the activation energy. Perturbative assumptions made in the quantum studies are shown to be accurate at all energies studied.« less

Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

NASA Astrophysics Data System (ADS)

Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

2018-05-01

Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

Extension of the Kohn-Sham formulation of density functional theory to finite temperature

NASA Astrophysics Data System (ADS)

Gonis, A.; Däne, M.

2018-05-01

Based on Mermin's extension of the Hohenberg and Kohn theorems to non-zero temperature, the Kohn-Sham formulation of density functional theory (KS-DFT) is generalized to finite temperature. We show that present formulations are inconsistent with Mermin's functional containing expressions, in particular describing the Coulomb energy, that defy derivation and are even in violation of rules of logical inference. More; current methodology is in violation of fundamental laws of both quantum and classical mechanics. Based on this feature, we demonstrate the impossibility of extending the KS formalism to finite temperature through the self-consistent solutions of the single-particle Schrödinger equation of T > 0. Guided by the form of Mermin's functional that depends on the eigenstates of a Hamiltonian, determined at T = 0, we base our extension of KS-DFT on the determination of the excited states of a non-interacting system at the zero of temperature. The resulting formulation is consistent with that of Mermin constructing the free energy at T > 0 in terms of the excited states of a non-interacting Hamiltonian (system) that, within the KS formalism, are described by Slater determinants. To determine the excited states at T = 0 use is made of the extension of the Hohenberg and Kohn theorems to excited states presented in previous work applied here to a non-interacting collection of replicas of a non-interacting N-particle system, whose ground state density is taken to match that of K non-interacting replicas of an interacting N-particle system at T = 0 . The formalism allows for an ever denser population of the excitation spectrum of a Hamiltonian, within the KS approximation. The form of the auxiliary potential, (Kohn-Sham potential), is formally identical to that in the ground state formalism with the contribution of the Coulomb energy provided by the derivative of the Coulomb energy in all excited states taken into account. Once the excited states are determined, the minimum of the free energy within the KS formalism follows immediately in the form of Mermin's functional, but with the exact excited states in that functional represented by Slater determinants obtained through self-consistency conditions at the zero of temperature. It is emphasized that, in departure from all existing formulations, no self-consistency conditions are implemented at finite T; as we show, in fact, such formulations are rigorously blocked.

Scalar gravitational waves in the effective theory of gravity

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

Mottola, Emil

As a low energy effective field theory, classical General Relativity receives an infrared relevant modification from the conformal trace anomaly of the energy-momentum tensor of massless, or nearly massless, quantum fields. The local form of the effective action associated with the trace anomaly is expressed in terms of a dynamical scalar field that couples to the conformal factor of the spacetime metric, allowing it to propagate over macroscopic distances. Linearized around flat spacetime, this semi-classical EFT admits scalar gravitational wave solutions in addition to the transversely polarized tensor waves of the classical Einstein theory. The amplitude of the scalar wavemore » modes, as well as their energy and energy flux which are positive and contain a monopole moment, are computed. As a result, astrophysical sources for scalar gravitational waves are considered, with the excited gluonic condensates in the interiors of neutron stars in merger events with other compact objects likely to provide the strongest burst signals.« less

Scalar gravitational waves in the effective theory of gravity

DOE PAGES

Mottola, Emil

2017-07-10

As a low energy effective field theory, classical General Relativity receives an infrared relevant modification from the conformal trace anomaly of the energy-momentum tensor of massless, or nearly massless, quantum fields. The local form of the effective action associated with the trace anomaly is expressed in terms of a dynamical scalar field that couples to the conformal factor of the spacetime metric, allowing it to propagate over macroscopic distances. Linearized around flat spacetime, this semi-classical EFT admits scalar gravitational wave solutions in addition to the transversely polarized tensor waves of the classical Einstein theory. The amplitude of the scalar wavemore » modes, as well as their energy and energy flux which are positive and contain a monopole moment, are computed. As a result, astrophysical sources for scalar gravitational waves are considered, with the excited gluonic condensates in the interiors of neutron stars in merger events with other compact objects likely to provide the strongest burst signals.« less

Linear and angular coherence momenta in the classical second-order coherence theory of vector electromagnetic fields.

PubMed

Wang, Wei; Takeda, Mitsuo

2006-09-01

A new concept of vector and tensor densities is introduced into the general coherence theory of vector electromagnetic fields that is based on energy and energy-flow coherence tensors. Related coherence conservation laws are presented in the form of continuity equations that provide new insights into the propagation of second-order correlation tensors associated with stationary random classical electromagnetic fields.

Communication: Classical threshold law for ion-neutral-neutral three-body recombination

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

Pérez-Ríos, Jesús; Greene, Chris H.

2015-07-28

A very recently method for classical trajectory calculations for three-body collision [Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014)] has been applied to describe ion-neutral-neutral ternary processes for low energy collisions: 0.1 mK–10 mK. As a result, a threshold law for the three-body recombination cross section is obtained and corroborated numerically. The derived threshold law predicts the formation of weakly bound dimers, with binding energies comparable to the collision energy of the collisional partners. In this low energy range, this analysis predicts that molecular ions should dominate over molecular neutrals as the most products formed.

Computer-simulation study of a disordered classical spin system in one dimension with long-range anisotropic ferromagnetic interactions

NASA Astrophysics Data System (ADS)

Romano, S.

1992-01-01

The present paper considers a classical system, consisting of n-component unit vectors (n=2 or 3), associated with a one-dimensional lattice \\{uk||k∈openZ\\}, and interacting via a translationally invariant pair potential of the long-range, ferromagnetic and anisotropic form W=Wjk=-ɛ||j-k||-2(auj,nuk,n +b tsumλ

Quantum and quasi-classical calculations for the S+ + H2(v, j) →SH+(v′, j′)+H reactive collisions

PubMed Central

Zanchet, Alexandre; Roncero, Octavio; Bulut, Niyazi

2016-01-01

State-to-state cross sections for the S+ + H2(v, j) → SH+ (v′, j′) + H endothermic reaction are obtained with quantum wave packet(WP) and quasi-classical (QCT) methods for different initial rovibrational H2(v, j) over a wide range of translation energies. Final state distribution as a function of the initial quantum number is obtained and discussed. Additionally, the effect of the internal excitation of H2 on the reactivity is carefully studied. It appears that energy transfer among modes is very inefficient, that vibrational energy is the most favorable for reaction and rotational excitation significantly enhance reactivity when vibrational energy is sufficient to reach the product. Special attention is also paid on an unusual discrepancy between classical and quantum dynamics for low rotational levels while agreement improves with rotational excitation of H2, An interesting resonant behaviour found in WP calculations is also discussed and is associated to the existence of roaming classical trajectories that enhance the reactivity of the title reaction. Finally, a comparison with the experimental results of Stowe et al.[1] for S+ + HD and S+ +D2 reactions, finding a reasonably good agreement with those results. PMID:27055725

Quantum and quasi-classical calculations for the S⁺ + H₂(v,j) → SH⁺(v',j') + H reactive collisions.

PubMed

Zanchet, Alexandre; Roncero, Octavio; Bulut, Niyazi

2016-04-28

State-to-state cross-sections for the S(+) + H2(v,j) → SH(+)(v',j') + H endothermic reaction are obtained using quantum wave packet (WP) and quasi-classical (QCT) methods for different initial ro-vibrational H2(v,j) over a wide range of translation energies. The final state distribution as a function of the initial quantum number is obtained and discussed. Additionally, the effect of the internal excitation of H2 on the reactivity is carefully studied. It appears that energy transfer among modes is very inefficient that vibrational energy is the most favorable for the reaction, and rotational excitation significantly enhances the reactivity when vibrational energy is sufficient to reach the product. Special attention is also paid to an unusual discrepancy between classical and quantum dynamics for low rotational levels while agreement improves with rotational excitation of H2. An interesting resonant behaviour found in WP calculations is also discussed and associated with the existence of roaming classical trajectories that enhance the reactivity of the title reaction. Finally, a comparison with the experimental results of Stowe et al. for S(+) + HD and S(+) + D2 reactions exhibits a reasonably good agreement with those results.

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

DOE PAGES

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

2017-04-24

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

Classical system boundaries cannot be determined within quantum Darwinism

NASA Astrophysics Data System (ADS)

Fields, Chris

Multiple observers who interact with environmental encodings of the states of a macroscopic quantum system S as required by quantum Darwinism cannot demonstrate that they are jointly observing S without a joint a priori assumption of a classical boundary separating S from its environment E. Quantum Darwinism cannot, therefore, be regarded as providing a purely quantum-mechanical explanation of the "emergence" of classicality.

Identification of non-classical C-H···M interactions in early and late transition metal complexes containing the CH(ArO)3 ligand.

PubMed

Lein, Matthias; Harrison, John A; Nielson, Alastair J

2013-08-14

The fully optimised DFT structure of the d(0) complex [{CH(ArO)3}Ti(NEt2)] (2) at the B3LYP level compares well with the distorted tetrahedral geometry shown by the X-ray crystal structure. QTAIM analysis of the electron density associated with the C-H···Ti interaction shows a well defined bond critical point, a bond path between the hydrogen and titanium centres and a negative value for the energy density indicative of covalency. A natural bond orbital (NBO) picture of the interaction shows that the C-H σ bond electron density donates to a d hybrid orbital on the metal in a linear fashion. Calculated IR and NMR data for the components of the interaction are consistent with experiment. The computed structures for [{CH(ArO)3}Ti(OPh)] (3), [{CH(ArO)3}Zr(NEt2)] (4), [{CH(ArO)3}Hf(NEt2)] (5), show tetrahedral geometries and QTAIM and NBO properties similar to (2). [{CH(ArO)3}Mo(NEt2)] (6) shows distortion of the tripodal ligand and a reduced C-H···M bond angle with properties more consistent with a C-H···M side-on donor interaction. In [{CH(ArO)3}Fe(NEt2)] (7) the C-H···M bond angle is linear and involves a donor interaction. An energy minimised structure maintaining the three fold coordination to the tripodal ligand was not obtained for [{CH(ArO)3}Ni(NEt2)](2-) but changing from a diethyl amide ligand to phenolato gave energy minimised [{CH(ArO)3}Ni(OPh)](2-) (8). This structure shows a distorted square planar geometry with a substantially bent phenoxo ligand and a near linear C-H···M covalent interaction with donor and back bonding properties. The work shows that linear C-H···M interactions can have both agostic and weak hydrogen bond-like covalency.

Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM.

PubMed

Sriwastava, Brijesh Kumar; Basu, Subhadip; Maulik, Ujjwal

2015-10-01

Protein-protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.

Physics of Gravitational Interaction: Geometry of Space or Quantum Field in Space

NASA Astrophysics Data System (ADS)

Baryshev, Yurij

2006-03-01

Thirring-Feynman's tensor field approach to gravitation opens new understanding on the physics of gravitational interaction and stimulates novel experiments on the nature of gravity. According to Field Gravity, the universal gravity force is caused by exchange of gravitons - the quanta of gravity field. Energy of this field is well-defined and excludes the singularity. All classical relativistic effects are the same as in General Relativity. The intrinsic scalar (spin 0) part of gravity field corresponds to ``antigravity'' and only together with the pure tensor (spin 2) part gives the usual Newtonian force. Laboratory and astrophysical experiments which may test the predictions of FG, will be performed in near future. In particular, observations at gravity observatories with bar and interferometric detectors, like Explorer, Nautilus, LIGO and VIRGO, will check the predicted scalar gravitational waves from supernova explosions. New types of cosmological models in Minkowski space are possible too.

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Monte Carlo simulations of kagome lattices with magnetic dipolar interactions

NASA Astrophysics Data System (ADS)

Plumer, Martin; Holden, Mark; Way, Andrew; Saika-Voivod, Ivan; Southern, Byron

Monte Carlo simulations of classical spins on the two-dimensional kagome lattice with only dipolar interactions are presented. In addition to revealing the sixfold-degenerate ground state, the nature of the finite-temperature phase transition to long-range magnetic order is discussed. Low-temperature states consisting of mixtures of degenerate ground-state configurations separated by domain walls can be explained as a result of competing exchange-like and shape-anisotropy-like terms in the dipolar coupling. Fluctuations between pairs of degenerate spin configurations are found to persist well into the ordered state as the temperature is lowered until locking in to a low-energy state. Results suggest that the system undergoes a continuous phase transition at T ~ 0 . 43 in agreement with previous MC simulations but the nature of the ordering process differs. Preliminary results which extend this analysis to the 3D fcc ABC-stacked kagome systems will be presented.

Coarse-graining, Electrostatics and pH effects in phospholipid systems

NASA Astrophysics Data System (ADS)

Travesset, Alex; Vangaveti, Sweta

2010-03-01

We introduce a minimal free energy describing the interaction of charged groups and counterions including both classical electrostatic and specific interactions. The predictions of the model are compared against the standard model for describing ions next to charged interfaces, consisting of Poisson-Boltzmann theory with additional constants describing ion binding, which are specific to the counterion and the interfacial charge (``chemical binding''). It is shown that the ``chemical'' model can be appropriately described by an underlying ``physical'' model over several decades in concentration, but the extracted binding constants are not uniquely defined, as they differ depending on the particular observable quantity being studied. It is also shown that electrostatic correlations for divalent (or higher valence) ions enhance the surface charge by increasing deprotonation, an effect not properly accounted within chemical models. The model is applied to the charged phospholipids phosphatidylserine, Phosphatidc acid and Phosphoinositides and implications for different biological processes are discussed.

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

Cui, Jie; Krems, Roman V.; Li, Zhiying

We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom–molecule interaction. We then compare the results of the atom–benzene calculations with those for benzene–benzene collisions. The comparison illustrates that the mean lifetimes of the benzene–benzene collision complexesmore » are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene–benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.« less

Polar order in nanostructured organic materials

NASA Astrophysics Data System (ADS)

Sayar, M.; Olvera de la Cruz, M.; Stupp, S. I.

2003-02-01

Achiral multi-block liquid crystals are not expected to form polar domains. Recently, however, films of nanoaggregates formed by multi-block rodcoil molecules were identified as the first example of achiral single-component materials with macroscopic polar properties. By solving an Ising-like model with dipolar and asymmetric short-range interactions, we show here that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a approx 8 nm), leading to a reduction in the repulsive dipolar interactions which oppose polar order within layers. In finite-thickness films of nanostructures, this effect enables the formation of polar domains. We compute exactly the energies of the possible structures consistent with the experiments as a function of film thickness at zero temperature (T). We also provide Monte Carlo simulations at non-zero T for a disordered hexagonal lattice that resembles the smectic-like packing in these nanofilms.

Quantum-mechanical analysis of the energetic contributions to π stacking in nucleic acids versus rise, twist, and slide.

PubMed

Parker, Trent M; Hohenstein, Edward G; Parrish, Robert M; Hud, Nicholas V; Sherrill, C David

2013-01-30

Symmetry-adapted perturbation theory (SAPT) is applied to pairs of hydrogen-bonded nucleobases to obtain the energetic components of base stacking (electrostatic, exchange-repulsion, induction/polarization, and London dispersion interactions) and how they vary as a function of the helical parameters Rise, Twist, and Slide. Computed average values of Rise and Twist agree well with experimental data for B-form DNA from the Nucleic Acids Database, even though the model computations omitted the backbone atoms (suggesting that the backbone in B-form DNA is compatible with having the bases adopt their ideal stacking geometries). London dispersion forces are the most important attractive component in base stacking, followed by electrostatic interactions. At values of Rise typical of those in DNA (3.36 Å), the electrostatic contribution is nearly always attractive, providing further evidence for the importance of charge-penetration effects in π-π interactions (a term neglected in classical force fields). Comparison of the computed stacking energies with those from model complexes made of the "parent" nucleobases purine and 2-pyrimidone indicates that chemical substituents in DNA and RNA account for 20-40% of the base-stacking energy. A lack of correspondence between the SAPT results and experiment for Slide in RNA base-pair steps suggests that the backbone plays a larger role in determining stacking geometries in RNA than in B-form DNA. In comparisons of base-pair steps with thymine versus uracil, the thymine methyl group tends to enhance the strength of the stacking interaction through a combination of dispersion and electrosatic interactions.

Classical Wigner method with an effective quantum force: application to reaction rates.

PubMed

Poulsen, Jens Aage; Li, Huaqing; Nyman, Gunnar

2009-07-14

We construct an effective "quantum force" to be used in the classical molecular dynamics part of the classical Wigner method when determining correlation functions. The quantum force is obtained by estimating the most important short time separation of the Feynman paths that enter into the expression for the correlation function. The evaluation of the force is then as easy as classical potential energy evaluations. The ideas are tested on three reaction rate problems. The resulting transmission coefficients are in much better agreement with accurate results than transmission coefficients from the ordinary classical Wigner method.

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

NASA Astrophysics Data System (ADS)

Ahlstrand, Emma; Zukerman Schpector, Julio; Friedman, Ran

2017-11-01

When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions are available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li+ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.

Quantum path integral simulation of isotope effects in the melting temperature of ice Ih.

PubMed

Ramírez, R; Herrero, C P

2010-10-14

The isotope effect in the melting temperature of ice Ih has been studied by free energy calculations within the path integral formulation of statistical mechanics. Free energy differences between isotopes are related to the dependence of their kinetic energy on the isotope mass. The water simulations were performed by using the q-TIP4P/F model, a point charge empirical potential that includes molecular flexibility and anharmonicity in the OH stretch of the water molecule. The reported melting temperature at ambient pressure of this model (T=251 K) increases by 6.5±0.5 and 8.2±0.5 K upon isotopic substitution of hydrogen by deuterium and tritium, respectively. These temperature shifts are larger than the experimental ones (3.8 and 4.5 K, respectively). In the classical limit, the melting temperature is nearly the same as that for tritiated ice. This unexpected behavior is rationalized by the coupling between intermolecular interactions and molecular flexibility. This coupling makes the kinetic energy of the OH stretching modes larger in the liquid than in the solid phase. However, the opposite behavior is found for intramolecular modes, which display larger kinetic energy in ice than in liquid water.

Exploring the importance of quantum effects in nucleation: The archetypical Nen case

NASA Astrophysics Data System (ADS)

Unn-Toc, Wesley; Halberstadt, Nadine; Meier, Christoph; Mella, Massimo

2012-07-01

The effect of quantum mechanics (QM) on the details of the nucleation process is explored employing Ne clusters as test cases due to their semi-quantal nature. In particular, we investigate the impact of quantum mechanics on both condensation and dissociation rates in the framework of the microcanonical ensemble. Using both classical trajectories and two semi-quantal approaches (zero point averaged dynamics, ZPAD, and Gaussian-based time dependent Hartree, G-TDH) to model cluster and collision dynamics, we simulate the dissociation and monomer capture for Ne8 as a function of the cluster internal energy, impact parameter and collision speed. The results for the capture probability Ps(b) as a function of the impact parameter suggest that classical trajectories always underestimate capture probabilities with respect to ZPAD, albeit at most by 15%-20% in the cases we studied. They also do so in some important situations when using G-TDH. More interestingly, dissociation rates kdiss are grossly overestimated by classical mechanics, at least by one order of magnitude. We interpret both behaviours as mainly due to the reduced amount of kinetic energy available to a quantum cluster for a chosen total internal energy. We also find that the decrease in monomer dissociation energy due to zero point energy effects plays a key role in defining dissociation rates. In fact, semi-quantal and classical results for kdiss seem to follow a common "corresponding states" behaviour when the proper definition of internal and dissociation energies are used in a transition state model estimation of the evaporation rate constants.

Simplified DFT methods for consistent structures and energies of large systems

NASA Astrophysics Data System (ADS)

Caldeweyher, Eike; Gerit Brandenburg, Jan

2018-05-01

Kohn–Sham density functional theory (DFT) is routinely used for the fast electronic structure computation of large systems and will most likely continue to be the method of choice for the generation of reliable geometries in the foreseeable future. Here, we present a hierarchy of simplified DFT methods designed for consistent structures and non-covalent interactions of large systems with particular focus on molecular crystals. The covered methods are a minimal basis set Hartree–Fock (HF-3c), a small basis set screened exchange hybrid functional (HSE-3c), and a generalized gradient approximated functional evaluated in a medium-sized basis set (B97-3c), all augmented with semi-classical correction potentials. We give an overview on the methods design, a comprehensive evaluation on established benchmark sets for geometries and lattice energies of molecular crystals, and highlight some realistic applications on large organic crystals with several hundreds of atoms in the primitive unit cell.

Theoretical investigation of the electron capture and loss processes in the collisions of He2+ + Ne.

PubMed

Hong, Xuhai; Wang, Feng; Jiao, Yalong; Su, Wenyong; Wang, Jianguo; Gou, Bingcong

2013-08-28

Based on the time-dependent density functional theory, a method is developed to study ion-atom collision dynamics, which self-consistently couples the quantum mechanical description of electron dynamics with the classical treatment of the ion motion. Employing real-time and real-space method, the coordinate space translation technique is introduced to allow one to focus on the region of target or projectile depending on the actual concerned process. The benchmark calculations are performed for the collisions of He(2+) + Ne, and the time evolution of electron density distribution is monitored, which provides interesting details of the interaction dynamics between the electrons and ion cores. The cross sections of single and many electron capture and loss have been calculated in the energy range of 1-1000 keV/amu, and the results show a good agreement with the available experiments over a wide range of impact energies.

Collisions of O+ with He at low energies

NASA Astrophysics Data System (ADS)

Joseph, Dwayne C.; Saha, B. C.; Zhao, L. B.

2009-05-01

We have investigated the following charge transfer processO^+( ^4S^0, ^2D^0, ^2P^0)+He->O( ^3P)+He^+-δE using the full quantum [1] and semi-classical molecular [2]orbital close-coupling (MOCC) approximations. The quantum MOCC equations are solved numerically in the adiabatic representation [3]. Using MRD-CI package [4] the ab initio configuration interaction calculation is carried out for potential energies. Details of our findings will be reported in the conference. [1] B. H. Bransden and M. R. C. McDowell, ``Charge Exchange and the Theory of Ion-Atom Collisions'', Clarendon Press, Oxford, 1992. [2] M. Kimura and N. F. Lane, At. Mol. Opt. Phys 26, 79 (1990). [3] J. P. Braga and J. C. Belchoir, J. Comput. Chem 17, 1559 (1996). [4] R. J. Buenker, ``Current Aspects of Quantum Chemistry 1981, Vol 21, edited by R. Carbo (Elsevier, Amsterdam), p 17.

Irreversible thermodynamic analysis and application for molecular heat engines

NASA Astrophysics Data System (ADS)

Lucia, Umberto; Açıkkalp, Emin

2017-09-01

Is there a link between the macroscopic approach to irreversibility and microscopic behaviour of the systems? Consumption of free energy keeps the system away from a stable equilibrium. Entropy generation results from the redistribution of energy, momentum, mass and charge. This concept represents the essence of the thermodynamic approach to irreversibility. Irreversibility is the result of the interaction between systems and their environment. The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible thermodynamics approaches are applied for a quantum heat engine with -1/2 spin system. Finally, lost works are determined for considered system and results show that macro and molecular heat engines obey same limitations. Moreover, a quantum thermodynamic approach is suggested in order to explain the results previously obtained from an atomic viewpoint.

Experimental and numerical analysis of the constitutive equation of rubber composites reinforced with random ceramic particle

NASA Astrophysics Data System (ADS)

Luo, D. M.; Xie, Y.; Su, X. R.; Zhou, Y. L.

2018-01-01

Based on the four classical models of Mooney-Rivlin (M-R), Yeoh, Ogden and Neo-Hookean (N-H) model, a strain energy constitutive equation with large deformation for rubber composites reinforced with random ceramic particles is proposed from the angle of continuum mechanics theory in this paper. By decoupling the interaction between matrix and random particles, the strain energy of each phase is obtained to derive the explicit constitutive equation for rubber composites. The tests results of uni-axial tensile, pure shear and equal bi-axial tensile are simulated by the non-linear finite element method on the ANSYS platform. The results from finite element method are compared with those from experiment, and the material parameters are determined by fitting the results from different test conditions, and the influence of radius of random ceramic particles on the effective mechanical properties are analyzed.

Extremely efficient internal exciton dissociation through edge states in layered 2D perovskites

DOE PAGES

Blancon, Jean -Christophe Robert; Tsai, Hsinhan; Nie, Wanyi; ...

2017-03-09

Understanding and controlling charge and energy flow in state-of-the-art semiconductor quantum wells has enabled high-efficiency optoelectronic devices. Two-dimensional (2D) Ruddlesden-Popper perovskites are solution-processed quantum wells wherein the band gap can be tuned by varying the perovskite-layer thickness, which modulates the effective electron-hole confinement. We report that, counterintuitive to classical quantum-confined systems where photogenerated electrons and holes are strongly bound by Coulomb interactions or excitons, the photophysics of thin films made of Ruddlesden-Popper perovskites with a thickness exceeding two perovskite-crystal units (>1.3 nanometers) is dominated by lower-energy states associated with the local intrinsic electronic structure of the edges of the perovskitemore » layers. Furthermore, these states provide a direct pathway for dissociating excitons into longer-lived free carriers that substantially improve the performance of optoelectronic devices.« less

Casimir-Polder shifts on quantum levitation states

NASA Astrophysics Data System (ADS)

Crépin, P.-P.; Dufour, G.; Guérout, R.; Lambrecht, A.; Reynaud, S.

2017-03-01

An ultracold atom above a horizontal mirror experiences quantum reflection from the attractive Casimir-Polder interaction, which holds it against gravity and leads to quantum levitation states. We analyze this system by using a Liouville transformation of the Schrödinger equation and a Langer coordinate adapted to problems with a classical turning point. Reflection on the Casimir-Polder attractive well is replaced by reflection on a repulsive wall, and the problem is then viewed as an ultracold atom trapped inside a cavity with gravity and Casimir-Polder potentials acting, respectively, as top and bottom mirrors. We calculate numerically Casimir-Polder shifts of the energies of the cavity resonances and propose an approximate treatment which is precise enough to discuss spectroscopy experiments aimed at tests of the weak-equivalence principle on antihydrogen. We also discuss the lifetimes by calculating complex energies associated with cavity resonances.

Polluted Pathways: Mechanisms of Metabolic Disruption by Endocrine Disrupting Chemicals.

PubMed

Mimoto, Mizuho S; Nadal, Angel; Sargis, Robert M

2017-06-01

Environmental toxicants are increasingly implicated in the global decline in metabolic health. Focusing on diabetes, herein, the molecular and cellular mechanisms by which metabolism disrupting chemicals (MDCs) impair energy homeostasis are discussed. Emerging data implicate MDC perturbations in a variety of pathways as contributors to metabolic disease pathogenesis, with effects in diverse tissues regulating fuel utilization. Potentiation of traditional metabolic risk factors, such as caloric excess, and emerging threats to metabolism, such as disruptions in circadian rhythms, are important areas of current and future MDC research. Increasing evidence also implicates deleterious effects of MDCs on metabolic programming that occur during vulnerable developmental windows, such as in utero and early post-natal life as well as pregnancy. Recent insights into the mechanisms by which MDCs alter energy homeostasis will advance the field's ability to predict interactions with classical metabolic disease risk factors and empower studies utilizing targeted therapeutics to treat MDC-mediated diabetes.

The dissociation and recombination rates of CH4 through the Ni(111) surface: The effect of lattice motion

NASA Astrophysics Data System (ADS)

Wang, Wenji; Zhao, Yi

2017-07-01

Methane dissociation is a prototypical system for the study of surface reaction dynamics. The dissociation and recombination rates of CH4 through the Ni(111) surface are calculated by using the quantum instanton method with an analytical potential energy surface. The Ni(111) lattice is treated rigidly, classically, and quantum mechanically so as to reveal the effect of lattice motion. The results demonstrate that it is the lateral displacements rather than the upward and downward movements of the surface nickel atoms that affect the rates a lot. Compared with the rigid lattice, the classical relaxation of the lattice can increase the rates by lowering the free energy barriers. For instance, at 300 K, the dissociation and recombination rates with the classical lattice exceed the ones with the rigid lattice by 6 and 10 orders of magnitude, respectively. Compared with the classical lattice, the quantum delocalization rather than the zero-point energy of the Ni atoms further enhances the rates by widening the reaction path. For instance, the dissociation rate with the quantum lattice is about 10 times larger than that with the classical lattice at 300 K. On the rigid lattice, due to the zero-point energy difference between CH4 and CD4, the kinetic isotope effects are larger than 1 for the dissociation process, while they are smaller than 1 for the recombination process. The increasing kinetic isotope effect with decreasing temperature demonstrates that the quantum tunneling effect is remarkable for the dissociation process.

Statistics of extreme waves in the framework of one-dimensional Nonlinear Schrodinger Equation

NASA Astrophysics Data System (ADS)

Agafontsev, Dmitry; Zakharov, Vladimir

2013-04-01

We examine the statistics of extreme waves for one-dimensional classical focusing Nonlinear Schrodinger (NLS) equation, iΨt + Ψxx + |Ψ |2Ψ = 0, (1) as well as the influence of the first nonlinear term beyond Eq. (1) - the six-wave interactions - on the statistics of waves in the framework of generalized NLS equation accounting for six-wave interactions, dumping (linear dissipation, two- and three-photon absorption) and pumping terms, We solve these equations numerically in the box with periodically boundary conditions starting from the initial data Ψt=0 = F(x) + ?(x), where F(x) is an exact modulationally unstable solution of Eq. (1) seeded by stochastic noise ?(x) with fixed statistical properties. We examine two types of initial conditions F(x): (a) condensate state F(x) = 1 for Eq. (1)-(2) and (b) cnoidal wave for Eq. (1). The development of modulation instability in Eq. (1)-(2) leads to formation of one-dimensional wave turbulence. In the integrable case the turbulence is called integrable and relaxes to one of infinite possible stationary states. Addition of six-wave interactions term leads to appearance of collapses that eventually are regularized by the dumping terms. The energy lost during regularization of collapses in (2) is restored by the pumping term. In the latter case the system does not demonstrate relaxation-like behavior. We measure evolution of spectra Ik =< |Ψk|2 >, spatial correlation functions and the PDFs for waves amplitudes |Ψ|, concentrating special attention on formation of "fat tails" on the PDFs. For the classical integrable NLS equation (1) with condensate initial condition we observe Rayleigh tails for extremely large waves and a "breathing region" for middle waves with oscillations of the frequency of waves appearance with time, while nonintegrable NLS equation with dumping and pumping terms (2) with the absence of six-wave interactions α = 0 demonstrates perfectly Rayleigh PDFs without any oscillations with time. In case of the cnoidal wave initial condition we observe severely non-Rayleigh PDFs for the classical NLS equation (1) with the regions corresponding to 2-, 3- and so on soliton collisions clearly seen of the PDFs. Addition of six-wave interactions in Eq. (2) for condensate initial condition results in appearance of non-Rayleigh addition to the PDFs that increase with six-wave interaction constant α and disappears with the absence of six-wave interactions α = 0. References: [1] D.S. Agafontsev, V.E. Zakharov, Rogue waves statistics in the framework of one-dimensional Generalized Nonlinear Schrodinger Equation, arXiv:1202.5763v3.

Experimental Blind Quantum Computing for a Classical Client.

PubMed

Huang, He-Liang; Zhao, Qi; Ma, Xiongfeng; Liu, Chang; Su, Zu-En; Wang, Xi-Lin; Li, Li; Liu, Nai-Le; Sanders, Barry C; Lu, Chao-Yang; Pan, Jian-Wei

2017-08-04

To date, blind quantum computing demonstrations require clients to have weak quantum devices. Here we implement a proof-of-principle experiment for completely classical clients. Via classically interacting with two quantum servers that share entanglement, the client accomplishes the task of having the number 15 factorized by servers who are denied information about the computation itself. This concealment is accompanied by a verification protocol that tests servers' honesty and correctness. Our demonstration shows the feasibility of completely classical clients and thus is a key milestone towards secure cloud quantum computing.

Experimental Blind Quantum Computing for a Classical Client

NASA Astrophysics Data System (ADS)

Huang, He-Liang; Zhao, Qi; Ma, Xiongfeng; Liu, Chang; Su, Zu-En; Wang, Xi-Lin; Li, Li; Liu, Nai-Le; Sanders, Barry C.; Lu, Chao-Yang; Pan, Jian-Wei

2017-08-01

To date, blind quantum computing demonstrations require clients to have weak quantum devices. Here we implement a proof-of-principle experiment for completely classical clients. Via classically interacting with two quantum servers that share entanglement, the client accomplishes the task of having the number 15 factorized by servers who are denied information about the computation itself. This concealment is accompanied by a verification protocol that tests servers' honesty and correctness. Our demonstration shows the feasibility of completely classical clients and thus is a key milestone towards secure cloud quantum computing.

Classical density functional theory and Monte Carlo simulation study of electric double layer in the vicinity of a cylindrical electrode

NASA Astrophysics Data System (ADS)

Zhou, Shiqi; Lamperski, Stanisław; Sokołowska, Marta

2017-07-01

We have performed extensive Monte-Carlo simulations and classical density functional theory (DFT) calculations of the electrical double layer (EDL) near a cylindrical electrode in a primitive model (PM) modified by incorporating interionic dispersion interactions. It is concluded that (i) in general, an unsophisticated use of the mean field (MF) approximation for the interionic dispersion interactions does not distinctly worsen the classical DFT performance, even if the salt ions considered are highly asymmetrical in size (3:1) and charge (5:1), the bulk molar concentration considered is high up to a total bulk ion packing fraction of 0.314, and the surface charge density of up to 0.5 C m-2. (ii) More specifically, considering the possible noises in the simulation, the local volume charge density profiles are the most accurately predicted by the classical DFT in all situations, and the co- and counter-ion singlet distributions are also rather accurately predicted; whereas the mean electrostatic potential profile is relatively less accurately predicted due to an integral amplification of minor inaccuracy of the singlet distributions. (iii) It is found that the layered structure of the co-ion distribution is abnormally possible only if the surface charge density is high enough (for example 0.5 C m-2) moreover, the co-ion valence abnormally influences the peak height of the first counter-ion layer, which decreases with the former. (iv) Even if both the simulation and DFT indicate an insignificant contribution of the interionic dispersion interaction to the above three ‘local’ quantities, it is clearly shown by the classical DFT that the interionic dispersion interaction does significantly influence a ‘global’ quantity like the cylinder surface-aqueous electrolyte interfacial tension, and this may imply the role of the interionic dispersion interaction in explaining the specific Hofmeister effects. We elucidate all of the above observations based on the arguments from the liquid state theory and at the molecular scale.

Quantum Landauer erasure with a molecular nanomagnet

NASA Astrophysics Data System (ADS)

Gaudenzi, R.; Burzurí, E.; Maegawa, S.; van der Zant, H. S. J.; Luis, F.

2018-06-01

The erasure of a bit of information is an irreversible operation whose minimal entropy production of kB ln 2 is set by the Landauer limit1. This limit has been verified in a variety of classical systems, including particles in traps2,3 and nanomagnets4. Here, we extend it to the quantum realm by using a crystal of molecular nanomagnets as a quantum spin memory and showing that its erasure is still governed by the Landauer principle. In contrast to classical systems, maximal energy efficiency is achieved while preserving fast operation owing to its high-speed spin dynamics. The performance of our spin register in terms of energy-time cost is orders of magnitude better than existing memory devices to date. The result shows that thermodynamics sets a limit on the energy cost of certain quantum operations and illustrates a way to enhance classical computations by using a quantum system.

Quantum Theory of (H,H{Sub 2}) Scattering: Approximate Treatments of Reactive Scattering

DOE R&D Accomplishments Database

Tang, K. T.; Karplus, M.

1970-10-01

A quantum mechanical study is made of reactive scattering in the (H, H{sub 2}) system. The problem is formulated in terms of a form of the distorted-wave Born approximation (DWBA) suitable for collisions in which all particles have finite mass. For certain incident energies, differential and total cross sections, as well as other attributes of the reactive collisions, (e.g. reaction configuration), are determined. Two limiting models in the DWBA formulation are compared; in one, the molecule is unperturbed by the incoming atom and in the other, the molecule adiabatically follows the incoming atom. For thermal incident energies and semi-empirical interaction potential employed, the adiabatic model seems to be more appropriate. Since the DWBA method is too complicated for a general study of the (H, H{sub 2}) reaction, a much simpler approximation method, the ?linear model? is developed. This model is very different in concept from treatments in which the three atoms are constrained to move on a line throughout the collision. The present model includes the full three-dimensional aspect of the collision and it is only the evaluation of the transition matrix element itself that is simplified. It is found that the linear model, when appropriately normalized, gives results in good agreement with that of the DWBA method. By application of this model, the energy dependence, rotational state of dependence and other properties of the total and differential reactions cross sections are determined. These results of the quantum mechanical treatment are compared with the classical calculation for the same potential surface. The most important result is that, in agreement with the classical treatment, the differential cross sections are strongly backward peaked at low energies and shifts in the forward direction as the energy increases. Finally, the implications of the present calculations for a theory of chemical kinetics are discussed.

DFT study of gases adsorption on sharp tip nano-catalysts surface for green fertilizer synthesis

NASA Astrophysics Data System (ADS)

Yahya, Noorhana; Irfan, Muhammad; Shafie, Afza; Soleimani, Hassan; Alqasem, Bilal; Rehman, Zia Ur; Qureshi, Saima

2016-11-01

The energy minimization and spin modifications of sorbates with sorbents in magnetic induction method (MIM) play a vital role in yield of fertilizer. Hence, in this article the focus of study is the interaction of sorbates/reactants (H2, N2 and CO2) in term of average total adsorption energies, average isosteric heats of adsorption energies, magnetic moments, band gaps energies and spin modifications over identical cone tips nanocatalyst (sorbents) of Fe2O3, Fe3O4 (magnetic), CuO and Al2O3 (non-magnetic) for green nano-fertilizer synthesis. Study of adsorption energy, band structures and density of states of reactants with sorbents are purely classical and quantum mechanical based concepts that are vividly illustrated and supported by ADSORPTION LOCATOR and Cambridge Seriel Total Energy Package (CASTEP) modules following classical and first principle DFT simulation study respectively. Maximum values of total average energies, total average adsorption energies and average adsorption energies of H2, N2 and CO2 molecules are reported as -14.688 kcal/mol, -13.444 kcal/mol, -3.130 kcal/mol, - kcal/mol and -6.348 kcal/mol over Al2O3 cone tips respectively and minimum over magnetic cone tips. Whereas, the maximum and average minimum values of average isosteric heats of adsorption energies of H2, N2 and CO2 molecules are figured out to be 3.081 kcal/mol, 4.842 kcal/mol and 6.848 kcal/mol, 0.988 kcal/mol, 1.554 kcal/mol and 2.236 kcal/mol over aluminum oxide and Fe3O4 cone tips respectively. In addition to the adsorption of reactants over identical cone sorbents the maximum and minimum values of net spin, electrons and number of bands for magnetite and aluminum oxide cone structures are attributed to 82 and zero, 260 and 196, 206 and 118 for Fe3O4 and Al2O3 cones respectively. Maximum and least observed values of band gap energies are figured out to be 0.188 eV and 0.018 eV with Al2O3 and Fe3O4 cone structures respectively. Ultimately, with the adsorption of reactants an identical increment of 14 electrons each in up and down spins is resulted.

Free energy of adhesion of lipid bilayers on silica surfaces

NASA Astrophysics Data System (ADS)

Schneemilch, M.; Quirke, N.

2018-05-01

The free energy of adhesion per unit area (hereafter referred to as the adhesion strength) of lipid arrays on surfaces is a key parameter that determines the nature of the interaction between materials and biological systems. Here we report classical molecular simulations of water and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayers at model silica surfaces with a range of silanol densities and structures. We employ a novel technique that enables us to estimate the adhesion strength of supported lipid bilayers in the presence of water. We find that silanols on the silica surface form hydrogen bonds with water molecules and that the water immersion enthalpy for all surfaces varies linearly with the surface density of these hydrogen bonds. The adhesion strength of lipid bilayers is a linear function of the surface density of hydrogen bonds formed between silanols and the lipid molecules on crystalline surfaces. Approximately 20% of isolated silanols form such bonds but more than 99% of mutually interacting geminal silanols do not engage in hydrogen bonding with water. On amorphous silica, the bilayer displays much stronger adhesion than expected from the crystalline surface data. We discuss the implications of these results for nanoparticle toxicity.

21cm Absorption Line Zeeman Observations And Modeling Of Physical Conditions In M16

NASA Astrophysics Data System (ADS)

Kiuchi, Furea; Brogan, C.; Troland, T.

2011-01-01

We present detailed 21 cm HI absorption line observations of M16 using the Very Large Array. The M16 "pillars of creation" are classic examples of the interaction of ISM with radiation from young, hot stars. Magnetic fields can affect these interactions, the 21 cm Zeeman effect reveals magnetic field strengths in the Photodissociation regions associated with the pillars. The present results yield a 3-sigma upper limit upon the line-of-sight magnetic field of about 300 microgauss. This limit is consistent with a total field strength of 500 microgauss, required in the molecular gas if magnetic energies and turbulent energies in the pillars are in equipartition. Most likely, magnetic fields do not play a dominant role in the dynamics of the M16 pillars. Another goal of this study is to determine the distribution of cold HI in the M16 region and to model the physical conditions in the neutral gas in the pillars. We used the spectral synthesis code Cloudy 08.00 for this purpose. We adopted the results of a published Cloudy HII region model and extended this model into the neutral gas to derive physical conditions therein.

π-π stacking tackled with density functional theory

PubMed Central

Swart, Marcel; van der Wijst, Tushar; Fonseca Guerra, Célia

2007-01-01

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing π-π interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson–Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing π-π stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound π-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the π-π stacking potential energy surface. Figure Additivity approximation for the π-π interaction between two stacked Watson–Crick base pairs in terms of pairwise interactions between individual bases Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0239-y) contains supplementary material, which is available to authorized users. PMID:17874150

Mean-field theory of baryonic matter for QCD in the large Nc and heavy quark mass limits

NASA Astrophysics Data System (ADS)

Adhikari, Prabal; Cohen, Thomas D.

2013-11-01

We discuss theoretical issues pertaining to baryonic matter in the combined heavy-quark and large Nc limits of QCD. Witten's classic argument that baryons and interacting systems of baryons can be described in a mean-field approximation with each of the quarks moving in an average potential due to the remaining quarks is heuristic. It is important to justify this heuristic description for the case of baryonic matter since systems of interacting baryons are intrinsically more complicated than single baryons due to the possibility of hidden color states—states in which the subsystems making up the entire baryon crystal are not color-singlet nucleons but rather colorful states coupled together to make a color-singlet state. In this work, we provide a formal justification of this heuristic prescription. In order to do this, we start by taking the heavy quark limit, thus effectively reducing the problem to a many-body quantum mechanical system. This problem can be formulated in terms of integrals over coherent states, which for this problem are simple Slater determinants. We show that for the many-body problem, the support region for these integrals becomes narrow at large Nc, yielding an energy which is well approximated by a single coherent state—that is a mean-field description. Corrections to the energy are of relative order 1/Nc. While hidden color states are present in the exact state of the heavy quark system, they only influence the interaction energy below leading order in 1/Nc.

Riemannian geometry of thermodynamics and systems with repulsive power-law interactions.

PubMed

Ruppeiner, George

2005-07-01

A Riemannian geometric theory of thermodynamics based on the postulate that the curvature scalar R is proportional to the inverse free energy density is used to investigate three-dimensional fluid systems of identical classical point particles interacting with each other via a power-law potential energy gamma r(-alpha) . Such systems are useful in modeling melting transitions. The limit alpha-->infinity corresponds to the hard sphere gas. A thermodynamic limit exists only for short-range (alpha>3) and repulsive (gamma>0) interactions. The geometric theory solutions for given alpha>3 , gamma>0 , and any constant temperature T have the following properties: (1) the thermodynamics follows from a single function b (rho T(-3/alpha) ) , where rho is the density; (2) all solutions are equivalent up to a single scaling constant for rho T(-3/alpha) , related to gamma via the virial theorem; (3) at low density, solutions correspond to the ideal gas; (4) at high density there are solutions with pressure and energy depending on density as expected from solid state physics, though not with a Dulong-Petit heat capacity limit; (5) for 33.7913 a phase transition is required to go between these regimes; (7) for any alpha>3 we may include a first-order phase transition, which is expected from computer simulations; and (8) if alpha-->infinity, the density approaches a finite value as the pressure increases to infinity, with the pressure diverging logarithmically in the density difference.

Serum Metabolomic Profiling of Piglets Infected with Virulent Classical Swine Fever Virus

PubMed Central

Gong, Wenjie; Jia, Junjie; Zhang, Bikai; Mi, Shijiang; Zhang, Li; Xie, Xiaoming; Guo, Huancheng; Shi, Jishu; Tu, Changchun

2017-01-01

Classical swine fever (CSF) is a highly contagious swine infectious disease and causes significant economic losses for the pig industry worldwide. The objective of this study was to determine whether small molecule metabolites contribute to the pathogenesis of CSF. Birefly, serum metabolomics of CSFV Shimen strain-infected piglets were analyzed by ultraperformance liquid chromatography/electrospray ionization time-of-flight mass spectrometry (UPLC/ESI-Q-TOF/MS) in combination with multivariate statistical analysis. In CSFV-infected piglets at days 3 and 7 post-infection changes were found in metabolites associated with several key metabolic pathways, including tryptophan catabolism and the kynurenine pathway, phenylalanine metabolism, fatty acid and lipid metabolism, the tricarboxylic acid and urea cycles, branched-chain amino acid metabolism, and nucleotide metabolism. Several pathways involved in energy metabolism including fatty acid biosynthesis and β-oxidation, branched-chain amino acid metabolism, and the tricarboxylic acid cycle were significantly inhibited. Changes were also observed in several metabolites exclusively associated with gut microbiota. The metabolomic profiles indicate that CSFV-host gut microbiome interactions play a role in the development of CSF. PMID:28496435

Effects of weakly coupled and dense quantum plasmas environments on charge exchange and ionization processes in Na+ + Rb(5s) atom collisions

NASA Astrophysics Data System (ADS)

Pandey, Mukesh Kumar; Lin, Yen-Chang; Ho, Yew Kam

2017-02-01

The effects of weakly coupled or classical and dense quantum plasmas environment on charge exchange and ionization processes in Na+ + Rb(5s) atom collision at keV energy range have been investigated using classical trajectory Monte Carlo (CTMC) method. The interaction of three charged particles are described by the Debye-Hückel screen potential for weakly coupled plasma, whereas exponential cosine-screened Coulomb potential have been used for dense quantum plasma environment and the effects of both conditions on the cross sections are compared. It is found that screening effects on cross sections in high Debye length condition is quite small in both plasma environments. However, enhanced screening effects on cross sections are observed in dense quantum plasmas for low Debye length condition, which becomes more effective while decreasing the Debye length. Also, we have found that our calculated results for plasma-free case are comparable with the available theoretical results. These results are analyzed in light of available theoretical data with the choice of model potentials.

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

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

The standard mean-field treatment of inter-particle attraction in classical DFT is better than one might expect

NASA Astrophysics Data System (ADS)

Archer, Andrew J.; Chacko, Blesson; Evans, Robert

2017-07-01

In classical density functional theory (DFT), the part of the Helmholtz free energy functional arising from attractive inter-particle interactions is often treated in a mean-field or van der Waals approximation. On the face of it, this is a somewhat crude treatment as the resulting functional generates the simple random phase approximation (RPA) for the bulk fluid pair direct correlation function. We explain why using standard mean-field DFT to describe inhomogeneous fluid structure and thermodynamics is more accurate than one might expect based on this observation. By considering the pair correlation function g(x) and structure factor S(k) of a one-dimensional model fluid, for which exact results are available, we show that the mean-field DFT, employed within the test-particle procedure, yields results much superior to those from the RPA closure of the bulk Ornstein-Zernike equation. We argue that one should not judge the quality of a DFT based solely on the approximation it generates for the bulk pair direct correlation function.

Efficient energy transfer in light-harvesting systems: Quantum-classical comparison, flux network, and robustness analysis

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

Wu Jianlan; Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139; Liu Fan

2012-11-07

Following the calculation of optimal energy transfer in thermal environment in our first paper [J. L. Wu, F. Liu, Y. Shen, J. S. Cao, and R. J. Silbey, New J. Phys. 12, 105012 (2010)], full quantum dynamics and leading-order 'classical' hopping kinetics are compared in the seven-site Fenna-Matthews-Olson (FMO) protein complex. The difference between these two dynamic descriptions is due to higher-order quantum corrections. Two thermal bath models, classical white noise (the Haken-Strobl-Reineker (HSR) model) and quantum Debye model, are considered. In the seven-site FMO model, we observe that higher-order corrections lead to negligible changes in the trapping time ormore » in energy transfer efficiency around the optimal and physiological conditions (2% in the HSR model and 0.1% in the quantum Debye model for the initial site at BChl 1). However, using the concept of integrated flux, we can identify significant differences in branching probabilities of the energy transfer network between hopping kinetics and quantum dynamics (26% in the HSR model and 32% in the quantum Debye model for the initial site at BChl 1). This observation indicates that the quantum coherence can significantly change the distribution of energy transfer pathways in the flux network with the efficiency nearly the same. The quantum-classical comparison of the average trapping time with the removal of the bottleneck site, BChl 4, demonstrates the robustness of the efficient energy transfer by the mechanism of multi-site quantum coherence. To reconcile with the latest eight-site FMO model which is also investigated in the third paper [J. Moix, J. L. Wu, P. F. Huo, D. F. Coker, and J. S. Cao, J. Phys. Chem. Lett. 2, 3045 (2011)], the quantum-classical comparison with the flux network analysis is summarized in Appendix C. The eight-site FMO model yields similar trapping time and network structure as the seven-site FMO model but leads to a more disperse distribution of energy transfer pathways.« less

One-electron propagation in Fermi, Pasta, Ulam disordered chains with Gaussian acoustic pulse pumping

NASA Astrophysics Data System (ADS)

Silva, L. D. Da; Dos Santos, J. L. L.; Ranciaro Neto, A.; Sales, M. O.; de Moura, F. A. B. F.

In this work, we consider a one-electron moving on a Fermi, Pasta, Ulam disordered chain under effect of electron-phonon interaction and a Gaussian acoustic pulse pumping. We describe electronic dynamics using quantum mechanics formalism and the nonlinear atomic vibrations using standard classical physics. Solving numerical equations related to coupled quantum/classical behavior of this system, we study electronic propagation properties. Our calculations suggest that the acoustic pumping associated with the electron-lattice interaction promote a sub-diffusive electronic dynamics.

Classical Optimal Control for Energy Minimization Based On Diffeomorphic Modulation under Observable-Response-Preserving Homotopy.

PubMed

Soley, Micheline B; Markmann, Andreas; Batista, Victor S

2018-06-12

We introduce the so-called "Classical Optimal Control Optimization" (COCO) method for global energy minimization based on the implementation of the diffeomorphic modulation under observable-response-preserving homotopy (DMORPH) gradient algorithm. A probe particle with time-dependent mass m( t;β) and dipole μ( r, t;β) is evolved classically on the potential energy surface V( r) coupled to an electric field E( t;β), as described by the time-dependent density of states represented on a grid, or otherwise as a linear combination of Gaussians generated by the k-means clustering algorithm. Control parameters β defining m( t;β), μ( r, t;β), and E( t;β) are optimized by following the gradients of the energy with respect to β, adapting them to steer the particle toward the global minimum energy configuration. We find that the resulting COCO algorithm is capable of resolving near-degenerate states separated by large energy barriers and successfully locates the global minima of golf potentials on flat and rugged surfaces, previously explored for testing quantum annealing methodologies and the quantum optimal control optimization (QuOCO) method. Preliminary results show successful energy minimization of multidimensional Lennard-Jones clusters. Beyond the analysis of energy minimization in the specific model systems investigated, we anticipate COCO should be valuable for solving minimization problems in general, including optimization of parameters in applications to machine learning and molecular structure determination.

Spectral Gap Energy Transfer in Atmospheric Boundary Layer

NASA Astrophysics Data System (ADS)

Bhushan, S.; Walters, K.; Barros, A. P.; Nogueira, M.

2012-12-01

Experimental measurements of atmospheric turbulence energy spectra show E(k) ~ k-3 slopes at synoptic scales (~ 600 km - 2000 km) and k-5/3 slopes at the mesoscales (< 400 km). The -5/3 spectra is presumably related to 3D turbulence which is dominated by the classical Kolmogrov energy cascade. The -3 spectra is related to 2D turbulence, which is dominated by strong forward scatter of enstrophy and weak forward scatter of energy. In classical 2D turbulence theory, it is expected that a strong backward energy cascade would develop at the synoptic scale, and that circulation would grow infinitely. To limit this backward transfer, energy arrest at macroscales must be introduced. The most commonly used turbulence models developed to mimic the above energy transfer include the energy backscatter model for 2D turbulence in the horizontal plane via Large Eddy Simulation (LES) models, dissipative URANS models in the vertical plane, and Ekman friction for the energy arrest. One of the controversial issues surrounding the atmospheric turbulence spectra is the explanation of the generation of the 2D and 3D spectra and transition between them, for energy injection at the synoptic scales. Lilly (1989) proposed that the existence of 2D and 3D spectra can only be explained by the presence of an additional energy injection in the meso-scale region. A second issue is related to the observations of dual peak spectra with small variance in meso-scale, suggesting that the energy transfer occurs across a spectral gap (Van Der Hoven, 1957). Several studies have confirmed the spectral gap for the meso-scale circulations, and have suggested that they are enhanced by smaller scale vertical convection rather than by the synoptic scales. Further, the widely accepted energy arrest mechanism by boundary layer friction is closely related to the spectral gap transfer. This study proposes an energy transfer mechanism for atmospheric turbulence with synoptic scale injection, wherein the generation of 2D and 3D spectra is explained using spectral gap energy transfer. The existence of the spectral gap energy transfer is validated by performing LES for the interaction of large scale circulation with a wall, and studying the evolution of the energy spectra both near to and far from the wall. Simulations are also performed using the Advanced Weather and Research Forecasting (WRF-ARW) for moist zonal flow over Gaussian ridge, and the energy spectra close and away from the ground are studied. The energy spectra predicted by WRF-ARW are qualitatively compared with LES results to emphasize the limitations of the currently used turbulence parameterizations. Ongoing validation efforts include: (1) extending the interaction of large scale circulation with wall simulations to finer grids to capture a wider range of wavenumbers; and (2) a coupled 2D-3D simulation is planned to predict the entire atmospheric turbulence spectra at a very low computational expense. The overarching objective of this study to develop turbulence modeling capability based on the energy transfer mechanisms proposed in this study. Such a model will be implemented in WRF-ARW, and applied to atmospheric simulations, for example the prediction of moisture convergence patterns at the meso-scale in the southeast United States (Tao & Barros, 2008).

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

NASA Astrophysics Data System (ADS)

Drukker, Karen; Hammes-Schiffer, Sharon

1997-07-01

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

On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

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

Zhu, Xiaolei, E-mail: virtualzx@gmail.com; Yarkony, David R., E-mail: yarkony@jhu.edu

2016-01-14

In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} to describe the photodissociation of phenolmore » from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 10{sup 6} configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct H{sup d}, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm{sup −1} for electronic energies <60 000 cm{sup −1}.« less

TiS2 and ZrS2 single- and double-wall nanotubes: first-principles study.

PubMed

Bandura, Andrei V; Evarestov, Robert A

2014-02-15

Hybrid density functional theory has been applied for investigations of the electronic and atomic structure of bulk phases, nanolayers, and nanotubes based on titanium and zirconium disulfides. Calculations have been performed on the basis of the localized atomic functions by means of the CRYSTAL-2009 computer code. The full optimization of all atomic positions in the regarded systems has been made to study the atomic relaxation and to determine the most favorable structures. The different layered and isotropic bulk phases have been considered as the possible precursors of the nanotubes. Calculations on single-walled TiS2 and ZrS2 nanotubes confirmed that the nanotubes obtained by rolling up the hexagonal crystalline layers with octahedral 1T morphology are the most stable. The strain energy of TiS2 and ZrS2 nanotubes is small, does not depend on the tube chirality, and approximately obeys to D(-2) law (D is nanotube diameter) of the classical elasticity theory. It is greater than the strain energy of the similar TiO2 and ZrO2 nanotubes; however, the formation energy of the disulfide nanotubes is considerably less than the formation energy of the dioxide nanotubes. The distance and interaction energy between the single-wall components of the double-wall nanotubes is proved to be close to the distance and interaction energy between layers in the layered crystals. Analysis of the relaxed nanotube shape using radial coordinate of the metal atoms demonstrates a small but noticeable deviation from completely cylindrical cross-section of the external walls in the armchair-like double-wall nanotubes. Copyright © 2013 Wiley Periodicals, Inc.

Three-body problem in d-dimensional space: Ground state, (quasi)-exact-solvability

NASA Astrophysics Data System (ADS)

Turbiner, Alexander V.; Miller, Willard; Escobar-Ruiz, M. A.

2018-02-01

As a straightforward generalization and extension of our previous paper [A. V. Turbiner et al., "Three-body problem in 3D space: Ground state, (quasi)-exact-solvability," J. Phys. A: Math. Theor. 50, 215201 (2017)], we study the aspects of the quantum and classical dynamics of a 3-body system with equal masses, each body with d degrees of freedom, with interaction depending only on mutual (relative) distances. The study is restricted to solutions in the space of relative motion which are functions of mutual (relative) distances only. It is shown that the ground state (and some other states) in the quantum case and the planar trajectories (which are in the interaction plane) in the classical case are of this type. The quantum (and classical) Hamiltonian for which these states are eigenfunctions is derived. It corresponds to a three-dimensional quantum particle moving in a curved space with special d-dimension-independent metric in a certain d-dependent singular potential, while at d = 1, it elegantly degenerates to a two-dimensional particle moving in flat space. It admits a description in terms of pure geometrical characteristics of the interaction triangle which is defined by the three relative distances. The kinetic energy of the system is d-independent; it has a hidden sl(4, R) Lie (Poisson) algebra structure, alternatively, the hidden algebra h(3) typical for the H3 Calogero model as in the d = 3 case. We find an exactly solvable three-body S3-permutationally invariant, generalized harmonic oscillator-type potential as well as a quasi-exactly solvable three-body sextic polynomial type potential with singular terms. For both models, an extra first order integral exists. For d = 1, the whole family of 3-body (two-dimensional) Calogero-Moser-Sutherland systems as well as the Tremblay-Turbiner-Winternitz model is reproduced. It is shown that a straightforward generalization of the 3-body (rational) Calogero model to d > 1 leads to two primitive quasi-exactly solvable problems. The extension to the case of non-equal masses is straightforward and is briefly discussed.

Signatures of chaos in the Brillouin zone.

PubMed

Barr, Aaron; Barr, Ariel; Porter, Max D; Reichl, Linda E

2017-10-01

When the classical dynamics of a particle in a finite two-dimensional billiard undergoes a transition to chaos, the quantum dynamics of the particle also shows manifestations of chaos in the form of scarring of wave functions and changes in energy level spacing distributions. If we "tile" an infinite plane with such billiards, we find that the Bloch states on the lattice undergo avoided crossings, energy level spacing statistics change from Poisson-like to Wigner-like, and energy sheets of the Brillouin zone begin to "mix" as the classical dynamics of the billiard changes from regular to chaotic behavior.

Enhanced energy transport in genetically engineered excitonic networks.

PubMed

Park, Heechul; Heldman, Nimrod; Rebentrost, Patrick; Abbondanza, Luigi; Iagatti, Alessandro; Alessi, Andrea; Patrizi, Barbara; Salvalaggio, Mario; Bussotti, Laura; Mohseni, Masoud; Caruso, Filippo; Johnsen, Hannah C; Fusco, Roberto; Foggi, Paolo; Scudo, Petra F; Lloyd, Seth; Belcher, Angela M

2016-02-01

One of the challenges for achieving efficient exciton transport in solar energy conversion systems is precise structural control of the light-harvesting building blocks. Here, we create a tunable material consisting of a connected chromophore network on an ordered biological virus template. Using genetic engineering, we establish a link between the inter-chromophoric distances and emerging transport properties. The combination of spectroscopy measurements and dynamic modelling enables us to elucidate quantum coherent and classical incoherent energy transport at room temperature. Through genetic modifications, we obtain a significant enhancement of exciton diffusion length of about 68% in an intermediate quantum-classical regime.

Effective Field Theory of Surface-mediated Forces in Soft Matter

NASA Astrophysics Data System (ADS)

Yolcu, Cem

We propose a field theoretic formalism for describing soft surfaces modified by the presence of inclusions. Examples include particles trapped at a fluid-fluid interface, proteins attached to (or embedded in) a biological membrane, etc. We derive the energy functional for near-flat surfaces by an effective field theory approach. The two disparate length scales, particle sizes and inter-particle separations, afford the expansion parameters for controlling the accuracy of the effective theory, which is arbitrary in principle. We consider the following two surface types: (i) one where tension determines the behavior, such as a fluid-fluid interface (referred to as a film), and (ii) one where bending-elasticity dominates (referred to as a membrane). We also restrict to rigid inclusions with a circular footprint, and discuss generalizations briefly. As a result of the localized constraints imposed on the surface by the inclusions, the free energy of the system depends on their spatial arrangement, i.e. forces arise between them. Such surface-mediated interactions are believed to play an important role in the aggregation behavior of colloidal particles at interfaces and proteins on membranes. The interaction free energy consists of two parts: (i) the ground-state of the surface determined by possible deformations imposed by the particles, and (ii) the fluctuation correction. The former is analogous to classical electrostatics with the height profile of the surface playing the role of the electrostatic potential, while the latter is analogous to the Casimir effect and originates from the mere presence of constraints. We compute both interactions in truncated expansions. The efficiency of the formalism allows us to predict, with remarkable ease, quite a few orders of subleading corrections to existing results which are only valid when the inclusions are infinitely far apart. We also found that the few previous studies on finite distance corrections were incomplete. In addition to pairwise additive interactions, we compute the leading behavior of several many-body interactions, as well as subleading corrections where the leading contribution was previously calculated.

The Saga of Light-Matter Interaction and Magneto-optical Effects Applications to Atomic Magnetometry, Laser-cooled Atoms, Atomic Clocks, Geomagnetism, and Plant Bio-magnetism

NASA Astrophysics Data System (ADS)

Corsini, Eric P.

The quest to expand the limited sensorial domain, in particular to bridge the inability to gauge magnetic fields near and far, has driven the fabrication of remedial tools. The interaction of ferromagnetic material with a magnetic field had been the only available technique to gauge that field for several millennium. The advent of electricity and associated classical phenomena captured in the four Maxwell equations, were a step forward. In the early 1900s, the model of quantum mechanics provided a two-way leap forward. One came from the newly understood interaction of light and matter, and more specifically the three-way coupling of photons, atoms' angular momenta, and magnetic field, which are the foundations of atomic magnetometry. The other came from magnetically sensitive quantum effects in a fabricated energy-ladder form of matter cooled to a temperature below that of the energy steps; these quantum effects gave rise to the superconducting quantum interference device (SQUID). Research using atomic magnetometers and SQUIDs has resulted in thousands of publications, text books, and conferences. The current status in each field is well described in Refs. [48,49,38,42] and all references therein. In this work we develop and investigate techniques and applications pertaining to atomic magnetometry. [Full text: eric.corsini gmail.com].

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Braun, N.; Hauth, T.; Pulvermacher, C.; Ritter, M.

2017-10-01

Today’s analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results is based on the execution of small scripts - often written in Python or ROOT macros which call complex compiled algorithms in the background - to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.

The spherical-harmonics representation for the interaction between diatomic molecules: The general case and applications to COsbnd CO and COsbnd HF

NASA Astrophysics Data System (ADS)

Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.; Barreto, Rodrigo L. P.; Palazzetti, Federico; Albernaz, Alessandra F.; Lombardi, Andrea; Maciel, Glauciete S.; Aquilanti, Vincenzo

2017-07-01

The spherical-harmonics expansion is a mathematically rigorous procedure and a powerful tool for the representation of potential energy surfaces of interacting molecular systems, determining their spectroscopic and dynamical properties, specifically in van der Waals clusters, with applications also to classical and quantum molecular dynamics simulations. The technique consists in the construction (by ab initio or semiempirical methods) of the expanded potential interaction up to terms that provide the generation of a number of leading configurations sufficient to account for faithful geometrical representations. This paper reports the full general description of the method of the spherical-harmonics expansion as applied to diatomic-molecule - diatomic-molecule systems of increasing complexity: the presentation of the mathematical background is given for providing both the application to the prototypical cases considered previously (O2sbnd O2, N2sbnd N2, and N2sbnd O2 systems) and the generalization to: (i) the COsbnd CO system, where a characteristic feature is the lower symmetry order with respect to the cases studied before, requiring a larger number of expansion terms necessary to adequately represent the potential energy surface; and (ii) the COsbnd HF system, which exhibits the lowest order of symmetry among this class of aggregates and therefore the highest number of leading configurations.

End-State Relative Equilibria in the Sphere-Restricted Full Three-Body Problem

NASA Astrophysics Data System (ADS)

Gabriel, Travis; Scheeres, Daniel J.

2015-05-01

The Sphere-Restricted Full Three-Body Problem studies the motion of three finite density spheres as they interact under surface and gravitational forces. When accounting for the dissipation of energy, full-body systems may achieve minimum energy states that are unatainable in the classic treatment of the N-Body Problem. This serves as a simple model for the mechanics of rubble pile asteroids, interacting grains in a protoplanetary disk, and potentially the interactions of planetary ring particles. Previous studies of this problem have been performed in the case where the three spheres are of equal size and mass, with all possible relative equilibria and their stability having been identified as a function of the total angular momentum of the system. These studies uncovered that at certain levels of angular momentum there exists more than one stable relative equilibrium state. Thus a question of interest is which of these states a dissipative system would preferentially settle in provided some domain of initial conditions, and whether this would be a function of the dissipation parameters. Using perfectly-rigid dynamics, three-equal-sphere systems are simulated in a purpose-written C-based code to uncover these details. Results from this study are relevant to the mechanics and dynamics in small solar system bodies where relative forces are not great enough to compromise the rigidity of the constituents.

Modifiying shallow-water equations as a model for wave-vortex turbulence

NASA Astrophysics Data System (ADS)

Mohanan, A. V.; Augier, P.; Lindborg, E.

2017-12-01

The one-layer shallow-water equations is a simple two-dimensional model to study the complex dynamics of the oceans and the atmosphere. We carry out forced-dissipative numerical simulations, either by forcing medium-scale wave modes, or by injecting available potential energy (APE). With pure wave forcing in non-rotating cases, a statistically stationary regime is obtained for a range of forcing Froude numbers Ff = ɛ /(kf c), where ɛ is the energy dissipation rate, kf the forcing wavenumber and c the wave speed. Interestingly, the spectra scale as k-2 and third and higher order structure functions scale as r. Such statistics is a manifestation of shock turbulence or Burgulence, which dominate the flow. Rotating cases exhibit some inverse energy cascade, along with a stronger forward energy cascade, dominated by wave-wave interactions. We also propose two modifications to the classical shallow-water equations to construct a toy model. The properties of the model are explored by forcing in APE at a small and a medium wavenumber. The toy model simulations are then compared with results from shallow-water equations and a full General Circulation Model (GCM) simulation. The most distinctive feature of this model is that, unlike shallow-water equations, it avoids shocks and conserves quadratic energy. In Fig. 1, for the shallow-water equations, shocks appear as thin dark lines in the divergence (∇ .{u}) field, and as discontinuities in potential temperature (θ ) field; whereas only waves appear in the corresponding fields from toy model simulation. Forward energy cascade results in a wave field with k-5/3 spectrum, along with equipartition of KE and APE at small scales. The vortical field develops into a k-3 spectrum. With medium forcing wavenumber, at large scales, energy converted from APE to KE undergoes inverse cascade as a result of nonlinear fluxes composed of vortical modes alone. Gradually, coherent vortices emerge with a strong preference for anticyclonic motion. The model can serve as a closer representation of real geophysical turbulence than the classical shallow-water equations. Fig 1. Divergence and potential temperature fields of shallow-water (top row) and toy model (bottom row) simulations.

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

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

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

Forces dictating colloidal interactions between viruses and soil

USGS Publications Warehouse

Chattopadhyay, Sandip; Puls, Robert W.

2000-01-01

The fate and transport of viruses in soil and aquatic environments were studied with respect to the different forces involved in the process of sorption of these viruses on soil particles. In accordance with the classical DLVO theory, we have calculated the repulsive electrostatic forces and the attractive van der Waals forces. Bacteriophages have been used as model sorbates, while different clays have been used as model sorbents. The equations used for the determination of the change in free energy for the process (ΔG) takes into consideration the roughness of the sorbent surfaces. Results indicate that attractive van der Waals forces predominate the process of sorption of the selected bacteriophages on clays.

A constructive model potential method for atomic interactions

NASA Technical Reports Server (NTRS)

Bottcher, C.; Dalgarno, A.

1974-01-01

A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.

Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

NASA Astrophysics Data System (ADS)

Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

Gegenbauer-solvable quantum chain model

NASA Astrophysics Data System (ADS)

Znojil, Miloslav

2010-11-01

An N-level quantum model is proposed in which the energies are represented by an N-plet of zeros of a suitable classical orthogonal polynomial. The family of Gegenbauer polynomials G(n,a,x) is selected for illustrative purposes. The main obstacle lies in the non-Hermiticity (aka crypto-Hermiticity) of Hamiltonians H≠H†. We managed to (i) start from elementary secular equation G(N,a,En)=0, (ii) keep our H, in the nearest-neighbor-interaction spirit, tridiagonal, (iii) render it Hermitian in an ad hoc, nonunique Hilbert space endowed with metric Θ≠I, (iv) construct eligible metrics in closed forms ordered by increasing nondiagonality, and (v) interpret the model as a smeared N-site lattice.

Quantum gap and spin-wave excitations in the Kitaev model on a triangular lattice

NASA Astrophysics Data System (ADS)

Avella, Adolfo; Di Ciolo, Andrea; Jackeli, George

2018-05-01

We study the effects of quantum fluctuations on the dynamical generation of a gap and on the evolution of the spin-wave spectra of a frustrated magnet on a triangular lattice with bond-dependent Ising couplings, analog of the Kitaev honeycomb model. The quantum fluctuations lift the subextensive degeneracy of the classical ground-state manifold by a quantum order-by-disorder mechanism. Nearest-neighbor chains remain decoupled and the surviving discrete degeneracy of the ground state is protected by a hidden model symmetry. We show how the four-spin interaction, emergent from the fluctuations, generates a spin gap shifting the nodal lines of the linear spin-wave spectrum to finite energies.

Tuning the Curie temperature of FeCo compounds by tetragonal distortion

NASA Astrophysics Data System (ADS)

Jakobsson, A.; Şaşıoǧlu, E.; Mavropoulos, Ph.; Ležaić, M.; Sanyal, B.; Bihlmayer, G.; Blügel, S.

2013-09-01

Combining density-functional theory calculations with a classical Monte Carlo method, we show that for B2-type FeCo compounds, tetragonal distortion gives rise to a strong reduction of the Curie temperature TC. The TC monotonically decreases from 1575 K (for c /a=1) to 940 K (for c /a=√2 ). We find that the nearest neighbor Fe-Co exchange interaction is sufficient to explain the c/a behavior of the TC. Combination of high magnetocrystalline anisotropy energy with a moderate TC value suggests tetragonal FeCo grown on the Rh substrate with c /a=1.24 to be a promising material for heat-assisted magnetic recording applications.

Unimolecular Logic Gate with Classical Input by Single Gold Atoms.

PubMed

Skidin, Dmitry; Faizy, Omid; Krüger, Justus; Eisenhut, Frank; Jancarik, Andrej; Nguyen, Khanh-Hung; Cuniberti, Gianaurelio; Gourdon, Andre; Moresco, Francesca; Joachim, Christian

2018-02-27

By a combination of solution and on-surface chemistry, we synthesized an asymmetric starphene molecule with two long anthracenyl input branches and a short naphthyl output branch on the Au(111) surface. Starting from this molecule, we could demonstrate the working principle of a single molecule NAND logic gate by selectively contacting single gold atoms by atomic manipulation to the longer branches of the molecule. The logical input "1" ("0") is defined by the interaction (noninteraction) of a gold atom with one of the input branches. The output is measured by scanning tunneling spectroscopy following the shift in energy of the electronic tunneling resonances at the end of the short branch of the molecule.

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

PubMed

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

2016-11-30

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

The cation-π interaction.

PubMed

Dougherty, Dennis A

2013-04-16

The chemistry community now recognizes the cation-π interaction as a major force for molecular recognition, joining the hydrophobic effect, the hydrogen bond, and the ion pair in determining macromolecular structure and drug-receptor interactions. This Account provides the author's perspective on the intellectual origins and fundamental nature of the cation-π interaction. Early studies on cyclophanes established that water-soluble, cationic molecules would forego aqueous solvation to enter a hydrophobic cavity if that cavity was lined with π systems. Important gas phase studies established the fundamental nature of the cation-π interaction. The strength of the cation-π interaction (Li(+) binds to benzene with 38 kcal/mol of binding energy; NH4(+) with 19 kcal/mol) distinguishes it from the weaker polar-π interactions observed in the benzene dimer or water-benzene complexes. In addition to the substantial intrinsic strength of the cation-π interaction in gas phase studies, the cation-π interaction remains energetically significant in aqueous media and under biological conditions. Many studies have shown that cation-π interactions can enhance binding energies by 2-5 kcal/mol, making them competitive with hydrogen bonds and ion pairs in drug-receptor and protein-protein interactions. As with other noncovalent interactions involving aromatic systems, the cation-π interaction includes a substantial electrostatic component. The six (four) C(δ-)-H(δ+) bond dipoles of a molecule like benzene (ethylene) combine to produce a region of negative electrostatic potential on the face of the π system. Simple electrostatics facilitate a natural attraction of cations to the surface. The trend for (gas phase) binding energies is Li(+) > Na(+) > K(+) > Rb(+): as the ion gets larger the charge is dispersed over a larger sphere and binding interactions weaken, a classical electrostatic effect. On other hand, polarizability does not define these interactions. Cyclohexane is more polarizable than benzene but a decidedly poorer cation binder. Many studies have documented cation-π interactions in protein structures, where lysine or arginine side chains interact with phenylalanine, tyrosine, or tryptophan. In addition, countless studies have established the importance of the cation-π interaction in a range of biological processes. Our work has focused on molecular neurobiology, and we have shown that neurotransmitters generally use a cation-π interaction to bind to their receptors. We have also shown that many drug-receptor interactions involve cation-π interactions. A cation-π interaction plays a critical role in the binding of nicotine to ACh receptors in the brain, an especially significant case. Other researchers have established important cation-π interactions in the recognition of the "histone code," in terpene biosynthesis, in chemical catalysis, and in many other systems.

The Cation-π Interaction

PubMed Central

DOUGHERTY, DENNIS A.

2014-01-01

CONSPECTUS The chemistry community now recognizes the cation-π interaction as a major force for molecular recognition, joining the hydrophobic effect, the hydrogen bond, and the ion pair in determining macromolecular structure and drug-receptor interactions. This Account provides the author’s perspective on the intellectual origins and fundamental nature of the cation-π interaction. Early studies on cyclophanes established that water-soluble, cationic molecules would forgo aqueous solvation to enter a hydrophobic cavity if that cavity was lined with π systems. Important gas phase studies established the fundamental nature of the cation-π interaction. The strength of the cation-π interaction – Li+ binds to benzene with 38 kcal/mol of binding energy; NH4+ with 19 kcal/mol– distinguishes it from the weaker polar-π interactions observed in the benzene dimer or water-benzene complexes. In addition to the substantial intrinsic strength of the cation-π interaction in gas phase studies, the cation-π interaction remains energetically significant in aqueous media and under biological conditions. Many studies have shown that cation-π interactions can enhance binding energies by 2 – 5 kcal/mol, making them competitive with hydrogen bonds and ion pairs in drug-receptor and protein-protein interactions. As with other noncovalent interactions involving aromatic systems, the cation-π interaction includes a substantial electrostatic component. The six (four) Cδ−–Hδ+ bond dipoles of a molecule like benzene (ethylene) combine to produce a region of negative electrostatic potential on the face of the π system. Simple electrostatics facilitate a natural attraction of cations to the surface. The trend for (gas phase) binding energies is Li+>Na+>K+>Rb+: as the ion gets larger the charge is dispersed over a larger sphere and binding interactions weaken, a classical electrostatic effect. On other hand, polarizability does not define these interactions. Cyclohexane is more polarizable than benzene, but a decidedly poorer cation binder. Many studies have documented cation-π interactions in protein structures, where Lys or Arg side chains interact with Phe, Tyr, or Trp. In addition, countless studies have established the importance of cation-π interaction in a range of biological processes. Our work has focused on molecular neurobiology, and we have shown that neurotransmitters generally use a cation-π interaction to bind to their receptors. We have also shown that many drug-receptor interactions involve cation-π interactions. A cation-π interaction plays a critical role in the binding of nicotine to ACh receptors in the brain, an especially significant case. Other researchers have established important cation-π interactions in the recognition of the “histone code,” in terpene biosynthesis, in chemical catalysis, and in many other systems. PMID:23214924

New insights into classical solutions of the local instability of the sandwich panels problem

NASA Astrophysics Data System (ADS)

Pozorska, Jolanta; Pozorski, Zbigniew

2016-06-01

The paper concerns the problem of local instability of thin facings of a sandwich panel. The classic analytical solutions are compared and examined. The Airy stress function is applied in the case of the state of plane stress and the state of plane strain. Wrinkling stress values are presented. The differences between the results obtained using the differential equations method and energy method are discussed. The relations between core strain energies are presented.

A study of the Merritt Island, Florida sea breeze flow regimes and their effect on surface heat and moisture fluxes

NASA Technical Reports Server (NTRS)

Rubes, M. T.; Cooper, H. J.; Smith, E. A.

1993-01-01

Data collected during the Convective and Precipitation/Electrification Experiment were analyzed as part of an investigation of the sea breeze in the vicinity of Merritt Island, Florida. Analysis of near-surface divergence fields shows that the classical 24-hour oscillation in divergence over the island due to the direct sea breeze circulation is frequently disrupted and exhibits two distinct modes: the classical sea breeze pattern and deviations from that pattern. A comparison of clear day surface energy fluxes with fluxes on other days indicates that changes in magnitudes were dominated by the presence or absence of clouds. Non-classical sea breeze days tended to lose more available energy in the morning than classical sea breeze days due to earlier development of small cumulus over the island. A composite storm of surface winds, surface energy fluxes, rainfall, and satellite visible data was constructed. A spectral transmittance over the visible wavelengths for the cloud cover resulting from the composite storm was calculated. It is shown that pre-storm transmittances of 0.8 fall to values near 0.1 as the downdraft moves directly over the site. It is also found that under post-composite storm conditions of continuous clear sky days, 3.5 days are required to evaporate back into the atmosphere the latent heat energy lost to the surface by rainfall.

Receptor interaction profiles of novel psychoactive tryptamines compared with classic hallucinogens.

PubMed

Rickli, Anna; Moning, Olivier D; Hoener, Marius C; Liechti, Matthias E

2016-08-01

The present study investigated interactions between the novel psychoactive tryptamines DiPT, 4-OH-DiPT, 4-OH-MET, 5-MeO-AMT, and 5-MeO-MiPT at monoamine receptors and transporters compared with the classic hallucinogens lysergic acid diethylamide (LSD), psilocin, N,N-dimethyltryptamine (DMT), and mescaline. We investigated binding affinities at human monoamine receptors and determined functional serotonin (5-hydroxytryptamine [5-HT]) 5-HT2A and 5-HT2B receptor activation. Binding at and the inhibition of human monoamine uptake transporters and transporter-mediated monoamine release were also determined. All of the novel tryptamines interacted with 5-HT2A receptors and were partial or full 5-HT2A agonists. Binding affinity to the 5-HT2A receptor was lower for all of the tryptamines, including psilocin and DMT, compared with LSD and correlated with the reported psychoactive doses in humans. Several tryptamines, including psilocin, DMT, DiPT, 4-OH-DiPT, and 4-OH-MET, interacted with the serotonin transporter and partially the norepinephrine transporter, similar to 3,4-methylenedioxymethamphetamine but in contrast to LSD and mescaline. LSD but not the tryptamines interacted with adrenergic and dopaminergic receptors. In conclusion, the receptor interaction profiles of the tryptamines predict hallucinogenic effects that are similar to classic serotonergic hallucinogens but also MDMA-like psychoactive properties. Copyright © 2016 Elsevier B.V. and ECNP. All rights reserved.

Beth-Uhlenbeck approach for repulsive interactions between baryons in a hadron gas

NASA Astrophysics Data System (ADS)

Vovchenko, Volodymyr; Motornenko, Anton; Gorenstein, Mark I.; Stoecker, Horst

2018-03-01

The quantum mechanical Beth-Uhlenbeck (BU) approach for repulsive hard-core interactions between baryons is applied to the thermodynamics of a hadron gas. The second virial coefficient a2—the "excluded volume" parameter—calculated within the BU approach is found to be temperature dependent, and it differs dramatically from the classical excluded volume (EV) model result. At temperatures T =100 -200 MeV, the widely used classical EV model underestimates the EV parameter for nucleons at a given value of the nucleon hard-core radius by large factors of 3-4. Previous studies, which employed the hard-core radii of hadrons as an input into the classical EV model, have to be re-evaluated using the appropriately rescaled EV parameters. The BU approach is used to model the repulsive baryonic interactions in the hadron resonance gas (HRG) model. Lattice data for the second- and fourth-order net baryon susceptibilities are described fairly well when the temperature dependent BU baryonic excluded volume parameter corresponds to nucleon hard-core radii of rc=0.25 -0.3 fm. Role of the attractive baryonic interactions is also considered. It is argued that HRG model with a constant baryon-baryon EV parameter vN N≃1 fm3 provides a simple yet efficient description of baryon-baryon interaction in the crossover temperature region.

Class II HLA interactions modulate genetic risk for multiple sclerosis

PubMed Central

Dilthey, Alexander T; Xifara, Dionysia K; Ban, Maria; Shah, Tejas S; Patsopoulos, Nikolaos A; Alfredsson, Lars; Anderson, Carl A; Attfield, Katherine E; Baranzini, Sergio E; Barrett, Jeffrey; Binder, Thomas M C; Booth, David; Buck, Dorothea; Celius, Elisabeth G; Cotsapas, Chris; D’Alfonso, Sandra; Dendrou, Calliope A; Donnelly, Peter; Dubois, Bénédicte; Fontaine, Bertrand; Fugger, Lars; Goris, An; Gourraud, Pierre-Antoine; Graetz, Christiane; Hemmer, Bernhard; Hillert, Jan; Kockum, Ingrid; Leslie, Stephen; Lill, Christina M; Martinelli-Boneschi, Filippo; Oksenberg, Jorge R; Olsson, Tomas; Oturai, Annette; Saarela, Janna; Søndergaard, Helle Bach; Spurkland, Anne; Taylor, Bruce; Winkelmann, Juliane; Zipp, Frauke; Haines, Jonathan L; Pericak-Vance, Margaret A; Spencer, Chris C A; Stewart, Graeme; Hafler, David A; Ivinson, Adrian J; Harbo, Hanne F; Hauser, Stephen L; De Jager, Philip L; Compston, Alastair; McCauley, Jacob L; Sawcer, Stephen; McVean, Gil

2016-01-01

Association studies have greatly refined the understanding of how variation within the human leukocyte antigen (HLA) genes influences risk of multiple sclerosis. However, the extent to which major effects are modulated by interactions is poorly characterized. We analyzed high-density SNP data on 17,465 cases and 30,385 controls from 11 cohorts of European ancestry, in combination with imputation of classical HLA alleles, to build a high-resolution map of HLA genetic risk and assess the evidence for interactions involving classical HLA alleles. Among new and previously identified class II risk alleles (HLA-DRB1*15:01, HLA-DRB1*13:03, HLA-DRB1*03:01, HLA-DRB1*08:01 and HLA-DQB1*03:02) and class I protective alleles (HLA-A*02:01, HLA-B*44:02, HLA-B*38:01 and HLA-B*55:01), we find evidence for two interactions involving pairs of class II alleles: HLA-DQA1*01:01–HLA-DRB1*15:01 and HLA-DQB1*03:01–HLA-DQB1*03:02. We find no evidence for interactions between classical HLA alleles and non-HLA risk-associated variants and estimate a minimal effect of polygenic epistasis in modulating major risk alleles. PMID:26343388

Complex trajectories in a classical periodic potential

NASA Astrophysics Data System (ADS)

Anderson, Alexander G.; Bender, Carl M.

2012-11-01

This paper examines the complex trajectories of a classical particle in the potential V(x) = -cos (x). Almost all the trajectories describe a particle that hops from one well to another in an erratic fashion. However, it is shown analytically that there are two special classes of trajectories x(t) determined only by the energy of the particle and not by the initial position of the particle. The first class consists of periodic trajectories; that is, trajectories that return to their initial position x(0) after some real time T. The second class consists of trajectories for which there exists a real time T such that x(t + T) = x(t) ± 2π. These two classes of classical trajectories are analogous to valence and conduction bands in quantum mechanics, where the quantum particle either remains localized or else tunnels resonantly (conducts) through a crystal lattice. These two special types of trajectories are associated with sets of energies of measure 0. For other energies, it is shown that for long times the average velocity of the particle becomes a fractal-like function of energy.

Classical strongly coupled quark-gluon plasma. VII. Energy loss

NASA Astrophysics Data System (ADS)

Cho, Sungtae; Zahed, Ismail

2010-12-01

We use linear response analysis and the fluctuation-dissipation theorem to derive the energy loss of a heavy quark in the SU(2) classical Coulomb plasma in terms of the l=1 monopole and nonstatic structure factor. The result is valid for all Coulomb couplings Γ=V/K, the ratio of the mean potential to kinetic energy. We use the Liouville equation in the collisionless limit to assess the SU(2) nonstatic structure factor. We find the energy loss to be strongly dependent on Γ. In the liquid phase with Γ≈4, the energy loss is mostly metallic and soundless with neither a Cerenkov nor a Mach cone. Our analytical results compare favorably with the SU(2) molecular dynamics simulations at large momentum and for heavy quark masses.

Fuzzy logic controller versus classical logic controller for residential hybrid solar-wind-storage energy system

NASA Astrophysics Data System (ADS)

Derrouazin, A.; Aillerie, M.; Mekkakia-Maaza, N.; Charles, J. P.

2016-07-01

Several researches for management of diverse hybrid energy systems and many techniques have been proposed for robustness, savings and environmental purpose. In this work we aim to make a comparative study between two supervision and control techniques: fuzzy and classic logics to manage the hybrid energy system applied for typical housing fed by solar and wind power, with rack of batteries for storage. The system is assisted by the electric grid during energy drop moments. A hydrogen production device is integrated into the system to retrieve surplus energy production from renewable sources for the household purposes, intending the maximum exploitation of these sources over years. The models have been achieved and generated signals for electronic switches command of proposed both techniques are presented and discussed in this paper.

On a Lagrange-Hamilton formalism describing position and momentum uncertainties

NASA Technical Reports Server (NTRS)

Schuch, Dieter

1993-01-01

According to Heisenberg's uncertainty relation, in quantum mechanics it is not possible to determine, simultaneously, exact values for the position and the momentum of a material system. Calculating the mean value of the Hamiltonian operator with the aid of exact analytic Gaussian wave packet solutions, these uncertainties cause an energy contribution additional to the classical energy of the system. For the harmonic oscillator, e.g., this nonclassical energy represents the ground state energy. It will be shown that this additional energy contribution can be considered as a Hamiltonian function, if it is written in appropriate variables. With the help of the usual Lagrange-Hamilton formalism known from classical particle mechanics, but now considering this new Hamiltonian function, it is possible to obtain the equations of motion for position and momentum uncertainties.

On the Monte Carlo simulation of electron transport in the sub-1 keV energy range.

PubMed

Thomson, Rowan M; Kawrakow, Iwan

2011-08-01

The validity of "classic" Monte Carlo (MC) simulations of electron and positron transport at sub-1 keV energies is investigated in the context of quantum theory. Quantum theory dictates that uncertainties on the position and energy-momentum four-vectors of radiation quanta obey Heisenberg's uncertainty relation; however, these uncertainties are neglected in "classical" MC simulations of radiation transport in which position and momentum are known precisely. Using the quantum uncertainty relation and electron mean free path, the magnitudes of uncertainties on electron position and momentum are calculated for different kinetic energies; a validity bound on the classical simulation of electron transport is derived. In order to satisfy the Heisenberg uncertainty principle, uncertainties of 5% must be assigned to position and momentum for 1 keV electrons in water; at 100 eV, these uncertainties are 17 to 20% and are even larger at lower energies. In gaseous media such as air, these uncertainties are much smaller (less than 1% for electrons with energy 20 eV or greater). The classical Monte Carlo transport treatment is questionable for sub-1 keV electrons in condensed water as uncertainties on position and momentum must be large (relative to electron momentum and mean free path) to satisfy the quantum uncertainty principle. Simulations which do not account for these uncertainties are not faithful representations of the physical processes, calling into question the results of MC track structure codes simulating sub-1 keV electron transport. Further, the large difference in the scale at which quantum effects are important in gaseous and condensed media suggests that track structure measurements in gases are not necessarily representative of track structure in condensed materials on a micrometer or a nanometer scale.

Initial angular momentum and flow in high energy nuclear collisions

NASA Astrophysics Data System (ADS)

Fries, Rainer J.; Chen, Guangyao; Somanathan, Sidharth

2018-03-01

We study the transfer of angular momentum in high energy nuclear collisions from the colliding nuclei to the region around midrapidity, using the classical approximation of the color glass condensate (CGC) picture. We find that the angular momentum shortly after the collision (up to times ˜1 /Qs , where Qs is the saturation scale) is carried by the "β -type" flow of the initial classical gluon field, introduced by some of us earlier. βi˜μ1∇iμ2-μ2∇iμ1 (i =1 ,2 ) describes the rapidity-odd transverse energy flow and emerges from Gauss's law for gluon fields. Here μ1 and μ2 are the averaged color charge fluctuation densities in the two nuclei, respectively. Interestingly, strong coupling calculations using anti-de Sitter/conformal field theory (AdS/CFT) techniques also find an energy flow term featuring this particular combination of nuclear densities. In classical CGC the order of magnitude of the initial angular momentum per rapidity in the reaction plane, at a time 1 /Qs , is |d L2/d η |≈ RAQs-3ɛ¯0/2 at midrapidity, where RA is the nuclear radius, and ɛ¯0 is the average initial energy density. This result emerges as a cancellation between a vortex of energy flow in the reaction plane aligned with the total angular momentum, and energy shear flow opposed to it. We discuss in detail the process of matching classical Yang-Mills results to fluid dynamics. We will argue that dissipative corrections should not be discarded to ensure that macroscopic conservation laws, e.g., for angular momentum, hold. Viscous fluid dynamics tends to dissipate the shear flow contribution that carries angular momentum in boost-invariant fluid systems. This leads to small residual angular momentum around midrapidity at late times for collisions at high energies.

Ion-neutral chemistry at ultralow energies: dynamics of reactive collisions between laser-cooled Ca+ ions and Rb atoms in an ion-atom hybrid trap†

NASA Astrophysics Data System (ADS)

Hall, Felix H. J.; Eberle, Pascal; Hegi, Gregor; Raoult, Maurice; Aymar, Mireille; Dulieu, Olivier; Willitsch, Stefan

2013-08-01

Cold chemical reactions between laser-cooled Ca+ ions and Rb atoms were studied in an ion-atom hybrid trap. Reaction rate constants were determined in the range of collision energies ⟨E coll⟩/k B=20 mK-20 K. The lowest energies were achieved in experiments using single localised Ca+ ions. Product branching ratios were studied using resonant-excitation mass spectrometry. The dynamics of the reactive processes in this system (non-radiative and radiative charge transfer as well as radiative association leading to the formation of CaRb+ molecular ions) have been analysed using high-level quantum-chemical calculations of the potential energy curves of CaRb+ and quantum-scattering calculations for the radiative channels. For the present low-energy scattering experiments, it is shown that the energy dependence of the reaction rate constants is governed by long-range interactions in line with the classical Langevin model, but their magnitude is determined by short-range non-adiabatic and radiative couplings which only weakly depend on the asymptotic energy. The quantum character of the collisions is predicted to manifest itself in the occurrence of narrow shape resonances at well-defined collision energies. The present results highlight both universal and system-specific phenomena in cold ion-neutral reactive collisions.

Energy expenditure for massage therapists during performing selected classical massage techniques.

PubMed

Więcek, Magdalena; Szymura, Jadwiga; Maciejczyk, Marcin; Szyguła, Zbigniew; Cempla, Jerzy; Borkowski, Mateusz

2018-04-11

The aim of the study is to evaluate the intensity of the effort and energy expenditure in the course of performing selected classical massage techniques and to assess the workload of a massage therapist during a work shift. Thirteen massage therapists (age: 21.9±1.9 years old, body mass index: 24.5±2.8 kg×m^-2, maximal oxygen consumption × body mass^-1 (VO_{2 max}×BM^-1): 42.3±7 ml×kg^-1×min^-1) were involved in the study. The stress test consisted in performing selected classical massage techniques in the following order: stroking, kneading, shaking, beating, rubbing and direct vibration, during which the cardio-respiratory responses and the subjective rating of perceived exertion (RPE) were assessed. Intensity of exercise during each massage technique was expressed as % VO_{2 max}, % maximal heart rate (HR_max) and % heart rate reserve (HRR). During each massage technique, net energy expenditure (EE) and energy cost of work using metabolic equivalent of task (MET) were determined. The intensity of exercise was 47.2±6.2% as expressed in terms of % VO_{2 max}, and 74.7±3.2% as expressed in terms of % HR_max, while it was 47.8±1.7% on average when expressed in terms of % HRR during the whole procedure. While performing the classical massage, the average EE and MET were 5.6±0.9 kcal×min^-1 and 5.6±0.2, respectively. The average RPE calculated for the entire procedure was 12.1±1.4. During the performance of a classical massage technique for a single treatment during the study, the average total EE was 176.5±29.6 kcal, resulting in an energy expenditure of 336.2±56.4 kcal×h^-1. In the case of the classical massage technique, rubbing was the highest intensity exercise for the masseur who performed the massage (%VO_{2 max} = 57.4±13.1%, HR_max = 79.6±7.7%, HRR = 58.5±13.1%, MET = 6.7±1.1, EE = 7.1±1.4 kcal×min^-1, RPE = 13.4±1.3). In the objective assessment, physical exercise while performing a single classical massage is characterized by hard work. The technique of classical massage during which the masseur performs the highest exercise intensity is rubbing. According to the classification of work intensity based on energy expenditure, the masseur's work is considered heavy during the whole work shift. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Ion specific effects: decoupling ion-ion and ion-water interactions

PubMed Central

Song, Jinsuk; Kang, Tae Hui; Kim, Mahn Won; Han, Songi

2015-01-01

Ion-specific effects in aqueous solution, known as the Hofmeister effect is prevalent in diverse systems ranging from pure ionic to complex protein solutions. The objective of this paper is to explicitly demonstrate how complex ion-ion and ion-water interactions manifest themselves in the Hofmeister effects, based on a series of recent experimental observation. These effects are not considered in the classical description of ion effects, such as the Deryaguin-Landau-Verwey-Overbeek (DLVO) theory that, likely for that reason, fail to describe the origin of the phenomenological Hofmeister effect. However, given that models considering the basic forces of electrostatic and van der Waals interactions can offer rationalization for the core experimental observations, a universal interaction model stands a chance to be developed. In this perspective, we separately derive the contribution from ion-ion electrostatic interaction and ion-water interaction from second harmonic generation (SHG) data at the air-ion solution interface, which yields an estimate of ion-water interactions in solution. Hofmeister ion effects observed on biological solutes in solution should be similarly influenced by contributions from ion-ion and ion-water interactions, where the same ion-water interaction parameters derived from SHG data at the air-ion solution interface could be applicable. A key experimental data set available from solution systems to probe ion-water interaction is the modulation of water diffusion dynamics near ions in bulk ion solution, as well as near biological liposome surfaces. It is obtained from Overhauser dynamic nuclear polarization (ODNP), a nuclear magnetic resonance (NMR) relaxometry technique. The surface water diffusivity is influenced by the contribution from ion-water interactions, both from localized surface charges and adsorbed ions, although the relative contribution of the former is larger on liposome surfaces. In this perspective, ion-water interaction energy values derived from experimental data for various ions are compared with theoretical values in the literature. Ultimately, quantifying ion-induced changes in surface energy for the purpose of developing valid theoretical models for ion-water interaction, will be critical to rationalizing the Hofmeister effect. PMID:25761273

Lean muscle mass in classic or ovulatory PCOS: association with central obesity and insulin resistance.

PubMed

Mario, F M; do Amarante, F; Toscani, M K; Spritzer, P M

2012-10-01

This age-matched case-control study assessed total and segmental lean muscle mass in classic or ovulatory polycystic ovary syndrome (PCOS) patients and investigated whether lean mass is associated with hormone and metabolic features. Participants underwent anthropometric and clinical evaluation. Habitual physical activity was assessed with a digital pedometer, and body composition by dual-energy X-ray absorptiometry. Laboratory measurements included total cholesterol, cholesterol fractions, triglycerides, glucose, total serum testosterone, serum insulin, estradiol, luteinizing hormone, and SHBG. Energy intake was calculated using a food frequency questionnaire. Classic PCOS patients had higher body mass index (BMI), waist circumference, testosterone and lipid accumulation product values than ovulatory PCOS and controls. Energy consumption, homeostasis model assessment index, SHBG, free androgen index and triglycerides, total and trunk lean mass were higher only in classic PCOS women vs. controls. Arm, leg, trunk, total or limb lean masses were not correlated with hormone levels in any of the groups. However, in PCOS women lipid accumulation product was positively correlated with total (r=0.56, p=0.001), trunk (r=0.59, p=0.001), arm (r=0.54, p=0.001), leg (r=0.44, p=0.03) and limb (r=0.48, p=0.001) lean masses. BMI was positively correlated with all lean mass segments and independently associated with total lean mass. Lipid accumulation product and BMI were independently associated with trunk lean mass variation. The increase in lean mass in classic PCOS appears to be associated with insulin resistance and central obesity rather than with energy intake, physical activity or androgens. © J. A. Barth Verlag in Georg Thieme Verlag KG Stuttgart · New York.

Classical Electrodynamics: Lecture notes

NASA Astrophysics Data System (ADS)

Likharev, Konstantin K.

2018-06-01

Essential Advanced Physics is a series comprising four parts: Classical Mechanics, Classical Electrodynamics, Quantum Mechanics and Statistical Mechanics. Each part consists of two volumes, Lecture notes and Problems with solutions, further supplemented by an additional collection of test problems and solutions available to qualifying university instructors. This volume, Classical Electrodynamics: Lecture notes is intended to be the basis for a two-semester graduate-level course on electricity and magnetism, including not only the interaction and dynamics charged point particles, but also properties of dielectric, conducting, and magnetic media. The course also covers special relativity, including its kinematics and particle-dynamics aspects, and electromagnetic radiation by relativistic particles.